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Everson HR, Neyra K, Scarton DV, Chandrasekhar S, Green CM, Schmidt TL, Medintz IL, Veneziano R, Mathur D. Purification of DNA Nanoparticles Using Photocleavable Biotin Tethers. ACS Appl Mater Interfaces 2024; 16:22334-22343. [PMID: 38635042 DOI: 10.1021/acsami.3c18955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
The number of applications of self-assembled deoxyribonucleic acid (DNA) origami nanoparticles (DNA NPs) has increased drastically, following the development of a variety of single-stranded template DNA (ssDNA) that can serve as the scaffold strand. In addition to viral genomes, such as M13 bacteriophage and lambda DNAs, enzymatically produced ssDNA from various template sources is rapidly gaining traction and being applied as the scaffold for DNA NP preparation. However, separating fully formed DNA NPs that have custom scaffolds from crude assembly mixes is often a multistep process of first separating the ssDNA scaffold from its enzymatic amplification process and then isolating the assembled DNA NPs from excess precursor strands. Only then is the DNA NP sample ready for downstream characterization and application. In this work, we highlight a single-step purification of custom sequence- or M13-derived scaffold-based DNA NPs using photocleavable biotin tethers. The process only requires an inexpensive ultraviolet (UV) lamp, and DNA NPs with up to 90% yield and high purity are obtained. We show the versatility of the process in separating two multihelix bundle structures and a wireframe polyhedral architecture.
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Affiliation(s)
- Heather R Everson
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Dylan V Scarton
- College of Science, Interdisciplinary Program in Neuroscience, George Mason University, Fairfax, Virginia 22030, United States
- Institute for Advanced Biomedical Research, George Mason University, Manassas, Virginia 20110, United States
| | | | - Christopher M Green
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, District of Columbia 20375, United States
| | | | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, District of Columbia 20375, United States
| | - Remi Veneziano
- Institute for Advanced Biomedical Research, George Mason University, Manassas, Virginia 20110, United States
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
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2
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Hastman DA, Oh E, Melinger JS, Green CM, Thielemann AJP, Medintz IL, Díaz SA. Smaller Gold Nanoparticles Release DNA More Efficiently During fs Laser Pulsed Optical Heating. Small 2024; 20:e2303136. [PMID: 37749947 DOI: 10.1002/smll.202303136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/05/2023] [Indexed: 09/27/2023]
Abstract
This work investigates the effect of plasmonic gold nanoparticle (AuNP) size on the rate of thermal release of single-stranded oligonucleotides under femtosecond (fs)-pulsed laser irradiation sources. Contrary to the theoretical predictions that larger AuNPs (50-60 nm diameter) would produce the most solution heating and fastest DNA release, it is found that smaller AuNP diameters (25 nm) lead to faster dsDNA denaturation rates. Controlling for the pulse energy fluence, AuNP concentration, DNA loading density, and the distance from the AuNP surface finds the same result. These results imply that the solution temperature increases around the AuNP during fs laser pulse optical heating may not be the only significant influence on dsDNA denaturation, suggesting that direct energy transfer from the AuNP to the DNA (phonon-phonon coupling), which is increased as AuNPs decrease in size, may play a significant role.
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Affiliation(s)
- David A Hastman
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC, 20375, USA
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC, 20375, USA
| | - Aaron J P Thielemann
- Department of Navy-US Naval Research Laboratory Historically Black Colleges and Universities/Minority Institutions Internship Program, Washington, DC, 20002, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC, 20375, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC, 20375, USA
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3
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Green CM, Sementa D, Mathur D, Melinger JS, Deshpande P, Elbaum-Garfinkle S, Medintz IL, Ulijn RV, Díaz SA. Sequestration within peptide coacervates improves the fluorescence intensity, kinetics, and limits of detection of dye-based DNA biosensors. Commun Chem 2024; 7:49. [PMID: 38424154 PMCID: PMC10904739 DOI: 10.1038/s42004-024-01124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Peptide-based liquid-liquid phase separated domains, or coacervates, are a biomaterial gaining new interest due to their exciting potential in fields ranging from biosensing to drug delivery. In this study, we demonstrate that coacervates provide a simple and biocompatible medium to improve nucleic acid biosensors through the sequestration of both the biosensor and target strands within the coacervate, thereby increasing their local concentration. Using the well-established polyarginine (R9) - ATP coacervate system and an energy transfer-based DNA molecular beacon we observed three key improvements: i) a greater than 20-fold reduction of the limit of detection within coacervates when compared to control buffer solutions; ii) an increase in the kinetics, equilibrium was reached more than 4-times faster in coacervates; and iii) enhancement in the dye fluorescent quantum yields within the coacervates, resulting in greater signal-to-noise. The observed benefits translate into coacervates greatly improving bioassay functionality.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Deborah Sementa
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Joseph S Melinger
- Electronics Sciences and Technology Division Code 6816, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Priyasha Deshpande
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
| | - Shana Elbaum-Garfinkle
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
- Department of Chemistry Hunter College, City University of New York, New York, NY, 10065, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA.
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4
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Hooe SL, Smith AD, Dean SN, Breger JC, Ellis GA, Medintz IL. Multienzymatic Cascades and Nanomaterial Scaffolding-A Potential Way Forward for the Efficient Biosynthesis of Novel Chemical Products. Adv Mater 2024; 36:e2309963. [PMID: 37944537 DOI: 10.1002/adma.202309963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/25/2023] [Indexed: 11/12/2023]
Abstract
Synthetic biology is touted as the next industrial revolution as it promises access to greener biocatalytic syntheses to replace many industrial organic chemistries. Here, it is shown to what synthetic biology can offer in the form of multienzyme cascades for the synthesis of the most basic of new materials-chemicals, including especially designer chemical products and their analogs. Since achieving this is predicated on dramatically expanding the chemical space that enzymes access, such chemistry will probably be undertaken in cell-free or minimalist formats to overcome the inherent toxicity of non-natural substrates to living cells. Laying out relevant aspects that need to be considered in the design of multi-enzymatic cascades for these purposes is begun. Representative multienzymatic cascades are critically reviewed, which have been specifically developed for the synthesis of compounds that have either been made only by traditional organic synthesis along with those cascades utilized for novel compound syntheses. Lastly, an overview of strategies that look toward exploiting bio/nanomaterials for accessing channeling and other nanoscale materials phenomena in vitro to direct novel enzymatic biosynthesis and improve catalytic efficiency is provided. Finally, a perspective on what is needed for this field to develop in the short and long term is presented.
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Affiliation(s)
- Shelby L Hooe
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- National Research Council, Washington, DC, 20001, USA
| | - Aaron D Smith
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Scott N Dean
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Joyce C Breger
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
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Hastman DA, Hooe S, Chiriboga M, Díaz SA, Susumu K, Stewart MH, Green CM, Hildebrandt N, Medintz IL. Multiplexed DNA and Protease Detection with Orthogonal Energy Transfer on a Single Quantum Dot Scaffolded Biosensor. ACS Sens 2024; 9:157-170. [PMID: 38160434 DOI: 10.1021/acssensors.3c01812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Almost all pathogens, whether viral or bacterial, utilize key proteolytic steps in their pathogenesis. The ability to detect a pathogen's genomic material along with its proteolytic activity represents one approach to identifying the pathogen and providing initial evidence of its viability. Here, we report on a prototype biosensor design assembled around a single semiconductor quantum dot (QD) scaffold that is capable of detecting both nucleic acid sequences and proteolytic activity by using orthogonal energy transfer (ET) processes. The sensor consists of a central QD assembled via peptidyl-PNA linkers with multiple DNA sequences that encode complements to genomic sequences originating from the Ebola, Influenza, and COVID-19 viruses, which we use as surrogate targets. These are hybridized to complement strands labeled with a terbium (Tb) chelate, AlexaFluor647 (AF647), and Cy5.5 dyes, giving rise to two potential FRET cascades: the first includes Tb → QD → AF647 → Cy5.5 (→ = ET step), which is detected in a time-gated modality, and QD → AF647 → Cy5.5, which is detected from direct excitation. The labeled DNA-displaying QD construct is then further assembled with a RuII-modified peptide, which quenches QD photoluminescence by charge transfer and is recognized by a protease to yield the full biosensor. Each of the labeled DNAs and peptides can be ratiometrically assembled to the QD in a controllable manner to tune each of the ET pathways. Addition of a given target DNA displaces its labeled complement on the QD, disrupting that FRET channel, while protease addition disrupts charge transfer quenching of the central QD scaffold and boosts its photoluminescence and FRET relay capabilities. Along with characterizing the ET pathways and verifying biosensing in both individual and multiplexed formats, we also demonstrate the ability of this construct to function in molecular logic and perform Boolean operations; this highlights the construct's ability to discriminate and transduce signals between different inputs or pathogens. The potential application space for such a sensor device is discussed.
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Affiliation(s)
- David A Hastman
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
- American Society for Engineering Education, Washington ,District of Columbia20036, United States
| | - Shelby Hooe
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Matthew Chiriboga
- Northrop Grumman Corporation, Mission Systems, Baltimore, Maryland, 21240, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Michael H Stewart
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton L8S 4L7, Canada
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
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6
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Hooe S, Thakur M, Lasarte-Aragonés G, Breger JC, Walper SA, Medintz IL, Ellis GA. Exploration of the In Vitro Violacein Synthetic Pathway with Substrate Analogues. ACS Omega 2024; 9:3894-3904. [PMID: 38284012 PMCID: PMC10809250 DOI: 10.1021/acsomega.3c08233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
Evolution has gifted enzymes with the ability to synthesize an abundance of small molecules with incredible control over efficiency and selectivity. Central to an enzyme's role is the ability to selectively catalyze reactions in the milieu of chemicals within a cell. However, for chemists it is often desirable to extend the substrate scope of reactions to produce analogue(s) of a desired product and therefore some degree of enzyme promiscuity is often desired. Herein, we examine this dichotomy in the context of the violacein biosynthetic pathway. Importantly, we chose to interrogate this pathway with tryptophan analogues in vitro, to mitigate possible interference from cellular components and endogenous tryptophan. A total of nine tryptophan analogues were screened for by analyzing the substrate promiscuity of the initial enzyme, VioA, and compared to the substrate tryptophan. These results suggested that for VioA, substitutions at either the 2- or 4-position of tryptophan were not viable. The seven analogues that showed successful substrate conversion by VioA were then applied to the five enzyme cascade (VioABEDC) for the production of violacein, where l-tryptophan and 6-fluoro-l-tryptophan were the only substrates which were successfully converted to the corresponding violacein derivative(s). However, many of the other tryptophan analogues did convert to various substituted intermediaries. Overall, our results show substrate promiscuity with the initial enzyme, VioA, but much less for the full pathway. This work demonstrates the complexity involved when attempting to analyze substrate analogues within multienzymatic cascades, where each enzyme involved within the cascade possesses its own inherent promiscuity, which must be compatible with the remaining enzymes in the cascade for successful formation of a desired product.
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Affiliation(s)
- Shelby
L. Hooe
- National
Research Council, Washington, D.C. 20001, United States
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Meghna Thakur
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Guillermo Lasarte-Aragonés
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Joyce C. Breger
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Scott A. Walper
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Gregory A. Ellis
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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7
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Rolczynski BS, Díaz SA, Goldman ER, Medintz IL, Melinger JS. Investigating the dissipation of heat and quantum information from DNA-scaffolded chromophore networks. J Chem Phys 2024; 160:034105. [PMID: 38230810 DOI: 10.1063/5.0181034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024] Open
Abstract
Scaffolded molecular networks are important building blocks in biological pigment-protein complexes, and DNA nanotechnology allows analogous systems to be designed and synthesized. System-environment interactions in these systems are responsible for important processes, such as the dissipation of heat and quantum information. This study investigates the role of nanoscale molecular parameters in tuning these vibronic system-environment dynamics. Here, genetic algorithm methods are used to obtain nanoscale parameters for a DNA-scaffolded chromophore network based on comparisons between its calculated and measured optical spectra. These parameters include the positions, orientations, and energy level characteristics within the network. This information is then used to compute the dynamics, including the vibronic population dynamics and system-environment heat currents, using the hierarchical equations of motion. The dissipation of quantum information is identified by the system's transient change in entropy, which is proportional to the heat currents according to the second law of thermodynamics. These results indicate that the dissipation of quantum information is highly dependent on the particular nanoscale characteristics of the molecular network, which is a necessary first step before gleaning the systematic optimization rules. Subsequently, the I-concurrence dynamics are calculated to understand the evolution of the vibronic system's quantum entanglement, which are found to be long-lived compared to these system-bath dissipation processes.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - Ellen R Goldman
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
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8
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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9
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Medintz IL, Mathur D. The potential of DNA nanotechnology to advance multiple therapeutic systems. Ther Deliv 2023; 14:615-618. [PMID: 38014467 DOI: 10.4155/tde-2023-0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Affiliation(s)
- Igor L Medintz
- Center for Bio/Molecular Science & Engineering, US Naval Research Laboratory, Code 6900, Washington DC 20375, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
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10
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Breger JC, Goldman ER, Susumu K, Oh E, Green CM, Hooe SL, Thakur M, Medintz IL, Ellis GA. Enzyme assembly on nanoparticle scaffolds enhances cofactor recycling and improves coupled reaction kinetics. Nanoscale 2023. [PMID: 37272342 DOI: 10.1039/d3nr00729d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Enzyme activity can be many times enhanced in configurations where they are displayed on a nanoparticle (NP) and this same format sometimes even provides access to channeling phenomena within multienzyme cascades. Here, we demonstrate that such enhancement phenomena can be expanded to enzymatic cofactor recycling along with the coupled enzymatic processes that they are associated with. We begin by showing that the efficiency of glucose driven reduction of nicotinamide adenine dinucleotide (NAD+ → NADH) by glucose dehydrogenase (GDH) is enhanced ca. 5-fold when the enzyme is displayed on nanocrystalline semiconductor quantum dots (QDs) which are utilized as prototypical NP materials in our experimental assays. Coupling this enzymatic step with NADH-dependent lactate dehydrogenase (LDH) conversion of lactate to pyruvate also increases the latter's rate by a similar amount when both enzymes were jointly incorporated into self-assembled QD-based nanoclusters. Detailed agarose gel mobility assays and transmission electron microscopy imaging studies confirm that both tetrameric enzymes assemble to and crosslink the QDs into structured nanoclusters via their multiple-pendant terminal (His)6 sequences. Unexpectedly, control experiments utilizing blocking peptides to prevent enzyme-crosslinking of QDs resulted in even further enhancement of individual enzyme on-QD kinetic activity. This activity was also probed revealing that 200-fold excess peptide/QD addition enhanced individual GDH and LDH on-QD kcat a further 2- and 1.5×, respectively, above that seen just by QD display to a maximum of ∼10-fold GDH enhancement. The potential implications for how these enzyme kinetics-enhancing phenomena can be applied to single and multi-enzyme cascaded reactions in the context of cofactor recycling and cell-free synthetic biology are discussed.
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Affiliation(s)
- Joyce C Breger
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
| | - Ellen R Goldman
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
| | - Kimihiro Susumu
- Optical Sciences Division Code 5600, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Eunkeu Oh
- Optical Sciences Division Code 5600, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
| | - Shelby L Hooe
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
- National Research Council, Washington, D.C., 20001, USA
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
- College of Science, George Mason University, Fairfax, Virginia, 22030, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
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11
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Oktay E, Bush J, Vargas M, Scarton DV, O'Shea B, Hartman A, Green CM, Neyra K, Gomes CM, Medintz IL, Mathur D, Veneziano R. Customized Scaffolds for Direct Assembly of Functionalized DNA Origami. ACS Appl Mater Interfaces 2023. [PMID: 37267624 DOI: 10.1021/acsami.3c05690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Functional DNA origami nanoparticles (DNA-NPs) are used as nanocarriers in a variety of biomedical applications including targeted drug delivery and vaccine development. DNA-NPs can be designed into a broad range of nanoarchitectures in one, two, and three dimensions with high structural fidelity. Moreover, the addressability of the DNA-NPs enables the precise organization of functional moieties, which improves targeting, actuation, and stability. DNA-NPs are usually functionalized via chemically modified staple strands, which can be further conjugated with additional polymers and proteins for the intended application. Although this method of functionalization is extremely efficient to control the stoichiometry and organization of functional moieties, fewer than half of the permissible sites are accessible through staple modifications. In addition, DNA-NP functionalization rapidly becomes expensive when a high number of functionalizations such as fluorophores for tracking and chemical modifications for stability that do not require spatially precise organization are used. To facilitate the synthesis of functional DNA-NPs, we propose a simple and robust strategy based on an asymmetric polymerase chain reaction (aPCR) protocol that allows direct synthesis of custom-length scaffolds that can be randomly modified and/or precisely modified via sequence design. We demonstrated the potential of our strategy by producing and characterizing heavily modified scaffold strands with amine groups for dye functionalization, phosphorothioate bonds for stability, and biotin for surface immobilization. We further validated our sequence design approach for precise conjugation of biomolecules by synthetizing scaffolds including binding loops and aptamer sequences that can be used for direct hybridization of nucleic acid tagged biomolecules or binding of protein targets.
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Affiliation(s)
- Esra Oktay
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Joshua Bush
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Merlyn Vargas
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Dylan Valerio Scarton
- College of Science, Interdisciplinary Program in Neuroscience, George Mason University, Fairfax, Virginia 22030-4444, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Bailey O'Shea
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Amber Hartman
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington DC 20375-0001, United States
| | - Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, United States
| | - Carolina M Gomes
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington DC 20375-0001, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, United States
| | - Remi Veneziano
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
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12
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Breger JC, Vranish JN, Oh E, Stewart MH, Susumu K, Lasarte-Aragonés G, Ellis GA, Walper SA, Díaz SA, Hooe SL, Klein WP, Thakur M, Ancona MG, Medintz IL. Self assembling nanoparticle enzyme clusters provide access to substrate channeling in multienzymatic cascades. Nat Commun 2023; 14:1757. [PMID: 36990995 PMCID: PMC10060375 DOI: 10.1038/s41467-023-37255-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/08/2023] [Indexed: 03/31/2023] Open
Abstract
Access to efficient enzymatic channeling is desired for improving all manner of designer biocatalysis. We demonstrate that enzymes constituting a multistep cascade can self-assemble with nanoparticle scaffolds into nanoclusters that access substrate channeling and improve catalytic flux by orders of magnitude. Utilizing saccharification and glycolytic enzymes with quantum dots (QDs) as a model system, nanoclustered-cascades incorporating from 4 to 10 enzymatic steps are prototyped. Along with confirming channeling using classical experiments, its efficiency is enhanced several fold more by optimizing enzymatic stoichiometry with numerical simulations, switching from spherical QDs to 2-D planar nanoplatelets, and by ordering the enzyme assembly. Detailed analyses characterize assembly formation and clarify structure-function properties. For extended cascades with unfavorable kinetics, channeled activity is maintained by splitting at a critical step, purifying end-product from the upstream sub-cascade, and feeding it as a concentrated substrate to the downstream sub-cascade. Generalized applicability is verified by extending to assemblies incorporating other hard and soft nanoparticles. Such self-assembled biocatalytic nanoclusters offer many benefits towards enabling minimalist cell-free synthetic biology.
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Affiliation(s)
- Joyce C Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - James N Vranish
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- Department of Chemistry, Engineering, and Physics, Franciscan University of Steubenville, Steubenville, OH, 43952, USA
| | - Eunkeu Oh
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Michael H Stewart
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- College of Science, George Mason University, Fairfax, VA, 22030, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Scott A Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Shelby L Hooe
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- National Research Council, Washington, D.C., 20001, USA
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- National Research Council, Washington, D.C., 20001, USA
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- College of Science, George Mason University, Fairfax, VA, 22030, USA
| | - Mario G Ancona
- Electronic Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL, 32310, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
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13
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Oktay E, Alem F, Hernandez K, Girgis M, Green C, Mathur D, Medintz IL, Narayanan A, Veneziano R. DNA origami presenting the receptor binding domain of SARS-CoV-2 elicit robust protective immune response. Commun Biol 2023; 6:308. [PMID: 36959304 PMCID: PMC10034259 DOI: 10.1038/s42003-023-04689-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/10/2023] [Indexed: 03/25/2023] Open
Abstract
Effective and safe vaccines are invaluable tools in the arsenal to fight infectious diseases. The rapid spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the coronavirus disease 2019 pandemic has highlighted the need to develop methods for rapid and efficient vaccine development. DNA origami nanoparticles (DNA-NPs) presenting multiple antigens in prescribed nanoscale patterns have recently emerged as a safe, efficient, and easily scalable alternative for rational design of vaccines. Here, we are leveraging the unique properties of these DNA-NPs and demonstrate that precisely patterning ten copies of a reconstituted trimer of the receptor binding domain (RBD) of SARS-CoV-2 along with CpG adjuvants on the DNA-NPs is able to elicit a robust protective immunity against SARS-CoV-2 in a mouse model. Our results demonstrate the potential of our DNA-NP-based approach for developing safe and effective nanovaccines against infectious diseases with prolonged antibody response and effective protection in the context of a viral challenge.
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Affiliation(s)
- Esra Oktay
- Department of Bioengineering, George Mason University, Fairfax, VA, 22030, USA
| | - Farhang Alem
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA
| | - Keziah Hernandez
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA
| | - Michael Girgis
- Department of Bioengineering, George Mason University, Fairfax, VA, 22030, USA
| | - Christopher Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA.
| | - Remi Veneziano
- Department of Bioengineering, George Mason University, Fairfax, VA, 22030, USA.
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14
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Díaz SA, Pascual G, Patten LK, Roy SK, Meares A, Chiriboga M, Susumu K, Knowlton WB, Cunningham PD, Mathur D, Yurke B, Medintz IL, Lee J, Melinger JS. Towards control of excitonic coupling in DNA-templated Cy5 aggregates: the principal role of chemical substituent hydrophobicity and steric interactions. Nanoscale 2023; 15:3284-3299. [PMID: 36723027 PMCID: PMC9932853 DOI: 10.1039/d2nr05544a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/16/2023] [Indexed: 05/27/2023]
Abstract
Understanding and controlling exciton coupling in dye aggregates has become a greater focus as potential applications such as coherent exciton devices, nanophotonics, and biosensing have been proposed. DNA nanostructure templates allow for a powerful modular approach. Using DNA Holliday junction (HJ) templates variations of dye combinations and precision dye positions can be rapidly assayed, as well as creating aggregates of dyes that could not be prepared (either due to excess or lack of solubility) through alternative means. Indodicarbocyanines (Cy5) have been studied in coupled systems due to their large transition dipole moment, which contributes to strong coupling. Cy5-R dyes were recently prepared by chemically modifying the 5,5'-substituents of indole rings, resulting in varying dye hydrophobicity/hydrophilicity, steric considerations, and electron-donating/withdrawing character. We utilized Cy5-R dyes to examine the formation and properties of 30 unique DNA templated homodimers. We find that in our system the sterics of Cy5-R dyes play the determining factor in orientation and coupling strength of dimers, with coupling strengths ranging from 50-138 meV. The hydrophobic properties of the Cy5-R modify the percentage of dimers formed, and have a secondary role in determining the packing characteristics of the dimers when sterics are equivalent. Similar to other reports, we find that positioning of the Cy5-R within the HJ template can favor particular dimer interactions, specifically oblique or H-type dimers.
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Affiliation(s)
- Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States.
| | - Gissela Pascual
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Lance K Patten
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Simon K Roy
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Adam Meares
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States.
| | - Matthew Chiriboga
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States.
- Volgenau School of Engineering, George Mason University, Fairfax, Virginia 22030, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC, USA
- Jacobs Corporation, Hanover, MD, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul D Cunningham
- Electronics Science and Technology Division Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA.
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States.
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA.
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15
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Mathur D, Galvan AR, Green CM, Liu K, Medintz IL. Uptake and stability of DNA nanostructures in cells: a cross-sectional overview of the current state of the art. Nanoscale 2023; 15:2516-2528. [PMID: 36722508 PMCID: PMC10407680 DOI: 10.1039/d2nr05868e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The physical and chemical properties of synthetic DNA have transformed this prototypical biopolymer into a versatile nanoscale building block material in the form of DNA nanotechnology. DNA nanotechnology is, in turn, providing unprecedented precision bioengineering for numerous biomedical applications at the nanoscale including next generation immune-modulatory materials, vectors for targeted delivery of nucleic acids, drugs, and contrast agents, intelligent sensors for diagnostics, and theranostics, which combines several of these functionalities into a single construct. Assembling a DNA nanostructure to be programmed with a specific number of targeting moieties on its surface to imbue it with concomitant cellular uptake and retention capabilities along with carrying a specific therapeutic dose is now eminently feasible due to the extraordinary self-assembling properties and high formation efficiency of these materials. However, what remains still only partially addressed is how exactly this class of materials is taken up into cells in both the native state and as targeted or chemically facilitated, along with how stable they are inside the cellular cytosol and other cellular organelles. In this minireview, we summarize what is currently reported in the literature about how (i) DNA nanostructures are taken up into cells along with (ii) what is understood about their subsequent stability in the complex multi-organelle environment of the cellular milieu along with biological fluids in general. This allows us to highlight the many challenges that still remain to overcome in understanding DNA nanostructure-cellular interactions in order to fully translate these exciting new materials.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Angelica Rose Galvan
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Kevin Liu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
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16
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Rolczynski BS, Díaz SA, Kim YC, Mathur D, Klein WP, Medintz IL, Melinger JS. Determining interchromophore effects for energy transport in molecular networks using machine-learning algorithms. Phys Chem Chem Phys 2023; 25:3651-3665. [PMID: 36648290 DOI: 10.1039/d2cp04960k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nature uses chromophore networks, with highly optimized structural and energetic characteristics, to perform important chemical functions. Due to its modularity, predictable aggregation characteristics, and established synthetic protocols, structural DNA nanotechnology is a promising medium for arranging chromophore networks with analogous structural and energetic controls. However, this high level of control creates a greater need to know how to optimize the systems precisely. This study uses the system's modularity to produce variations of a coupled 14-Site chromophore network. It uses machine-learning algorithms and spectroscopy measurements to reveal the energy-transport roles of these Sites, paying particular attention to the cooperative and inhibitive effects they impose on each other for transport across the network. The physical significance of these patterns is contextualized, using molecular dynamics simulations and energy-transport modeling. This analysis yields insights about how energy transfers across the Donor-Relay and Relay-Acceptor interfaces, as well as the energy-transport pathways through the homogeneous Relay segment. Overall, this report establishes an approach that uses machine-learning methods to understand, in fine detail, the role that each Site plays in an optoelectronic molecular network.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Young C Kim
- Materials Science and Technology Division, Code 6300, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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17
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Chiriboga M, Green CM, Mathur D, Hastman DA, Melinger JS, Veneziano R, Medintz IL, Díaz SA. Structural and optical variation of pseudoisocyanine aggregates nucleated on DNA substrates. Methods Appl Fluoresc 2023; 11. [PMID: 36719011 PMCID: PMC10362908 DOI: 10.1088/2050-6120/acb2b4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/12/2023] [Indexed: 02/01/2023]
Abstract
Coherently coupled pseudoisocyanine (PIC) dye aggregates have demonstrated the ability to delocalize electronic excitations and ultimately migrate excitons with much higher efficiency than similar designs where excitations are isolated to individual chromophores. Here, we report initial evidence of a new type of PIC aggregate, formed through heterogeneous nucleation on DNA oligonucleotides, displaying photophysical properties that differ significantly from previously reported aggregates. This new aggregate, which we call the super aggregate (SA) due to the need for elevated dye excess to form it, is clearly differentiated from previously reported aggregates by spectroscopic and biophysical characterization. In emission spectra, the SA exhibits peak narrowing and, in some cases, significant quantum yield variation, indicative of stronger coupling in cyanine dyes. The SA was further characterized with circular dichroism and atomic force microscopy observing unique features depending on the DNA substrate. Then by integrating an AlexaFluorTM647 (AF) dye as an energy transfer acceptor into the system, we observed mixed energy transfer characteristics using the different DNA. For example, SA formed with a rigid DNA double crossover tile (DX-tile) substrate resulted in AF emission sensitization. While SA formed with more flexible non-DX-tile DNA (i.e. duplex and single strand DNA) resulted in AF emission quenching. These combined characterizations strongly imply that DNA-based PIC aggregate properties can be controlled through simple modifications to the DNA substrate's sequence and geometry. Ultimately, we aim to inform rational design principles for future device prototyping. For example, one key conclusion of the study is that the high absorbance cross-section and efficient energy transfer observed with rigid substrates made for better photonic antennae, compared to flexible DNA substrates.
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Affiliation(s)
- Matthew Chiriboga
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America.,Department of Bioengineering. College of Engineering and Computing, George Mason University, 4400 University Drive, Fairfax, VA 22030, United States of America
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
| | - Divita Mathur
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America.,Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States of America
| | - David A Hastman
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
| | - Joseph S Melinger
- Electronics Sciences and Technology Division, U.S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
| | - Remi Veneziano
- Department of Bioengineering. College of Engineering and Computing, George Mason University, 4400 University Drive, Fairfax, VA 22030, United States of America
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
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18
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Green CM, Spangler J, Susumu K, Stenger DA, Medintz IL, Díaz SA. Quantum Dot-Based Molecular Beacons for Quantitative Detection of Nucleic Acids with CRISPR/Cas(N) Nucleases. ACS Nano 2022; 16:20693-20704. [PMID: 36378103 DOI: 10.1021/acsnano.2c07749] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Strategies utilizing the CRISPR/Cas nucleases Cas13 and Cas12 have shown great promise in the development of highly sensitive and rapid diagnostic assays for the detection of pathogenic nucleic acids. The most common approaches utilizing fluorophore-quencher molecular beacons require strand amplification strategies or highly sensitive optical setups to overcome the limitations of the readout. Here, we demonstrate a flexible strategy for assembling highly luminescent and colorimetric quantum dot-nucleic acid hairpin (QD-HP) molecular beacons for use in CRISPR/Cas diagnostics. This strategy utilizes a chimeric peptide-peptide nucleic acid (peptide-PNA) to conjugate fluorescently labeled DNA or RNA hairpins to ZnS-coated QDs. QDs are particularly promising alternatives for molecular beacons due to their greater brightness, strong UV absorbance with large emission offset, exceptional photostability, and potential for multiplexing due to their sharp emission peaks. Using Förster resonance energy transfer (FRET), we have developed ratiometric reporters capable of pM target detection (without nucleotide amplification) for both target DNA and RNA, and we further demonstrated their capabilities for multiplexing and camera-phone detection. The flexibility of this system is imparted by the dual functionality of the QD as both a FRET donor and a central nanoscaffold for arranging nucleic acids and fluorescent acceptors on its surface. This method also provides a generalized approach that could be applied for use in other CRISPR/Cas nuclease systems.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Joseph Spangler
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
- Jacobs Corporation, Hanover, Maryland21076, United States
| | - David A Stenger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
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19
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Mathur D, Thakur M, Díaz SA, Susumu K, Stewart MH, Oh E, Walper SA, Medintz IL. Hybrid Nucleic Acid-Quantum Dot Assemblies as Multiplexed Reporter Platforms for Cell-Free Transcription Translation-Based Biosensors. ACS Synth Biol 2022; 11:4089-4102. [PMID: 36441919 PMCID: PMC9829448 DOI: 10.1021/acssynbio.2c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cell-free synthetic biology has emerged as a valuable tool for the development of rapid, portable biosensors that can be readily transported in the freeze-dried form to the point of need eliminating cold chain requirements. One of the challenges associated with cell-free sensors is the ability to simultaneously detect multiple analytes within a single reaction due to the availability of a limited set of fluorescent and colorimetric reporters. To potentially provide multiplexing capabilities to cell-free biosensors, we designed a modular semiconductor quantum dot (QD)-based reporter platform that is plugged in downstream of the transcription-translation functionality in the cell-free reaction and which converts enzymatic activity in the reaction into distinct optical signals. We demonstrate proof of concept by converting restriction enzyme activity, utilized as our prototypical sensing output, into optical changes across several distinct spectral output channels that all use a common excitation wavelength. These hybrid Förster resonance energy transfer (FRET)-based QD peptide PNA-DNA-Dye reporters (QD-PDDs) are completely self-assembled and consist of differentially emissive QD donors paired to a dye-acceptor displayed on a unique DNA encoding a given enzyme's cleavage site. Three QD-based PDDs, independently activated by the enzymes BamHI, EcoRI, and NcoI, were prototyped in mixed enzyme assays where all three demonstrated the ability to convert enzymatic activity into fluorescent output. Simultaneous monitoring of each of the three paired QD-donor dye-acceptor spectral channels in cell-free biosensing reactions supplemented with added linear genes encoding each enzyme confirmed robust multiplexing capabilities for at least two enzymes when co-expressed. The modular QD-PDDs are easily adapted to respond to other restriction enzymes or even proteases if desired.
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Affiliation(s)
| | | | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Kimihiro Susumu
- Jacobs Corporation, Hanover, Maryland 21076, United States; Optical Sciences Division Code 5600, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Michael H. Stewart
- Optical Sciences Division Code 5600, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Eunkeu Oh
- Optical Sciences Division Code 5600, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington 20375, United States
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20
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Huff J, Díaz S, Barclay MS, Chowdhury AU, Chiriboga M, Ellis GA, Mathur D, Patten LK, Roy SK, Sup A, Biaggne A, Rolczynski BS, Cunningham PD, Li L, Lee J, Davis PH, Yurke B, Knowlton WB, Medintz IL, Turner DB, Melinger JS, Pensack RD. Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes. J Phys Chem C Nanomater Interfaces 2022; 126:17164-17175. [PMID: 36268205 PMCID: PMC9575151 DOI: 10.1021/acs.jpcc.2c04336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/08/2022] [Indexed: 06/01/2023]
Abstract
Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates-aggregates of chemically distinct dyes-rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to assemble homo- and heterotetramer aggregates of the prototypical cyanine dyes Cy5 and Cy5.5. In addition to permitting control over the number of dyes within an aggregate, DNA-templated assembly confers control over aggregate composition, i.e., the ratio of constituent Cy5 and Cy5.5 dyes. By varying the ratio of Cy5 and Cy5.5, we show that the most intense absorption feature of the resulting tetramer can be shifted in energy over a range of almost 200 meV (1600 cm-1). All tetramers pack in the form of H-aggregates and exhibit quenched emission and drastically reduced excited-state lifetimes compared to the monomeric dyes. We apply a purely electronic exciton theory model to describe the observed progression of the absorption spectra. This model agrees with both the measured data and a more sophisticated vibronic model of the absorption and circular dichroism spectra, indicating that Cy5 and Cy5.5 heteroaggregates are largely described by molecular exciton theory. Finally, we extend the purely electronic exciton model to describe an idealized J-aggregate based on Förster resonance energy transfer (FRET) and discuss the potential advantages of such a device over traditional FRET relays.
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Affiliation(s)
- Jonathan
S. Huff
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Sebastián
A. Díaz
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Matthew S. Barclay
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Azhad U. Chowdhury
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Matthew Chiriboga
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
- Volgenau
School of Engineering, George Mason University, Fairfax, Virginia 22030, United States
| | - Gregory A. Ellis
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Divita Mathur
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Lance K. Patten
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Simon K. Roy
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Aaron Sup
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Austin Biaggne
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Brian S. Rolczynski
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Paul D. Cunningham
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Lan Li
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul H. Davis
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Daniel B. Turner
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Joseph S. Melinger
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Ryan D. Pensack
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
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21
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Johnson ZT, Jared N, Peterson JK, Li J, Smith EA, Walper SA, Hooe SL, Breger JC, Medintz IL, Gomes C, Claussen JC. Enzymatic Laser-Induced Graphene Biosensor for Electrochemical Sensing of the Herbicide Glyphosate. Glob Chall 2022; 6:2200057. [PMID: 36176938 PMCID: PMC9463521 DOI: 10.1002/gch2.202200057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Glyphosate is a globally applied herbicide yet it has been relatively undetectable in-field samples outside of gold-standard techniques. Its presumed nontoxicity toward humans has been contested by the International Agency for Research on Cancer, while it has been detected in farmers' urine, surface waters and crop residues. Rapid, on-site detection of glyphosate is hindered by lack of field-deployable and easy-to-use sensors that circumvent sample transportation to limited laboratories that possess the equipment needed for detection. Herein, the flavoenzyme, glycine oxidase, immobilized on platinum-decorated laser-induced graphene (LIG) is used for selective detection of glyphosate as it is a substrate for GlyOx. The LIG platform provides a scaffold for enzyme attachment while maintaining the electronic and surface properties of graphene. The sensor exhibits a linear range of 10-260 µ m, detection limit of 3.03 µ m, and sensitivity of 0.991 nA µ m -1. The sensor shows minimal interference from the commonly used herbicides and insecticides: atrazine, 2,4-dichlorophenoxyacetic acid, dicamba, parathion-methyl, paraoxon-methyl, malathion, chlorpyrifos, thiamethoxam, clothianidin, and imidacloprid. Sensor function is further tested in complex river water and crop residue fluids, which validate this platform as a scalable, direct-write, and selective method of glyphosate detection for herbicide mapping and food analysis.
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Affiliation(s)
| | - Nathan Jared
- Department of Mechanical EngineeringIowa State UniversityAmesIA50011USA
| | - John K. Peterson
- Department of Mechanical EngineeringIowa State UniversityAmesIA50011USA
| | - Jingzhe Li
- Department of ChemistryIowa State UniversityAmesIA50011USA
- The Ames LaboratoryU.S. Department of EnergyAmesIA50011USA
| | - Emily A. Smith
- Department of ChemistryIowa State UniversityAmesIA50011USA
- The Ames LaboratoryU.S. Department of EnergyAmesIA50011USA
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900U.S. Naval Research LaboratoryWashington, D.C20375USA
| | - Shelby L. Hooe
- Center for Bio/Molecular Science and Engineering, Code 6900U.S. Naval Research LaboratoryWashington, D.C20375USA
- National Research CouncilWashington, DC20001USA
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900U.S. Naval Research LaboratoryWashington, D.C20375USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900U.S. Naval Research LaboratoryWashington, D.C20375USA
| | - Carmen Gomes
- Department of Mechanical EngineeringIowa State UniversityAmesIA50011USA
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22
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Su R, Wu Y, Doulkeridou S, Qiu X, Sørensen TJ, Susumu K, Medintz IL, van Bergen en Henegouwen PMP, Hildebrandt N. A Nanobody‐on‐Quantum Dot Displacement Assay for Rapid and Sensitive Quantification of the Epidermal Growth Factor Receptor (EGFR). Angew Chem Int Ed Engl 2022; 61:e202207797. [PMID: 35759268 PMCID: PMC9542526 DOI: 10.1002/anie.202207797] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Indexed: 11/26/2022]
Abstract
Biosensing approaches that combine small, engineered antibodies (nanobodies) with nanoparticles are often complicated. Here, we show that nanobodies with different C‐terminal tags can be efficiently attached to a range of the most widely used biocompatible semiconductor quantum dots (QDs). Direct implementation into simplified assay formats was demonstrated by designing a rapid and wash‐free mix‐and‐measure immunoassay for the epidermal growth factor receptor (EGFR). Terbium complex (Tb)‐labeled hexahistidine‐tagged nanobodies were specifically displaced from QD surfaces via EGFR‐nanobody binding, leading to an EGFR concentration‐dependent decrease of the Tb‐to‐QD Förster resonance energy transfer (FRET) signal. The detection limit of 80±20 pM (16±4 ng mL−1) was 3‐fold lower than the clinical cut‐off concentration for soluble EGFR and up to 10‐fold lower compared to conventional sandwich FRET assays that required a pair of different nanobodies.
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Affiliation(s)
- Ruifang Su
- nanoFRET.comLaboratoire COBRA (UMR6014 & FR3038)Université de Rouen Normandie, CNRS, INSANormandie Université76000RouenFrance
- Nano-Science Center & Department of ChemistryUniversity of CopenhagenUniversitetsparken 52100CopenhagenDenmark
| | - Yu‐Tang Wu
- Université Paris-Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)91198Gif-sur-YvetteFrance
| | - Sofia Doulkeridou
- Cell BiologyNeurobiology and BiophysicsDepartment of BiologyScience FacultyUtrecht University3508 TBUtrechtThe Netherlands
- Princess Maxima CenterHeidelberglaan 253584CSUtrechtThe Netherlands
| | - Xue Qiu
- Université Paris-Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)91198Gif-sur-YvetteFrance
- Key Laboratory of Marine DrugMinistry of EducationSchool of Medicine and PharmacyOcean University of China266003QingdaoChina
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology266237QingdaoChina
| | - Thomas Just Sørensen
- Nano-Science Center & Department of ChemistryUniversity of CopenhagenUniversitetsparken 52100CopenhagenDenmark
| | - Kimihiro Susumu
- Jacobs CorporationHanoverMD 21076USA
- Optical Sciences Division, Code 5600, Code 6900U.S. Naval Research LaboratoryWashingtonDC 20375USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900U.S. Naval Research LaboratoryWashingtonDC 20375USA
| | | | - Niko Hildebrandt
- nanoFRET.comLaboratoire COBRA (UMR6014 & FR3038)Université de Rouen Normandie, CNRS, INSANormandie Université76000RouenFrance
- Université Paris-Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)91198Gif-sur-YvetteFrance
- Department of ChemistrySeoul National UniversitySeoul08826South Korea
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23
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Su R, Wu Y, Doulkeridou S, Qiu X, Sørensen TJ, Susumu K, Medintz IL, van Bergen en Henegouwen PMP, Hildebrandt N. A Nanobody‐on‐Quantum Dot Displacement Assay for Rapid and Sensitive Quantification of the Epidermal Growth Factor Receptor (EGFR). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ruifang Su
- nanoFRET.com Laboratoire COBRA (UMR6014 & FR3038) Université de Rouen Normandie, CNRS, INSA Normandie Université 76000 Rouen France
- Nano-Science Center & Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Yu‐Tang Wu
- Université Paris-Saclay, CEA, CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Sofia Doulkeridou
- Cell Biology Neurobiology and Biophysics Department of Biology Science Faculty Utrecht University 3508 TB Utrecht The Netherlands
- Princess Maxima Center Heidelberglaan 25 3584CS Utrecht The Netherlands
| | - Xue Qiu
- Université Paris-Saclay, CEA, CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
- Key Laboratory of Marine Drug Ministry of Education School of Medicine and Pharmacy Ocean University of China 266003 Qingdao China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology 266237 Qingdao China
| | - Thomas Just Sørensen
- Nano-Science Center & Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Kimihiro Susumu
- Jacobs Corporation Hanover MD 21076 USA
- Optical Sciences Division, Code 5600, Code 6900 U.S. Naval Research Laboratory Washington DC 20375 USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900 U.S. Naval Research Laboratory Washington DC 20375 USA
| | | | - Niko Hildebrandt
- nanoFRET.com Laboratoire COBRA (UMR6014 & FR3038) Université de Rouen Normandie, CNRS, INSA Normandie Université 76000 Rouen France
- Université Paris-Saclay, CEA, CNRS Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
- Department of Chemistry Seoul National University Seoul 08826 South Korea
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24
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Mathur D, Rogers KE, Díaz SA, Muroski ME, Klein WP, Nag OK, Lee K, Field LD, Delehanty JB, Medintz IL. Determining the Cytosolic Stability of Small DNA Nanostructures In Cellula. Nano Lett 2022; 22:5037-5045. [PMID: 35580267 PMCID: PMC9233082 DOI: 10.1021/acs.nanolett.2c00917] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
DNA nanostructures have proven potential in biomedicine. However, their intracellular interactions─especially cytosolic stability─remain mostly unknown and attempts to discern this are confounded by the complexities of endocytic uptake and entrapment. Here, we bypass the endocytic uptake and evaluate the DNA structural stability directly in live cells. Commonly used DNA structures─crosshairs and a tetrahedron─were labeled with a multistep Förster resonance energy transfer dye cascade and microinjected into the cytosol of transformed and primary cells. Energy transfer loss, as monitored by fluorescence microscopy, reported the structure's direct time-resolved breakdown in cellula. The results showed rapid degradation of the DNA crosshair within 20 min, while the tetrahedron remained consistently intact for at least 1 h postinjection. Nuclease assays in conjunction with a current understanding of the tetrahedron's torsional rigidity confirmed its higher stability. Such studies can inform design parameters for future DNA nanostructures where programmable degradation rates may be required.
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Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Katherine E Rogers
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Megan E Muroski
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- American Society of Engineering Education, Washington, DC 20036, United States
| | - William P Klein
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- National Research Council, Washington, DC 20001, United States
| | - Okhil K Nag
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Kwahun Lee
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- American Society of Engineering Education, Washington, DC 20036, United States
| | - Lauren D Field
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- National Research Council, Washington, DC 20001, United States
| | - James B Delehanty
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
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25
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Meares A, Susumu K, Mathur D, Lee SH, Mass OA, Lee J, Pensack RD, Yurke B, Knowlton WB, Melinger JS, Medintz IL. Synthesis of Substituted Cy5 Phosphoramidite Derivatives and Their Incorporation into Oligonucleotides Using Automated DNA Synthesis. ACS Omega 2022; 7:11002-11016. [PMID: 35415341 PMCID: PMC8991898 DOI: 10.1021/acsomega.1c06921] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/14/2022] [Indexed: 05/03/2023]
Abstract
Cyanine dyes represent a family of organic fluorophores with widespread utility in biological-based applications ranging from real-time PCR probes to protein labeling. One burgeoning use currently being explored with indodicarbocyanine (Cy5) in particular is that of accessing exciton delocalization in designer DNA dye aggregate structures for potential development of light-harvesting devices and room-temperature quantum computers. Tuning the hydrophilicity/hydrophobicity of Cy5 dyes in such DNA structures should influence the strength of their excitonic coupling; however, the requisite commercial Cy5 derivatives available for direct incorporation into DNA are nonexistent. Here, we prepare a series of Cy5 derivatives that possess different 5,5'-substituents and detail their incorporation into a set of DNA sequences. In addition to varying dye hydrophobicity/hydrophilicity, the 5,5'-substituents, including hexyloxy, triethyleneglycol monomethyl ether, tert-butyl, and chloro groups were chosen so as to vary the inherent electron-donating/withdrawing character while also tuning their resulting absorption and emission properties. Following the synthesis of parent dyes, one of their pendant alkyl chains was functionalized with a monomethoxytrityl protective group with the remaining hydroxyl-terminated N-propyl linker permitting rapid, same-day phosphoramidite conversion and direct internal DNA incorporation into nascent oligonucleotides with moderate to good yields using a 1 μmole scale automated DNA synthesis. Labeled sequences were cleaved from the controlled pore glass matrix, purified by HPLC, and their photophysical properties were characterized. The DNA-labeled Cy5 derivatives displayed spectroscopic properties that paralleled the parent dyes, with either no change or an increase in fluorescence quantum yield depending upon sequence.
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Affiliation(s)
- Adam Meares
- Center
for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, Washington, D.C., Virginia 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Kimihiro Susumu
- Optical
Sciences Division Code 5600, U. S. Naval
Research Laboratory, Washington,
D.C., Virginia 20375, United States
- Jacobs
Corporation, Hanover, Maryland 21076, United
States
| | - Divita Mathur
- Center
for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, Washington, D.C., Virginia 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Sang Ho Lee
- Optical
Sciences Division Code 5600, U. S. Naval
Research Laboratory, Washington,
D.C., Virginia 20375, United States
- Jacobs
Corporation, Hanover, Maryland 21076, United
States
| | - Olga A. Mass
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Chemistry & Biochemistry, Boise State
University, Boise, Idaho 83725, United
States
| | - Ryan D. Pensack
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Joseph S. Melinger
- Electronics
Science and Technology Division Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, Washington, D.C., Virginia 20375, United States
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26
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Chowdhury A, Díaz S, Huff JS, Barclay MS, Chiriboga M, Ellis GA, Mathur D, Patten LK, Sup A, Hallstrom N, Cunningham PD, Lee J, Davis PH, Turner DB, Yurke B, Knowlton WB, Medintz IL, Melinger JS, Pensack RD. Tuning between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates. J Phys Chem Lett 2022; 13:2782-2791. [PMID: 35319215 PMCID: PMC8978177 DOI: 10.1021/acs.jpclett.2c00017] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Molecular excitons, which propagate spatially via electronic energy transfer, are central to numerous applications including light harvesting, organic optoelectronics, and nanoscale computing; they may also benefit applications such as photothermal therapy and photoacoustic imaging through the local generation of heat via rapid excited-state quenching. Here we show how to tune between energy transfer and quenching for heterodimers of the same pair of cyanine dyes by altering their spatial configuration on a DNA template. We assemble "transverse" and "adjacent" heterodimers of Cy5 and Cy5.5 using DNA Holliday junctions. We find that the transverse heterodimers exhibit optical properties consistent with excitonically interacting dyes and fluorescence quenching, while the adjacent heterodimers exhibit optical properties consistent with nonexcitonically interacting dyes and disproportionately large Cy5.5 emission, suggestive of energy transfer between dyes. We use transient absorption spectroscopy to show that quenching in the transverse heterodimer occurs via rapid nonradiative decay to the ground state (∼31 ps) and that in the adjacent heterodimer rapid energy transfer from Cy5 to Cy5.5 (∼420 fs) is followed by Cy5.5 excited-state relaxation (∼700 ps). Accessing such drastically different photophysics, which may be tuned on demand for different target applications, highlights the utility of DNA as a template for dye aggregation.
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Affiliation(s)
- Azhad
U. Chowdhury
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Sebastián
A. Díaz
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Jonathan S. Huff
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Matthew S. Barclay
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Matthew Chiriboga
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
- Volgenau
School of Engineering, George Mason University, Fairfax, Virginia 22030, United States
| | - Gregory A. Ellis
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Divita Mathur
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of
Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Lance K. Patten
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Aaron Sup
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Natalya Hallstrom
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul D. Cunningham
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul H. Davis
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Daniel B. Turner
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Igor L. Medintz
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S. Melinger
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ryan D. Pensack
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
- (R.D.P.) Email
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27
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Thakur M, Breger JC, Susumu K, Oh E, Spangler JR, Medintz IL, Walper SA, Ellis GA. Self-assembled nanoparticle-enzyme aggregates enhance functional protein production in pure transcription-translation systems. PLoS One 2022; 17:e0265274. [PMID: 35298538 PMCID: PMC8929567 DOI: 10.1371/journal.pone.0265274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/27/2022] [Indexed: 11/19/2022] Open
Abstract
Cell-free protein synthesis systems (CFPS) utilize cellular transcription and translation (TX-TL) machinery to synthesize proteins in vitro. These systems are useful for multiple applications including production of difficult proteins, as high-throughput tools for genetic circuit screening, and as systems for biosensor development. Though rapidly evolving, CFPS suffer from some disadvantages such as limited reaction rates due to longer diffusion times, significant cost per assay when using commercially sourced materials, and reduced reagent stability over prolonged periods. To address some of these challenges, we conducted a series of proof-of-concept experiments to demonstrate enhancement of CFPS productivity via nanoparticle assembly driven nanoaggregation of its constituent proteins. We combined a commercially available CFPS that utilizes purified polyhistidine-tagged (His-tag) TX-TL machinery with CdSe/CdS/ZnS core/shell/shell quantum dots (QDs) known to readily coordinate His-tagged proteins in an oriented fashion. We show that nanoparticle scaffolding of the CFPS cross-links the QDs into nanoaggregate structures while enhancing the production of functional recombinant super-folder green fluorescent protein and phosphotriesterase, an organophosphate hydrolase; the latter by up to 12-fold. This enhancement, which occurs by an undetermined mechanism, has the potential to improve CFPS in general and specifically CFPS-based biosensors (faster response time) while also enabling rapid detoxification/bioremediation through point-of-concern synthesis of similar catalytic enzymes. We further show that such nanoaggregates improve production in diluted CFPS reactions, which can help to save money and extend the amount of these costly reagents. The results are discussed in the context of what may contribute mechanistically to the enhancement and how this can be applied to other CFPS application scenarios.
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Affiliation(s)
- Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
- College of Science, George Mason University, Fairfax, Virginia, United States of America
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
- Jacobs Corporation, Dallas, Texas, United States of America
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Joseph R. Spangler
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
- * E-mail:
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28
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Xiao Z, Darwish GH, Susumu K, Medintz IL, Algar WR. Prototype Smartphone-Based Device for Flow Cytometry with Immunolabeling via Supra-nanoparticle Assemblies of Quantum Dots. ACS Meas Sci Au 2022; 2:57-66. [PMID: 36785592 PMCID: PMC9838726 DOI: 10.1021/acsmeasuresciau.1c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Methods for the detection, enumeration, and typing of cells are important in many areas of research and healthcare. In this context, flow cytometers are a widely used research and clinical tool but are also an example of a large and expensive instrument that is limited to specialized laboratories. Smartphones have been shown to have excellent potential to serve as portable and lower-cost platforms for analyses that would normally be done in a laboratory. Here, we developed a prototype smartphone-based flow cytometer (FC). This compact 3D-printed device incorporated a laser diode and a microfluidic flow cell and used the built-in camera of a smartphone to track immunofluorescently labeled cells in suspension and measure their color. This capability was enabled by high-brightness supra-nanoparticle assemblies of colloidal semiconductor quantum dots (SiO2@QDs) as well as a support vector machine (SVM) classification algorithm. The smartphone-based FC device detected and enumerated target cells against a background of other cells, simultaneously and selectively counted two different cell types in a mixture, and used multiple colors of SiO2@QD-antibody conjugates to screen for and identify a particular cell type. The potential limits of multicolor detection are discussed alongside ideas for further development. Our results suggest that innovations in materials and engineering should enable eventual smartphone-based FC assays for clinical applications.
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Affiliation(s)
- Zhujun Xiao
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ghinwa H. Darwish
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Kimihiro Susumu
- Jacobs
Corporation, Hanover, Maryland 21076, United
States
- Optical
Sciences Division, Code 5600, U.S. Naval
Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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29
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Hastman DA, Chaturvedi P, Oh E, Melinger JS, Medintz IL, Vuković L, Díaz SA. Mechanistic Understanding of DNA Denaturation in Nanoscale Thermal Gradients Created by Femtosecond Excitation of Gold Nanoparticles. ACS Appl Mater Interfaces 2022; 14:3404-3417. [PMID: 34982525 DOI: 10.1021/acsami.1c19411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
There is significant interest in developing photothermal systems that can precisely control the structure and function of biomolecules through local temperature modulation. One specific application is the denaturation of double-stranded (ds) DNA through femtosecond (fs) laser pulse optical heating of gold nanoparticles (AuNPs); however, the mechanism of DNA melting in these systems is not fully understood. Here, we utilize 55 nm AuNPs with surface-tethered dsDNA, which are locally heated using fs laser pulses to induce DNA melting. By varying the dsDNA distance from the AuNP surface and the laser pulse energy fluence, this system is used to study how the nanosecond duration temperature increase and the steep temperature gradient around the AuNP affect dsDNA dehybridization. Through modifying the distance between the dsDNA and AuNP surface by 3.8 nm in total and the pulse energy fluence from 7.1 to 14.1 J/m2, the dehybridization rates ranged from 0.002 to 0.05 DNA per pulse, and the total amount of DNA released into solution was controlled over a range of 26-93% in only 100 s of irradiation. By shifting the dsDNA position as little as ∼1.1 nm, the average dsDNA dehybridization rate is altered up to 30 ± 2%, providing a high level of control over DNA melting and release. By comparing the theoretical temperature around the dsDNA to the experimentally derived temperature, we find that maximum or peak temperatures have a greater influence on the dehybridization rate when the dsDNA is closer to the AuNP surface and when lower laser pulse fluences are used. Furthermore, molecular dynamics simulations mimicking the photothermal heat pulse around a AuNP provide mechanistic insight into the stochastic nature of dehybridization and demonstrate increased base pair separation near the AuNP surface during laser pulse heating when compared to steady-state heating. Understanding how biological materials respond to the short-lived and non-uniform temperature increases innate to fs laser pulse optical heating of AuNPs is critical to improving the functionality and precision of this technique so that it may be implemented into more complex biological systems.
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Affiliation(s)
- David A Hastman
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, D.C. 20375, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Parth Chaturvedi
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, D.C. 20375, United States
| | - Lela Vuković
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, D.C. 20375, United States
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30
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Thakur M, Dean SN, Moore M, Spangler JR, Johnson BJ, Medintz IL, Walper SA. Packaging of Diisopropyl Fluorophosphatase (DFPase) in Bacterial Outer Membrane Vesicles Protects Its Activity at Extreme Temperature. ACS Biomater Sci Eng 2022; 8:493-501. [DOI: 10.1021/acsbiomaterials.1c01192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meghna Thakur
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
- College of Science, George Mason University, 4400 University Drive, Fairfax, Virginia 22030, United States
| | - Scott N. Dean
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Martin Moore
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Joseph R. Spangler
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Brandy J. Johnson
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
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31
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Kyriazi ME, El-Sagheer AH, Medintz IL, Brown T, Kanaras AG. An Investigation into the Resistance of Spherical Nucleic Acids against DNA Enzymatic Degradation. Bioconjug Chem 2022; 33:219-225. [PMID: 35001632 DOI: 10.1021/acs.bioconjchem.1c00540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nanoparticles coated with oligonucleotides, also termed spherical nucleic acids (SNAs), are at the forefront of scientific research and have been applied in vitro and in vivo for sensing, gene regulation, and drug delivery. They demonstrate unique properties stemming from the three-dimensional shell of oligonucleotides and present high cellular uptake. However, their resistance to enzymatic degradation is highly dependent on their physicochemical characteristics. In particular, the oligonucleotide loading of SNAs has been determined to be a critical parameter in SNA design. In order to ensure the successful function of SNAs, the degree of oligonucleotide loading has to be quantitatively determined to confirm that a dense oligonucleotide shell has been achieved. However, this can be time-consuming and may lead to multiple syntheses being required to achieve the necessary degree of surface functionalization. In this work we show how this limitation can be overcome by introducing an oligonucleotide modification. By replacing the phosphodiester bond on the oligonucleotide backbone with a phosphorothioate bond, SNAs even with a low DNA loading showed remarkable stability in the presence of nucleases. Furthermore, these chemically modified SNAs exhibited high selectivity and specificity toward the detection of mRNA in cellulo.
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Affiliation(s)
- Maria-Eleni Kyriazi
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton SO171BJ, United Kingdom.,College of Engineering and Technology, American University of the Middle East, Kuwait City, 15453, Kuwait
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Antonios G Kanaras
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton SO171BJ, United Kingdom.,Institute for Life Science, University of Southampton, Southampton, SO171BJ, United Kingdom
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32
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Hooe SL, Ellis GA, Medintz IL. Alternative design strategies to help build the enzymatic retrosynthesis toolbox. RSC Chem Biol 2022; 3:1301-1313. [DOI: 10.1039/d2cb00096b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/11/2022] [Indexed: 11/21/2022] Open
Abstract
Developing the field of enzymatic retrosynthesis can benefit from other research approaches including: minimalist multi-enzyme synthesis, substrate tolerance/specificity studies, optimizing enzyme activity in vitro, and elucidating relevant thermodynamic-kinetic properties.
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Affiliation(s)
- Shelby L. Hooe
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- National Research Council, Washington, DC 20001, USA
| | - Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
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33
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Abstract
DNA nanostructures self-assemble into almost any arbitrary architecture, and when combined with their capability to precisely position and orient dyes, nanoparticles, and biological moieties, the technology reaches its potential. We present a simple yet multifaceted conjugation strategy based on metal coordination by a multi-histidine peptide tag (Histag). The versatility of the Histag as a means to conjugate to DNA nanostructures is shown by using Histags to capture semiconductor quantum dots (QDs) with numerical and positional precision onto a DNA origami breadboard. Additionally, Histag-expressing enzymes, such as the bioluminescent luciferase, can also be captured to the DNA origami breadboard with similar precision. DNA nanostructure conjugation of the QDs or luciferase is confirmed through imaging and/or energy transfer to organic dyes integrated into the DNA nanostructure.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC, USA
- National Research Council, Washington, DC, USA
| | - Divita Mathur
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC, USA
- College of Science, George Mason University, Fairfax, VA, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC, USA
- Jacobs Corporation, Hanover, MD, USA
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC, USA.
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34
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Breger JC, Ellis GA, Walper SA, Susumu K, Medintz IL. Implementing Multi-Enzyme Biocatalytic Systems Using Nanoparticle Scaffolds. Methods Mol Biol 2022; 2487:227-262. [PMID: 35687240 DOI: 10.1007/978-1-0716-2269-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Interest in multi-enzyme synthesis outside of cells (in vitro) is becoming far more prevalent as the field of cell-free synthetic biology grows exponentially. Such synthesis would allow for complex chemical transformations based on the exquisite specificity of enzymes in a "greener" manner as compared to organic chemical transformations. Here, we describe how nanoparticles, and in this specific case-semiconductor quantum dots, can be used to both stabilize enzymes and further allow them to self-assemble into nanocomplexes that facilitate high-efficiency channeling phenomena. Pertinent protocol information is provided on enzyme expression, choice of nanoparticulate material, confirmation of enzyme attachment to nanoparticles, assay format and tracking, data analysis, and optimization of assay formats to draw the best analytical information from the underlying processes.
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Affiliation(s)
- Joyce C Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA
| | - Scott A Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC, USA
- Jacobs Corporation, Hanover, MD, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA.
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35
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Chiriboga M, Diaz SA, Mathur D, Hastman DA, Melinger JS, Veneziano R, Medintz IL. Understanding Self-Assembled Pseudoisocyanine Dye Aggregates in DNA Nanostructures and Their Exciton Relay Transfer Capabilities. J Phys Chem B 2021; 126:110-122. [PMID: 34962787 DOI: 10.1021/acs.jpcb.1c09048] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Progress has been made using B-form DNA duplex strands to template chromophores in ordered molecular aggregates known as J-aggregates. These aggregates can exhibit strong electronic coupling, extended coherent lifetimes, and long-range exciton delocalization under appropriate conditions. Certain cyanine dyes such as pseudoisocyanine (PIC) dye have shown a proclivity to form aggregates in specific DNA sequences. In particular, DX-tiles containing nonalternating poly(dA)-poly(dT) dinucleotide tracks (AT-tracks), which template noncovalent PIC dye aggregates, have been demonstrated to exhibit interesting emergent photonic properties. These DNA-based aggregates are referred to as J-bits for their similarity to J-aggregates. Here, we assemble multifluorophore DX-tile scaffolds which template J-bits into both contiguous and noncontiguous linear arrays. Our goal is to understand the relay capability of noncontiguous J-bit arrays and probe the effects that orientation and position have on the energy transfer between them. We find that linearly contiguous J-bits can relay excitons from an initial AlexaFluor 405 donor to a terminal AlexaFluor 647 acceptor across a distance of up to 16.3 nm. We observed a maximum increase in energy transfer of 41% in the shortest scaffold and an 11% increase in energy transfer across the maximum distance. However, in nonlinear arrays, exciton transfer is not detectable, even when off-axis J-bit-to-J-bit transfer distances were <2 nm. These results, in conjunction with the previous work on PIC-DNA systems, suggest that PIC-DNA-based systems may currently be limited to simple 1-D designs, which prevent isolating J-bits for enhanced energy-transfer characteristics until further understanding and improvements to the system can be made.
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Affiliation(s)
- Matthew Chiriboga
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,Volgenau School of Engineering, Department of Bioengineering, Institute for Advanced Biomedical Research George Mason University, Manassas, Virginia 22030, United States
| | - Sebastian A Diaz
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
| | - Divita Mathur
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - David A Hastman
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,A. James Clark School of Engineering, Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland 20742, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division Code 6800, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
| | - Remi Veneziano
- Volgenau School of Engineering, Department of Bioengineering, Institute for Advanced Biomedical Research George Mason University, Manassas, Virginia 22030, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
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36
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Rolczynski BS, Díaz SA, Kim YC, Medintz IL, Cunningham PD, Melinger JS. Understanding Disorder, Vibronic Structure, and Delocalization in Electronically Coupled Dimers on DNA Duplexes. J Phys Chem A 2021; 125:9632-9644. [PMID: 34709821 DOI: 10.1021/acs.jpca.1c07205] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Structural DNA nanotechnology is a promising approach to create chromophore networks with modular structures and Hamiltonians to control the material's functions. The functional behaviors of these systems depend on the interactions of the chromophores' vibronic states, as well as interactions with their environment. To optimize their functions, it is necessary to characterize the chromophore network's structural and energetic properties, including the electronic delocalization in some cases. In this study, parameters of interest are deduced in DNA-scaffolded Cyanine 3 and Cyanine 5 dimers. The methods include steady-state optical measurements, physical modeling, and a genetic algorithm approach. The parameters include the chromophore network's vibronic Hamiltonian, molecular positions, transition dipole orientations, and environmentally induced energy broadening. Additionally, the study uses temperature-dependent optical measurements to characterize the spectral broadening further. These combined results reveal the quantum mechanical delocalization, which is important for functions like coherent energy transport and quantum information applications.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Young C Kim
- Materials Science and Technology Division, Code 6300, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Paul D Cunningham
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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37
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Mathur D, Samanta A, Ancona MG, Díaz SA, Kim Y, Melinger JS, Goldman ER, Sadowski JP, Ong LL, Yin P, Medintz IL. Understanding Förster Resonance Energy Transfer in the Sheet Regime with DNA Brick-Based Dye Networks. ACS Nano 2021; 15:16452-16468. [PMID: 34609842 PMCID: PMC8823280 DOI: 10.1021/acsnano.1c05871] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Controlling excitonic energy transfer at the molecular level is a key requirement for transitioning nanophotonics research to viable devices with the main inspiration coming from biological light-harvesting antennas that collect and direct light energy with near-unity efficiency using Förster resonance energy transfer (FRET). Among putative FRET processes, point-to-plane FRET between donors and acceptors arrayed in two-dimensional sheets is predicted to be particularly efficient with a theoretical 1/r4 energy transfer distance (r) dependency versus the 1/r6 dependency seen for a single donor-acceptor interaction. However, quantitative validation has been confounded by a lack of robust experimental approaches that can rigidly place dyes in the required nanoscale arrangements. To create such assemblies, we utilize a DNA brick scaffold, referred to as a DNA block, which incorporates up to five two-dimensional planes with each displaying from 1 to 12 copies of five different donor, acceptor, or intermediary relay dyes. Nanostructure characterization along with steady-state and time-resolved spectroscopic data were combined with molecular dynamics modeling and detailed numerical simulations to compare the energy transfer efficiencies observed in the experimental DNA block assemblies to theoretical expectations. Overall, we demonstrate clear signatures of sheet regime FRET, and from this we provide a better understanding of what is needed to realize the benefits of such energy transfer in artificial dye networks along with FRET-based sensing and imaging.
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Affiliation(s)
| | | | | | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Youngchan Kim
- Center for Materials Physics and Technology Code 6390, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S. Melinger
- Electronic Science and Technology Division Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ellen R. Goldman
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - John Paul Sadowski
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States; American Society for Engineering Education, Washington, D.C. 20001, United States
| | - Luvena L. Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Ellis GA, Díaz SA, Medintz IL. Enhancing enzymatic performance with nanoparticle immobilization: improved analytical and control capability for synthetic biochemistry. Curr Opin Biotechnol 2021; 71:77-90. [PMID: 34293630 DOI: 10.1016/j.copbio.2021.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/26/2021] [Accepted: 06/28/2021] [Indexed: 12/25/2022]
Abstract
Enzymes are incredibly potent catalysts with the potential for rapid turnover rates and exquisite specificity, leading to their desired use in multiple biotechnological processes. Yet using these natural catalysts outside of their evolved role can necessitate significant engineering. Immobilization onto microscale (or larger) scaffolds can impart industrially-desired properties but often sacrifices enzymatic activity for long-term stability; in contrast, nanoparticle (NP) conjugation of enzymes can preserve or even enhance their activity. Here, we focus on recent examples of enzyme immobilization onto NPs as a method to improve their industrial applicability. We highlight the analytical methods that are used to both characterize such enhancement along with provide insight into the phenomena that give rise to it. Finally, a short perspective addresses how to adapt lessons learned at the bench about this phenomena to larger-scale biotechnological applications.
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Affiliation(s)
- Gregory A Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Sebastían A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
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Green CM, Hastman DA, Mathur D, Susumu K, Oh E, Medintz IL, Díaz SA. Direct and Efficient Conjugation of Quantum Dots to DNA Nanostructures with Peptide-PNA. ACS Nano 2021; 15:9101-9110. [PMID: 33955735 DOI: 10.1021/acsnano.1c02296] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA nanotechnology has proven to be a powerful strategy for the bottom-up preparation of colloidal nanoparticle (NP) superstructures, enabling the coordination of multiple NPs with orientation and separation approaching nanometer precision. To do this, NPs are often conjugated with chemically modified, single-stranded (ss) DNA that can recognize complementary ssDNA on the DNA nanostructure. The limitation is that many NPs cannot be easily conjugated with ssDNA, and other conjugation strategies are expensive, inefficient, or reduce the specificity and/or precision with which NPs can be placed. As an alternative, the conjugation of nanoparticle-binding peptides and peptide nucleic acids (PNA) can produce peptide-PNA with distinct NP-binding and DNA-binding domains. Here, we demonstrate a simple application of this method to conjugate semiconductor quantum dots (QDs) directly to DNA nanostructures by means of a peptide-PNA with a six-histidine peptide motif that binds to the QD surface. With this method, we achieved greater than 90% capture efficiency for multiple QDs on a single DNA nanostructure while preserving both site specificity and precise spatial control of QD placement. Additionally, we investigated the effects of peptide-PNA charge on the efficacy of QD immobilization in suboptimal conditions. The results validate peptide-PNA as a viable alternative to ssDNA conjugation of NPs and warrant studies of other NP-binding peptides for peptide-PNA conjugation.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
- National Research Council, 500 Fifth St NW, Washington, DC 20001, United States
| | - David A Hastman
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Divita Mathur
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC 20375, United States
- Jacobs Corporation, Hanover, Maryland 21076, United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
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Spangler JR, Caruana JC, Medintz IL, Walper SA. Harnessing the potential of Lactobacillus species for therapeutic delivery at the lumenal-mucosal interface. Future Sci OA 2021; 7:FSO671. [PMID: 33815818 PMCID: PMC8015674 DOI: 10.2144/fsoa-2020-0153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lactobacillus species have been studied for over 30 years in their role as commensal organisms in the human gut. Recently there has been a surge of interest in their abilities to natively and recombinantly stimulate immune activities, and studies have identified strains and novel molecules that convey particular advantages for applications as both immune adjuvants and immunomodulators. In this review, we discuss the recent advances in Lactobacillus-related activity at the gut/microbiota interface, the efforts to probe the boundaries of the direct and indirect therapeutic potential of these bacteria, and highlight the continued interest in harnessing the native capacity for the production of biogenic compounds shown to influence nervous system activity. Taken together, these aspects underscore Lactobacillus species as versatile therapeutic delivery vehicles capable of effector production at the lumenal-mucosal interface, and further establish a foundation of efficacy upon which future engineered strains can expand.
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Affiliation(s)
- Joseph R Spangler
- National Research Council Postdoctoral Fellow sited in US Naval Research Laboratory, Code 6900, Center for Bio/Molecular Science & Engineering, 4555 Overlook Ave SW, Washington DC, 20375, USA
| | - Julie C Caruana
- American Society for Engineering Education Postdoctoral Fellow sited in US Naval Research Laboratory, Code 6900, Center for Bio/Molecular Science & Engineering, 4555 Overlook Ave SW, Washington DC, 20375, USA
| | - Igor L Medintz
- US Naval Research Laboratory, Code 6900, Center for Bio/Molecular Science & Engineering, 4555 Overlook Ave SW, Washington DC, 20375, USA
| | - Scott A Walper
- US Naval Research Laboratory, Code 6900, Center for Bio/Molecular Science & Engineering, 4555 Overlook Ave SW, Washington DC, 20375, USA
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Díaz SA, Choo P, Oh E, Susumu K, Klein WP, Walper SA, Hastman DA, Odom TW, Medintz IL. Gold Nanoparticle Templating Increases the Catalytic Rate of an Amylase, Maltase, and Glucokinase Multienzyme Cascade through Substrate Channeling Independent of Surface Curvature. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03602] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
| | - Priscilla Choo
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- Jacobs Corporation, Hanover, Maryland 21076, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
| | - David A. Hastman
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
- Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland 20742, United States
| | - Teri W. Odom
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
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Kim H, Tran MV, Petryayeva E, Solodova O, Susumu K, Oh E, Medintz IL, Algar WR. Affinity Immobilization of Semiconductor Quantum Dots and Metal Nanoparticles on Cellulose Paper Substrates. ACS Appl Mater Interfaces 2020; 12:53462-53474. [PMID: 33180467 DOI: 10.1021/acsami.0c14559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Colloidal semiconductor quantum dots (QDs), metal nanoparticles, and cellulose paper are materials with numerous applications in bioanalysis and beyond. The functional properties of QDs and metal NPs are substantially different than those of cellulose, such that their integration with cellulose paper is potentially enabling for many applications. Here, we characterize and evaluate multiple chemistries that modify cellulose paper substrates for the affinity-based immobilization of QDs, gold nanoparticles (Au NPs), and platinum nanoparticles (Pt NPs). These chemistries include grafting of cellulose fibers with imidazole and dithiol groups, as well as the aminosilanization of cellulose fibers (both with and without subsequent grafting with dithiol groups). Cellulose modifications and nanoparticle immobilization are characterized by multiple techniques, including, but not limited to, X-ray photoelectron spectroscopy, scanning electron microscopy, and optical imaging, extinction, and fluorescence measurements. We demonstrate the on-paper immobilization of color-tuned mixtures of QDs, on-paper patterning of QDs by microcontact printing, and post-immobilization enhancement of energy transfer and model assays of protease activity. The robustness of QD photoluminescence is also evaluated between immobilization chemistries. Paper-immobilized Au NPs and Pt NPs are evaluated as potential substrates for SERS and as supported catalysts for a model decolorization reaction. Our cumulative results indicate that there may not be a one-size-fits-all immobilization chemistry. Instead, the immobilization chemistry should be tailored and optimized for the downstream application.
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Affiliation(s)
- Hyungki Kim
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Michael V Tran
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Eleonora Petryayeva
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Olga Solodova
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kimihiro Susumu
- Jacobs Corporation, Hanover, Maryland 21076, United States
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, United States
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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Cardoso Dos Santos M, Colin I, Ribeiro Dos Santos G, Susumu K, Demarque M, Medintz IL, Hildebrandt N. Time-Gated FRET Nanoprobes for Autofluorescence-Free Long-Term In Vivo Imaging of Developing Zebrafish. Adv Mater 2020; 32:e2003912. [PMID: 33252168 DOI: 10.1002/adma.202003912] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/16/2020] [Indexed: 05/25/2023]
Abstract
The zebrafish is an important vertebrate model for disease, drug discovery, toxicity, embryogenesis, and neuroscience. In vivo fluorescence microscopy can reveal cellular and subcellular details down to the molecular level with fluorescent proteins (FPs) currently the main tool for zebrafish imaging. However, long maturation times, low brightness, photobleaching, broad emission spectra, and sample autofluorescence are disadvantages that cannot be easily overcome by FPs. Here, a bright and photostable terbium-to-quantum dot (QD) Förster resonance energy transfer (FRET) nanoprobe with narrow and tunable emission bands for intracellular in vivo imaging is presented. The long photoluminescence (PL) lifetime enables time-gated (TG) detection without autofluorescence background. Intracellular four-color multiplexing with a single excitation wavelength and in situ assembly and FRET to mCherry demonstrate the versatility of the TG-FRET nanoprobes and the possibility of in vivo bioconjugation to FPs and combined nanoprobe-FP FRET sensing. Upon injection at the one-cell stage, FRET nanoprobes can be imaged in developing zebrafish embryos over seven days with toxicity similar to injected RNA and strongly improved signal-to-background ratios compared to non-TG imaging. This work provides a strategy for advancing in vivo fluorescence imaging applications beyond the capabilities of FPs.
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Affiliation(s)
- Marcelina Cardoso Dos Santos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, Orsay Cedex, 91405, France
| | - Ingrid Colin
- Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, CNRS, Gif-sur-Yvette, 91190, France
| | - Gabriel Ribeiro Dos Santos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, Orsay Cedex, 91405, France
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- KeyW Corporation, Hanover, MD, 21076, USA
| | - Michaël Demarque
- Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, CNRS, Gif-sur-Yvette, 91190, France
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Niko Hildebrandt
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, Orsay Cedex, 91405, France
- Laboratoire COBRA (Chimie Organique, Bioorganique Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, Mont-Saint-Aignan, 76821, France
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Abstract
The engineering and manipulation of delocalized molecular exciton states is a key component for artificial biomimetic light harvesting complexes as well as alternative circuitry platforms based on exciton propagation. Here we examine the consequences of strong electronic coupling in cyanine homodimers on DNA duplex scaffolds. The most closely spaced dyes, attached to positions directly across the double-helix from one another, exhibit pronounced Davydov splitting due to strong electronic coupling. We demonstrate that the DNA scaffold is sufficiently robust to support observation of the transition from the lowest energy (J-like) one-exciton state to the nonlocal two-exciton state, where each cyanine dye is in the excited state. This transition proceeds via sequential photon absorption and persists for the lifetime of the exciton, establishing this as a controlled method for creating two-exciton states. Our observations suggest that DNA-organized dye networks have potential as platforms for molecular logic gates and entangled photon emission based on delocalized two-exciton states.
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Affiliation(s)
- Paul D Cunningham
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Sebastián A Díaz
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Bernard Yurke
- Boise State University, Boise, Idaho 83725, United States
| | - Igor L Medintz
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Hastman DA, Melinger JS, Aragonés GL, Cunningham PD, Chiriboga M, Salvato ZJ, Salvato TM, Brown CW, Mathur D, Medintz IL, Oh E, Díaz SA. Femtosecond Laser Pulse Excitation of DNA-Labeled Gold Nanoparticles: Establishing a Quantitative Local Nanothermometer for Biological Applications. ACS Nano 2020; 14:8570-8583. [PMID: 32677822 DOI: 10.1021/acsnano.0c02899] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Femtosecond (fs) laser pulsed excitation of plasmonic nanoparticle (NP)-biomolecule conjugates is a promising method to locally heat biological materials. Studies have demonstrated that fs pulses of light can modulate the activity of DNA or proteins when attached to plasmonic NPs; however, the precision over subsequent biological function remains largely undetermined. Specifically, the temperature the localized biomolecules "experience" remains unknown. We used 55 nm gold nanoparticles (AuNPs) displaying double-stranded (ds) DNA to examine how, for dsDNA with different melting temperatures, the laser pulse energy fluence and bulk solution temperature affect the rate of local DNA denaturation. A universal "template" single-stranded DNA was attached to the AuNP surface, and three dye-labeled probe strands, distinct in length and melting temperature, were hybridized to it creating three individual dsDNA-AuNP bioconjugates. The dye-labeled probe strands were used to quantify the rate and amount of DNA release after a given number of light pulses, which was then correlated to the dsDNA denaturation temperature, resulting in a quantitative nanothermometer. The localized DNA denaturation rate could be modulated by more than threefold over the biologically relevant range of 8-53 °C by varying pulse energy fluence, DNA melting temperature, and surrounding bath temperature. With a modified dissociation equation tailored for this system, a "sensed" temperature parameter was extracted and compared to simulated AuNP temperature profiles. Determining actual biological responses in such systems can allow researchers to design precision nanoscale photothermal heating sources.
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Affiliation(s)
- David A Hastman
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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Hallaj T, Amjadi M, Qiu X, Susumu K, Medintz IL, Hildebrandt N. Terbium-to-quantum dot Förster resonance energy transfer for homogeneous and sensitive detection of histone methyltransferase activity. Nanoscale 2020; 12:13719-13730. [PMID: 32573632 DOI: 10.1039/d0nr03383a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The development of rapid, simple, and versatile biosensors for monitoring the activity of histone modifying enzymes (HMEs) is needed for the improvement of diagnostic assays, screening of HME inhibitors, and a better understanding of HME kinetics in different environments. Nanoparticles can play an important role in this regard by improving or complementing currently available enzyme detection technologies. Here, we present the development and application of a homogeneous methyltransferase (SET7/9) assay based on time-gated Förster resonance energy transfer (TG-FRET) between terbium complexes (Tb) and luminescent semiconductor quantum dots (QDs). Specific binding of a Tb-antibody conjugate to a SET7/9-methylated Lys4 on a histone H3(1-21) peptide substrate attached to the QD surface resulted in efficient FRET and provided the mechanism for monitoring the SET7/9 activity. Two common peptide-QD attachment strategies (biotin-streptavidin and polyhistidine-mediated self-assembly), two different QD colors (625 and 705 nm), and enzyme sensing with post- or pre-assembled QD-peptide conjugates demonstrated the broad applicability of this assay design. Limits of detection in the low picomolar concentration range, high selectivity tested against non-specific antibodies, enzymes, and co-factors, determination of the inhibition constants of the SET7/9 inhibitors SAH and (R)-PFI-2, and analysis of the co-factor (SAM) concentration-dependent enzyme kinetics of SET7/9 which followed the Michaelis-Menten model highlighted the excellent performance of this TG-FRET HME activity assay.
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Affiliation(s)
- Tooba Hallaj
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran. and Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia 5714783734, Iran
| | - Mohammad Amjadi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran.
| | - Xue Qiu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France and School of Medicine and Pharmacy, Ocean University of China. 5, Yushan Road, 266003 Qingdao, Shandong, China
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA and KeyW Corporation, Hanover, Maryland 21076, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA
| | - Niko Hildebrandt
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France and nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France.
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Léger C, Yahia-Ammar A, Susumu K, Medintz IL, Urvoas A, Valerio-Lepiniec M, Minard P, Hildebrandt N. Picomolar Biosensing and Conformational Analysis Using Artificial Bidomain Proteins and Terbium-to-Quantum Dot Förster Resonance Energy Transfer. ACS Nano 2020; 14:5956-5967. [PMID: 32216328 DOI: 10.1021/acsnano.0c01410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although antibodies remain a primary recognition element in all forms of biosensing, functional limitations arising from their size, stability, and structure have motivated the development and production of many different artificial scaffold proteins for biological recognition. However, implementing such artificial binders into functional high-performance biosensors remains a challenging task. Here, we present the design and application of Förster resonance energy transfer (FRET) nanoprobes comprising small artificial proteins (αRep bidomains) labeled with a Tb complex (Tb) donor on the C-terminus and a semiconductor quantum dot (QD) acceptor on the N-terminus. Specific binding of one or two protein targets to the αReps induced a conformational change that could be detected by time-resolved Tb-to-QD FRET. These single-probe FRET switches were used in a separation-free solution-phase assay to quantify different protein targets at sub-nanomolar concentrations and to measure the conformational changes with sub-nanometer resolution. Probing ligand-receptor binding under physiological conditions at very low concentrations in solution is a special feature of FRET that can be efficiently combined with other structural characterization methods to develop, understand, and optimize artificial biosensors. Our results suggest that the αRep FRET nanoprobes have a strong potential for their application in advanced diagnostics and intracellular live-cell imaging of ligand-receptor interactions.
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Affiliation(s)
- Corentin Léger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Akram Yahia-Ammar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | - Agathe Urvoas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie Valerio-Lepiniec
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Minard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Niko Hildebrandt
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France
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Breger JC, Susumu K, Lasarte-Aragonés G, Díaz SA, Brask J, Medintz IL. Quantum Dot Lipase Biosensor Utilizing a Custom-Synthesized Peptidyl-Ester Substrate. ACS Sens 2020; 5:1295-1304. [PMID: 32096987 DOI: 10.1021/acssensors.9b02291] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lipases are an important class of lipid hydrolyzing enzymes that play significant roles in many aspects of cell biology and digestion; they also have large roles in commercial food and biofuel preparation and are being targeted for pharmaceutical development. Given these, and many other biotechnological roles, sensitive and specific biosensors capable of monitoring lipase activity in a quantitative manner are critical. Here, we describe a Förster resonance energy transfer (FRET)-based biosensor that originates from a custom-synthesized ester substrate displaying a peptide at one end and a dye acceptor at the other. These substrates were ratiometrically self-assembled to luminescent semiconductor quantum dot (QD) donors by metal affinity coordination using the appended peptide's terminal hexahistidine motif to give rise to the full biosensing construct. This resulted in a high rate of FRET between the QD donor and the proximal substrate's dye acceptor. The lipase hydrolyzed the intervening target ester bond in the peptide substrate which, in turn, displaced the dye acceptor containing component and altered the rate of FRET in a concentration-dependent manner. Specifics of the substrate's stepwise synthesis are described along with the sensors assembly, characterization, and application in a quantitative proof-of-concept demonstration assay that is based on an integrated Michaelis-Menten kinetic approach. The utility of this unique nanoparticle-based architecture within a sensor configuration is then discussed.
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Affiliation(s)
- Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, U.S. Naval Research Laboratory, Code 5600, Washington, District of Columbia 20375, United States
- KeyW Corporation, Hanover, Maryland 21076, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
- Department of Bioengineering, George Mason University, Fairfax, Virginia 22030, United States
| | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
| | - Jesper Brask
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
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Mazuski RJ, Díaz SA, Wood RE, Lloyd LT, Klein WP, Mathur D, Melinger JS, Engel GS, Medintz IL. Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency. J Phys Chem Lett 2020; 11:4163-4172. [PMID: 32391695 DOI: 10.1021/acs.jpclett.0c01020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
DNA scaffolds enable base-pair-specific positioning of fluorescent molecules, allowing for nanometer-scale precision in controlling multidye interactions. Expanding on this concept, DNA-based molecular photonic wires (MPWs) allow for light harvesting and directional propagation of photonic energy on the nanometer scale. The most common MPW examples exploit Förster resonance energy transfer (FRET), and FRET between the same dye species (HomoFRET) was recently shown to increase the distance and efficiency at which MPWs can function. Although increased proximity between adjacent fluorophores can be used to increase the energy transfer efficiency, FRET assumptions break down as the distance between the dye molecules becomes comparable to their size (∼2 nm). Here we compare dye conjugation with single versus dimer Cy5 dye repeats as HomoFRET MPW components on a double-crossover DNA scaffold. At room temperature (RT) under low-light conditions, end-labeled uncoupled dye molecules provide optimal transfer, while the Cy5 dimers show ultrafast (<100 ps) nonradiative decay that severely limits their functionality. Of particular interest is the observation that through increased excitation fluence as well as cryogenic temperatures, the dimeric MPW shows suppression of the ultrafast decay, demonstrating fluorescence lifetimes similar to the single Cy5 MPWs. This work points to the complex dynamic capabilities of dye-based nanophotonic networks, where dye positioning and interactions can become critical, and could be used to extend the lengths and complexities of such dye-DNA devices, enabling multiparameter nanophotonic circuitry.
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Affiliation(s)
- Richard J Mazuski
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ryan E Wood
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Lawson T Lloyd
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Divita Mathur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Joseph S Melinger
- Electronic Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Gregory S Engel
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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