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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] [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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2
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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] [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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3
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Li J, Shi J, Wang Y, Yao H, Meng L, Liu H. An elaborate biomolecular keypad lock based on electrochromism of viologen derivatives and bioelectrocatalytic reduction of CO 2 at supramolecular hydrogel film electrodes. Biosens Bioelectron 2023; 238:115560. [PMID: 37542980 DOI: 10.1016/j.bios.2023.115560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/01/2023] [Accepted: 07/30/2023] [Indexed: 08/07/2023]
Abstract
Herein, the short peptide N-fluorenemethoxycarbonyl diphenylalanine (Fmoc-FF) was used to immobilize both diallyl viologen (DAV) and the enzyme formate dehydrogenase (FDH) to form Fmoc-FF/DAV/FDH supramolecular hydrogel films on an electrode surface by a simple solvent-controlled self-assembly method. The DAV component in the films exhibited multiple properties, such as electrochromism and electrofluorochromism, and acted as an electrochemical mediator. A high efficiency of bioelectrocatalytic reduction of CO2 to formate (HCOO-) was obtained by the natural FDH enzyme and the artificial coenzyme factor DAV both immobilized in the same films. The supramolecular hydrogel films with CO2, voltage and light as stimulating factors and current, fluorescence and UV-vis extinction as responsive signals, were further applied for the construction of complex biomolecular logic systems and information encryption. A 3-input/7-output biomolecular logic gate and several logic devices, including an encoder/decoder, a parity checker, and a keypad lock, were constructed. Especially, the biomolecular keypad lock with 3 types of signals as outputs significantly enhanced the security level of information encryption. In this work, a supramolecular self-assembly interface was simply fabricated with complex biomolecular computational functions using immobilized molecules as the computational core, greatly broadening the application range of supramolecular hydrogel films and providing an idea for new designs of bioinformation encryption through the use of a simple film system.
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Affiliation(s)
- Jiaxuan Li
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Jiaqi Shi
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Yizhu Wang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Huiqin Yao
- School of Public Health, Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Lingchen Meng
- School of Public Health, Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Hongyun Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China.
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4
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Mougkogiannis P, Adamatzky A. Logical gates in ensembles of proteinoid microspheres. PLoS One 2023; 18:e0289433. [PMID: 37721941 PMCID: PMC10506713 DOI: 10.1371/journal.pone.0289433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023] Open
Abstract
Proteinoids are thermal proteins which swell into microspheres in aqueous solution. Ensembles of proteinoids produce electrical spiking activity similar to that of neurons. We introduce a novel method for implementing logical gates in the ensembles of proteinoid microspheres using chronoamperometry. Chronoamperometry is a technique that involves applying a voltage pulse to proteinoid microspheres and measuring their current response. We have observed that proteinoids exhibit distinct current patterns that align with various logical outputs. We identify four types of logical gates: AND, OR, XOR, and NAND. These gates are determined by the current response of proteinoid microspheres. Additionally, we demonstrate that proteinoid microspheres have the ability to modify their current response over time, which is influenced by their previous exposure to voltage. This indicates that they possess a capacity for learning and are capable of adapting to their environment. Our research showcases the ability of proteinoid microspheres to perform logical operations and computations through their inherent electrical properties.
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Affiliation(s)
| | - Andrew Adamatzky
- Unconventional Computing Lab, University of the West of England, Bristol, United Kingdom
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5
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Kubba R, Kumar Singh M, Yadav O, Kumar A. Fӧrster resonance energy transfer (FRET) between CdSe quantum dots and ABA phosphorus(V) corroles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 291:122345. [PMID: 36657286 DOI: 10.1016/j.saa.2023.122345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 12/21/2022] [Accepted: 01/08/2023] [Indexed: 06/17/2023]
Abstract
In this article, highly fluorescent phosphorus(V) corrole was synthesised which was then combined with CdSe quantum dots (QDs) in order to study Förster resonance energy transfer (FRET) mechanism between CdSe QDs (donor) and phosphorus corrole (acceptor). Spectral overlap between QD's emission profile and corrole's absorption profile was found to be significant enough to result into Förster resonance energy transfer (FRET). The UV-vis spectrum experienced increase in the absorption bands on addition of phosphorus corrole to CdSe QDs suggesting QD-corrole conjugation. In the steady state fluorescence measurements, emission spectrum observed quenching in the fluorescence intensity of prepared CdSe QDs on addition of phosphorus corrole. Likewise, in case of time-resolved fluorescence measurements it was noticed that the CdSe QD's lifetime was greatly quenched by the presence of a corrole acceptor. Stern-Volmer plot was made to show quenching in this case was dynamic in nature. Based on the results of UV-vis, steady state and time-resolved fluorescence measurements the plausible mechanism behind such observations is considered to be FRET.
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Affiliation(s)
- Ritika Kubba
- Department of Applied Chemistry, Delhi Technological University, Delhi 42, India
| | | | - Omprakash Yadav
- Department of Chemistry, ARSD College, University of Delhi, Delhi, India
| | - Anil Kumar
- Department of Applied Chemistry, Delhi Technological University, Delhi 42, India.
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6
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Chen C, Wei X, Parsons MF, Guo J, Banal JL, Zhao Y, Scott MN, Schlau-Cohen GS, Hernandez R, Bathe M. Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami. Nat Commun 2022; 13:4935. [PMID: 35999227 PMCID: PMC9399249 DOI: 10.1038/s41467-022-32662-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
Control over the copy number and nanoscale positioning of quantum dots (QDs) is critical to their application to functional nanomaterials design. However, the multiple non-specific binding sites intrinsic to the surface of QDs have prevented their fabrication into multi-QD assemblies with programmed spatial positions. To overcome this challenge, we developed a general synthetic framework to selectively attach spatially addressable QDs on 3D wireframe DNA origami scaffolds using interfacial control of the QD surface. Using optical spectroscopy and molecular dynamics simulation, we investigated the fabrication of monovalent QDs of different sizes using chimeric single-stranded DNA to control QD surface chemistry. By understanding the relationship between chimeric single-stranded DNA length and QD size, we integrated single QDs into wireframe DNA origami objects and visualized the resulting QD-DNA assemblies using electron microscopy. Using these advances, we demonstrated the ability to program arbitrary 3D spatial relationships between QDs and dyes on DNA origami objects by fabricating energy-transfer circuits and colloidal molecules. Our design and fabrication approach enables the geometric control and spatial addressing of QDs together with the integration of other materials including dyes to fabricate hybrid materials for functional nanoscale photonic devices.
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Affiliation(s)
- Chi Chen
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Xingfei Wei
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Molly F. Parsons
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Jiajia Guo
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,grid.458489.c0000 0001 0483 7922Present Address: Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - James L. Banal
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,Present Address: Cache DNA, Inc., 200 Lincoln Centre Drive, Foster City, CA 94404 USA
| | - Yinong Zhao
- grid.21107.350000 0001 2171 9311Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Madelyn N. Scott
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Gabriela S. Schlau-Cohen
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Rigoberto Hernandez
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA ,grid.21107.350000 0001 2171 9311Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218 USA ,grid.21107.350000 0001 2171 9311Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Mark Bathe
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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7
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Tate N, Miyata Y, Sakai SI, Nakamura A, Shimomura S, Nishimura T, Kozuka J, Ogura Y, Tanida J. Quantitative analysis of nonlinear optical input/output of a quantum-dot network based on the echo state property. OPTICS EXPRESS 2022; 30:14669-14676. [PMID: 35473206 DOI: 10.1364/oe.450132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The echo state property, which is related to the dynamics of a neural network excited by input driving signals, is one of the well-known fundamental properties of recurrent neural networks. During the echo state, the neural network reveals an internal memory function that enables it to remember past inputs. Due to the echo state property, the neural network will asymptotically update its condition from the initial condition and is expected to exhibit temporally nonlinear input/output. As a physical neural network, we fabricated a quantum-dot network that is driven by sequential optical-pulse inputs and reveals corresponding outputs, by random dispersion of quantum-dots as its components. In the network, the localized optical energy of excited quantum-dots is allowed to transfer to neighboring quantum-dots, and its stagnation time due to multi-step transfers corresponds to the hold time of the echo state of the network. From the experimental results of photon counting of the fluorescence outputs, we observed nonlinear optical input/output of the quantum-dot network due to its echo state property. Its nonlinearity was quantitatively verified by a correlation analysis. As a result, the relation between the nonlinear input/outputs and the individual compositions of the quantum-dot network was clarified.
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8
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Wei W, Li J, Yao H, Liu H. A molecular keypad lock with 3-output signals built on stimulus-responsive polymer film electrodes containing diallyl viologen. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.139839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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9
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Glionna C, Kumar V, Le Saux G, Pramanik B, Wagner N, Cohen-Luria R, Ashkenasy G, Ashkenasy N. Dynamic Surface Layer Coiled Coil Proteins Processing Analog-to-Digital Information. J Am Chem Soc 2021; 143:17441-17451. [PMID: 34652148 DOI: 10.1021/jacs.1c06356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Surface layer proteins perform multiple functions in prokaryotic cells, including cellular defense, cell-shape maintenance, and regulation of import and export of materials. However, mimicking the complex and dynamic behavior of such two-dimensional biochemical systems is challenging, and hence research has so far focused mainly on the design and manipulation of the structure and functionality of protein assemblies in solution. Motivated by the new opportunities that dynamic surface layer proteins may offer for modern technology, we herein demonstrate that immobilization of coiled coil proteins onto an inorganic surface facilitates complex behavior, manifested by reversible chemical reactions that can be rapidly monitored as digital surface readouts. Using multiple chemical triggers as inputs and several surface characteristics as outputs, we can realize reversible switching and logic gate operations that are read in parallel. Moreover, using the same coiled coil protein monolayers for derivatization of nanopores drilled into silicon nitride membranes facilitates control over ion and mass transport through the pores, thereby expanding the applicability of the dynamic coiled coil system for contemporary stochastic biosensing applications.
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Affiliation(s)
- Chiara Glionna
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Vinod Kumar
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Guillaume Le Saux
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bapan Pramanik
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nurit Ashkenasy
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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10
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DNA Microsystems for Biodiagnosis. MICROMACHINES 2020; 11:mi11040445. [PMID: 32340280 PMCID: PMC7231314 DOI: 10.3390/mi11040445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022]
Abstract
Researchers are continuously making progress towards diagnosis and treatment of numerous diseases. However, there are still major issues that are presenting many challenges for current medical diagnosis. On the other hand, DNA nanotechnology has evolved significantly over the last three decades and is highly interdisciplinary. With many potential technologies derived from the field, it is natural to begin exploring and incorporating its knowledge to develop DNA microsystems for biodiagnosis in order to help address current obstacles, such as disease detection and drug resistance. Here, current challenges in disease detection are presented along with standard methods for diagnosis. Then, a brief overview of DNA nanotechnology is introduced along with its main attractive features for constructing biodiagnostic microsystems. Lastly, suggested DNA-based microsystems are discussed through proof-of-concept demonstrations with improvement strategies for standard diagnostic approaches.
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Cardoso Dos Santos M, Algar WR, Medintz IL, Hildebrandt N. Quantum dots for Förster Resonance Energy Transfer (FRET). Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115819] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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12
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Liang J, Wei W, Yao H, Shi K, Liu H. A biocomputing platform with electrochemical and fluorescent signal outputs based on multi-sensitive copolymer film electrodes with entrapped Au nanoclusters and tetraphenylethene and electrocatalysis of NADH. Phys Chem Chem Phys 2019; 21:24572-24583. [PMID: 31663551 DOI: 10.1039/c9cp03687c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this work, poly(N,N'-dimethylaminoethylmethacrylate-co-N-isopropylacrylamide) copolymer films were polymerized on the surface of Au electrodes with a facile one-step method, and Au nanoclusters (AuNCs) and tetraphenylethene (TPE) were synchronously embedded in the films, designated as P(DMA-co-NIPA)/AuNCs/TPE. Ferrocene dicarboxylic acid (FDA), an electroactive probe in solution displayed inverse pH- and SO42--sensitive on-off cyclic voltammetric (CV) behaviors at the film electrodes. The electrocatalytic oxidation of nicotinamide adenine dinucleotide (NADH) mediated by FDA in solution could substantially amplify the CV response difference between the on and off states. Moreover, the two fluorescence emission (FL) signals from the TPE constituent at 450 nm and AuNCs component at 660 nm in the films also demonstrated SO42-- and pH-sensitive behaviors. Based on the aforementioned results, a 4-input/9-output biomolecular logic circuit was constructed with pH, Na2SO4, FDA and NADH as the inputs, and the CV signals and the FL responses at 450 and 660 nm at different levels as the outputs. Additionally, some functional non-Boolean devices were elaborately designed on an identical platform, including a 1-to-2 decoder, a 2-to-1 encoder, a 1-to-2 demultiplexer and different types of keypad locks. This work combines copolymer films, bioelectrocatalysis, and fluorescence together so that more complicated biocomputing systems could be established. This work may pave a new way to develop advanced and sophisticated biocomputing logic circuits and functional devices in the future.
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Affiliation(s)
- Jiying Liang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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13
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Tsai HY, Kim H, Massey M, Krause KD, Algar WR. Concentric FRET: a review of the emerging concept, theory, and applications. Methods Appl Fluoresc 2019; 7:042001. [DOI: 10.1088/2050-6120/ab2b2f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Anni M. Polymer-II-VI Nanocrystals Blends: Basic Physics and Device Applications to Lasers and LEDs. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E1036. [PMID: 31331048 PMCID: PMC6669662 DOI: 10.3390/nano9071036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/08/2019] [Accepted: 07/16/2019] [Indexed: 02/04/2023]
Abstract
Hybrid thin films that combine organic conjugated molecules and semiconductors nanocrystals (NCs) have been deeply investigated in the previous years, due to their capability to provide an extremely broad tuning of their electronic and optical properties. In this paper we review the main aspects of the basic physics of the organic-inorganic interaction and the actual state of the art of lasers and light emitting diodes based on hybrid active materials.
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Affiliation(s)
- Marco Anni
- Dipartimento di Matematica e Fisica "Ennio De Giorgi", Università del Salento, Via per Arnesano, 73100 Lecce, Italy.
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15
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Chen C, Corry B, Huang L, Hildebrandt N. FRET-Modulated Multihybrid Nanoparticles for Brightness-Equalized Single-Wavelength Barcoding. J Am Chem Soc 2019; 141:11123-11141. [DOI: 10.1021/jacs.9b03383] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chi Chen
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
| | - Ben Corry
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Liang Huang
- College of Chemical Engineering, Zhejiang University of Technology, 310014, Hangzhou, People’s Republic of China
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
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Seo J, Kim S, Park HH, Nam JM. Biocomputing with Nanostructures on Lipid Bilayers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900998. [PMID: 31026121 DOI: 10.1002/smll.201900998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Biocomputation is the algorithmic manipulation of biomolecules. Nanostructures, most notably DNA nanostructures and nanoparticles, become active substrates for biocomputation when modified with stimuli-responsive, programmable biomolecular ligands. This approach-biocomputing with nanostructures ("nano-bio computing")-allows autonomous control of matter and information at the nanoscale; their dynamic assemblies and beneficial properties can be directed without human intervention. Recently, lipid bilayers interfaced with nanostructures have emerged as a new biocomputing platform. This new nano-bio interface, which exploits lipid bilayers as a chemical circuit board for information processing, offers a unique reaction space for realizing nanostructure-based computation at a previously unexplored dimension. In this Concept, recent advances in nano-bio computing are briefly reviewed and the newly emerging concept of biocomputing with nanostructures on lipid bilayers is introduced.
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Affiliation(s)
- Jinyoung Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Sungi Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Ha H Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
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17
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Bui H, Brown CW, Buckhout-White S, Díaz SA, Stewart MH, Susumu K, Oh E, Ancona MG, Goldman ER, Medintz IL. Transducing Protease Activity into DNA Output for Developing Smart Bionanosensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805384. [PMID: 30803148 DOI: 10.1002/smll.201805384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/28/2019] [Indexed: 06/09/2023]
Abstract
DNA can process information through sequence-based reorganization but cannot typically receive input information from most biological processes and translate that into DNA compatible language. Coupling DNA to a substrate responsive to biological events can address this limitation. A two-component sensor incorporating a chimeric peptide-DNA substrate is evaluated here as a protease-to-DNA signal convertor which transduces protease activity through DNA gates that discriminate between different input proteases. Acceptor dye-labeled peptide-DNAs are assembled onto semiconductor quantum dot (QD) donors as the input gate. Addition of trypsin or chymotrypsin cleaves their cognate peptide sequence altering the efficiency of Förster resonance energy transfer (FRET) with the QD and frees a DNA output which interacts with a tetrahedral output gate. Downstream output gate rearrangement results in FRET sensitization of a new acceptor dye. Following characterization of component assembly and optimization of individual steps, sensor ability to discriminate between the two proteases is confirmed along with effects from joint interactions where potential for cross-talk is highest. Processing multiple bits of information for a sensing outcome provides more confidence than relying on a single change especially for the discrimination between different targets. Coupling other substrates to DNA that respond similarly could help target other types of enzymes.
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Affiliation(s)
- Hieu Bui
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- National Research Council, 500 Fifth Street NW, Keck 576, Washington, DC, 20001, USA
| | - Carl W Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- College of Science, George Mason University, Fairfax, VA, 22030, USA
| | - Susan Buckhout-White
- Center for Bio/Molecular Science and Engineering, Code 6900, 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
| | - Michael H Stewart
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- KeyW Corporation, Hanover, MD, 21076, USA
| | - Eunkeu Oh
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- KeyW Corporation, Hanover, MD, 21076, USA
| | - Mario G Ancona
- Electronic Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Ellen R Goldman
- 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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18
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Chen C, Ao L, Wu Y, Cifliku V, Cardoso Dos Santos M, Bourrier E, Delbianco M, Parker D, Zwier JM, Huang L, Hildebrandt N. Single-Nanoparticle Cell Barcoding by Tunable FRET from Lanthanides to Quantum Dots. Angew Chem Int Ed Engl 2018; 57:13686-13690. [PMID: 30084526 PMCID: PMC6391968 DOI: 10.1002/anie.201807585] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/06/2018] [Indexed: 12/19/2022]
Abstract
Fluorescence barcoding based on nanoparticles provides many advantages for multiparameter imaging. However, creating different concentration-independent codes without mixing various nanoparticles and by using single-wavelength excitation and emission for multiplexed cellular imaging is extremely challenging. Herein, we report the development of quantum dots (QDs) with two different SiO2 shell thicknesses (6 and 12 nm) that are coated with two different lanthanide complexes (Tb and Eu). FRET from the Tb or Eu donors to the QD acceptors resulted in four distinct photoluminescence (PL) decays, which were encoded by simple time-gated (TG) PL intensity detection in three individual temporal detection windows. The well-defined single-nanoparticle codes were used for live cell imaging and a one-measurement distinction of four different cells in a single field of view. This single-color barcoding strategy opens new opportunities for multiplexed labeling and tracking of cells.
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Affiliation(s)
- Chi Chen
- NanoBioPhotonicsInstitute for Integrative Biology of the Cell (I2BC)Université Paris-Saclay, Université Paris-Sud, CNRS, CEA91400OrsayFrance
| | - Lijiao Ao
- Institute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences518055ShenzhenP. R. China
| | - Yu‐Tang Wu
- NanoBioPhotonicsInstitute for Integrative Biology of the Cell (I2BC)Université Paris-Saclay, Université Paris-Sud, CNRS, CEA91400OrsayFrance
| | - Vjona Cifliku
- NanoBioPhotonicsInstitute for Integrative Biology of the Cell (I2BC)Université Paris-Saclay, Université Paris-Sud, CNRS, CEA91400OrsayFrance
| | - Marcelina Cardoso Dos Santos
- NanoBioPhotonicsInstitute for Integrative Biology of the Cell (I2BC)Université Paris-Saclay, Université Paris-Sud, CNRS, CEA91400OrsayFrance
| | | | - Martina Delbianco
- Department of ChemistryDurham UniversitySouth RoadDH13LEDurhamUK
- Current affiliation: Max Planck Institute of Colloids and InterfacesPotsdamGermany
| | - David Parker
- Department of ChemistryDurham UniversitySouth RoadDH13LEDurhamUK
| | | | - Liang Huang
- College of Chemical EngineeringZhejiang University of Technology310014HangzhouP. R. China
| | - Niko Hildebrandt
- NanoBioPhotonicsInstitute for Integrative Biology of the Cell (I2BC)Université Paris-Saclay, Université Paris-Sud, CNRS, CEA91400OrsayFrance
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19
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Tregubov AA, Nikitin PI, Nikitin MP. Advanced Smart Nanomaterials with Integrated Logic-Gating and Biocomputing: Dawn of Theranostic Nanorobots. Chem Rev 2018; 118:10294-10348. [DOI: 10.1021/acs.chemrev.8b00198] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Andrey A. Tregubov
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
| | - Petr I. Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, Moscow 119991, Russia
| | - Maxim P. Nikitin
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
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20
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Wang Y, Howes PD, Kim E, Spicer CD, Thomas MR, Lin Y, Crowder SW, Pence IJ, Stevens MM. Duplex-Specific Nuclease-Amplified Detection of MicroRNA Using Compact Quantum Dot-DNA Conjugates. ACS APPLIED MATERIALS & INTERFACES 2018; 10:28290-28300. [PMID: 30113161 PMCID: PMC6141140 DOI: 10.1021/acsami.8b07250] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/31/2018] [Indexed: 05/18/2023]
Abstract
Advances in nanotechnology have provided new opportunities for the design of next-generation nucleic acid biosensors and diagnostics. Indeed, combining advances in functional nanoparticles, DNA nanotechnology, and nuclease-enzyme-based amplification can give rise to new assays with advantageous properties. In this work, we developed a microRNA (miRNA) assay using bright fluorescent quantum dots (QDs), simple DNA probes, and the enzyme duplex-specific nuclease. We employed an isothermal target-recycling mechanism, where a single miRNA target triggers the cleavage of many DNA signal probes. The incorporation of DNA-functionalized QDs enabled a quantitative fluorescent readout, mediated by Förster resonance energy transfer (FRET)-based interaction with the DNA signal probes. Our approach splits the reaction in two, performing the enzyme-mediated amplification and QD-based detection steps separately such that each reaction could be optimized for performance of the active components. Target recycling gave ca. 3 orders of magnitude amplification, yielding highly sensitive detection with a limit of 42 fM (or 1.2 amol) of miR-148, with excellent selectivity versus mismatched sequences and other miRNAs. Furthermore, we used an alternative target (miR-21) and FRET pair for direct and absolute quantification of miR-21 in RNA extracts from human cancer and normal cell lines.
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Affiliation(s)
- Ye Wang
- Department of Materials, Department of
Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K.
| | | | - Eunjung Kim
- Department of Materials, Department of
Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K.
| | | | - Michael R. Thomas
- Department of Materials, Department of
Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K.
| | - Yiyang Lin
- Department of Materials, Department of
Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K.
| | - Spencer W. Crowder
- Department of Materials, Department of
Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K.
| | - Isaac J. Pence
- Department of Materials, Department of
Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K.
| | - Molly M. Stevens
- Department of Materials, Department of
Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K.
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21
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Chen C, Ao L, Wu YT, Cifliku V, Cardoso Dos Santos M, Bourrier E, Delbianco M, Parker D, Zwier JM, Huang L, Hildebrandt N. Einzelnanopartikel-Strichkodierung von Zellen mittels durchstimmbarem FRET von Lanthanoiden auf Quantenpunkte. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807585] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Chi Chen
- NanoBioPhotonics; Institute for Integrative Biology of the Cell (I2BC); Université Paris-Saclay, Université Paris-Sud, CNRS, CEA; 91400 Orsay Frankreich
| | - Lijiao Ao
- Institute of Biomedicine and Biotechnology; Shenzhen Institutes of Advanced Technology; Chinese Academy of Sciences; 518055 Shenzhen P. R. China
| | - Yu-Tang Wu
- NanoBioPhotonics; Institute for Integrative Biology of the Cell (I2BC); Université Paris-Saclay, Université Paris-Sud, CNRS, CEA; 91400 Orsay Frankreich
| | - Vjona Cifliku
- NanoBioPhotonics; Institute for Integrative Biology of the Cell (I2BC); Université Paris-Saclay, Université Paris-Sud, CNRS, CEA; 91400 Orsay Frankreich
| | - Marcelina Cardoso Dos Santos
- NanoBioPhotonics; Institute for Integrative Biology of the Cell (I2BC); Université Paris-Saclay, Université Paris-Sud, CNRS, CEA; 91400 Orsay Frankreich
| | | | - Martina Delbianco
- Department of Chemistry; Durham University; South Road DH13LE Durham Großbritannien
- Derzeitige Adresse: Max-Planck-Institut für Kolloide und Grenzflächen; Potsdam Deutschland
| | - David Parker
- Department of Chemistry; Durham University; South Road DH13LE Durham Großbritannien
| | | | - Liang Huang
- College of Chemical Engineering; Zhejiang University of Technology; 310014 Hangzhou P. R. China
| | - Niko Hildebrandt
- NanoBioPhotonics; Institute for Integrative Biology of the Cell (I2BC); Université Paris-Saclay, Université Paris-Sud, CNRS, CEA; 91400 Orsay Frankreich
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22
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Qiu X, Guo J, Xu J, Hildebrandt N. Three-Dimensional FRET Multiplexing for DNA Quantification with Attomolar Detection Limits. J Phys Chem Lett 2018; 9:4379-4384. [PMID: 30016106 DOI: 10.1021/acs.jpclett.8b01944] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Photoluminescence (PL) multiplexing usually relies on spectral or temporal separation. A combination into higher-order multiplexing for biosensing is extremely challenging because the PL intensity is required for target quantification at very low concentrations and the interplay of color, lifetime, and intensity must be carefully adapted. Here, we demonstrate time-gated Förster resonance energy transfer (TG-FRET) from a long-lifetime Tb complex to Cy3.5 and Cy5.5 dyes for spectrotemporal multiplexing of four different DNA targets in the same sample by single-color excitation and two-color detection. We used rolling circle amplification (RCA) for high specificity and sensitivity and for placing Tb donors and dye acceptors at controlled distances within the amplified DNA concatemers. This precise distance tuning led to target-specific PL decays of the FRET pairs and simple, separation-free, and higher-order multiplexed quantification of DNA. The RCA-FRET DNA assay could distinguish very homologous target sequences and provided limits of detection down to 40 zeptomoles (300 aM).
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Affiliation(s)
- Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC) , Université Paris-Saclay, Université Paris-Sud, CNRS, CEA , Orsay 91400 , France
| | - Jiajia Guo
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC) , Université Paris-Saclay, Université Paris-Sud, CNRS, CEA , Orsay 91400 , France
| | - Jingyue Xu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC) , Université Paris-Saclay, Université Paris-Sud, CNRS, CEA , Orsay 91400 , France
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC) , Université Paris-Saclay, Université Paris-Sud, CNRS, CEA , Orsay 91400 , France
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23
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24
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Bhuyan T, Bhattacharjee M, Singh AK, Ghosh SS, Bandyopadhyay D. Boolean-chemotaxis of logibots deciphering the motions of self-propelling microorganisms. SOFT MATTER 2018; 14:3182-3191. [PMID: 29645047 DOI: 10.1039/c8sm00132d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We demonstrate the feasibility of a self-propelling mushroom motor, namely a 'logibot', as a functional unit for the construction of a host of optimized binary logic gates. Emulating the chemokinesis of unicellular prokaryotes or eukaryotes, the logibots made stimuli responsive conditional movements at varied speeds towards a pair of acid-alkali triggers. A series of integrative logic operations and cascaded logic circuits, namely, AND, NAND, NOT, OR, NOR, and NIMPLY, have been constructed employing the decisive chemotactic migrations of the logibot in the presence of the pH gradient established by the sole or coupled effects of acid (HCl-catalase) and alkali (NaOH) drips inside a peroxide bath. The imposed acid and/or alkali triggers across the logibots were realized as inputs while the logic gates were functionally reconfigured to several operational modes by varying the pH of the acid-alkali inputs. The self-propelling logibot could rapidly sense the external stimuli, decide, and act on the basis of intensities of the pH triggers. The impulsive responses of the logibots towards and away from the external acid-alkali stimuli were interpreted as the potential outputs of the logic gates. The external stimuli responsive self-propulsion of the logibots following different logic gates and circuits can not only be an eco-friendly alternative to the silicon-based computing operations but also be a promising strategy for the development of intelligent pH-responsive drug delivery devices.
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Affiliation(s)
- Tamanna Bhuyan
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Assam-781039, India.
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25
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Vranish JN, Ancona MG, Walper SA, Medintz IL. Pursuing the Promise of Enzymatic Enhancement with Nanoparticle Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2901-2925. [PMID: 29115133 DOI: 10.1021/acs.langmuir.7b02588] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The growing emphasis on green chemistry, renewable resources, synthetic biology, regio-/stereospecific chemical transformations, and nanotechnology for providing new biological products and therapeutics is reinvigorating research into enzymatic catalysis. Although the promise is profound, many complex issues remain to be addressed before this effort will have a significant impact. Prime among these is to combat the degradation of enzymes frequently seen in ex vivo formats following immobilization to stabilize the enzymes for long-term application and to find ways of enhancing their activity. One promising avenue for progress on these issues is via nanoparticle (NP) display, which has been found in a number of cases to enhance enzyme activity while also improving long-term stability. In this feature article, we discuss the phenomenon of enhanced enzymatic activity at NP interfaces with an emphasis on our own work in this area. Important factors such as NP surface chemistry, bioconjugation approaches, and assay formats are first discussed because they can critically affect the observed enhancement. Examples are given of improved performance for enzymes such as phosphotriesterase, alkaline phosphatase, trypsin, horseradish peroxidase, and β-galactosidase and in configurations with either the enzyme or the substrate attached to the NP. The putative mechanisms that give rise to the performance boost are discussed along with how detailed kinetic modeling can contribute to their understanding. Given the importance of biosensing, we also highlight how this configuration is already making a significant contribution to NP-based enzymatic sensors. Finally, a perspective is provided on how this field may develop and how NP-based enzymatic enhancement can be extended to coupled systems and multienzyme cascades.
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26
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Chashchikhin OV, Budyka MF. Hybrid nanosystems based on colloidal quantum dots and organic ligands (Review). HIGH ENERGY CHEMISTRY 2018. [DOI: 10.1134/s0018143918010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Massey M, Medintz IL, Ancona MG, Algar WR. Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR. ACS Sens 2017; 2:1205-1214. [PMID: 28787151 DOI: 10.1021/acssensors.7b00355] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular logic devices (MLDs) constructed from DNA are promising for applications in bioanalysis, computing, and other applications requiring Boolean logic. These MLDs accept oligonucleotide inputs and generate fluorescence output through changes in structure. Although fluorescent dyes are most common in MLD designs, nontraditional luminescent materials with unique optical properties can potentially enhance MLD capabilities. In this context, luminescent lanthanide complexes (LLCs) have been largely overlooked. Here, we demonstrate a set of high-contrast DNA photonic logic gates based on toehold-mediated strand displacement and time-gated FRET. The gates include NAND, NOR, OR, and AND designs that accept two unlabeled target oligonucleotide sequences as inputs. Bright "true" output states utilize time-gated, FRET-sensitized emission from an Alexa Fluor 546 (A546) dye acceptor paired with a luminescent terbium cryptate (Tb) donor. Dark "false" output states are generated through either displacement of the A546, or through competitive and sequential quenching of the Tb or A546 by a dark quencher. Time-gated FRET and the long luminescence lifetime and spectrally narrow emission lines of the Tb donor enable 4-10-fold contrast between Boolean outputs, ≤10% signal variation for a common output, multicolor implementation of two logic gates in parallel, and effective performance in buffer and serum. These metrics exceed those reported for many other logic gate designs with only fluorescent dyes and with other non-LLC materials. Preliminary three-input AND and NAND gates are also demonstrated. The powerful combination of an LLC FRET donor with DNA-based logic gates is anticipated to have many future applications in bioanalysis.
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Affiliation(s)
- Melissa Massey
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | | | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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28
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Qiu X, Guo J, Jin Z, Petreto A, Medintz IL, Hildebrandt N. Multiplexed Nucleic Acid Hybridization Assays Using Single-FRET-Pair Distance-Tuning. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13. [PMID: 28371153 DOI: 10.1002/smll.201700332] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 05/04/2023]
Abstract
Multiplexed photoluminescence (PL) detection plays an important role in chemical and biological sensing. Here, it is shown that time-gated (TG) detection of a single terbium-donor-based Förster resonance energy transfer (FRET) pair can be used to selectively quantify low nanomolar concentrations of multiple DNAs or microRNAs in a single sample. This study demonstrates the applicability of single-TG-FRET-pair multiplexing for molecular (Tb-to-dye) and nanoparticle (Tb-to-quantum-dot) biosensing. Both systems use acceptor-sensitization and donor-quenching for quantifying biomolecular recognition and modification of the donor-acceptor distance for tuning the PL decays. TG intensity detection provides extremely low background noise and a quick and simple one-step assay format. Single-TG-FRET-pair multiplexing can be combined with spectral and spatial resolution, paving the way for biosensing with unprecedented high-order multiplexing capabilities.
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Affiliation(s)
- Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405, Orsay Cedex, France
| | - Jiajia Guo
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405, Orsay Cedex, France
| | - Zongwen Jin
- CAS/CUHK Research Centre for Biosensing and Medical Instrumentation, SIAT/CAS, Shenzhen, 518055, P. R. China
| | - Alexandra Petreto
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405, Orsay Cedex, France
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, DC, 20375, USA
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405, Orsay Cedex, France
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29
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User Authorization at the Molecular Scale. Chemphyschem 2017; 18:1678-1687. [DOI: 10.1002/cphc.201700506] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/01/2017] [Indexed: 12/31/2022]
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30
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Affiliation(s)
- Patricia Remón
- CIQSO-Center for Research in Sustainable Chemistry and Department of Chemistry; University of Huelva; Campus de El Carmen s/n 21071 Huelva Spain
| | - Uwe Pischel
- CIQSO-Center for Research in Sustainable Chemistry and Department of Chemistry; University of Huelva; Campus de El Carmen s/n 21071 Huelva Spain
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31
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Truman LK, Bradberry SJ, Comby S, Kotova O, Gunnlaugsson T. Surface-Modified Gold Nanoparticles Possessing Two-Channel Responsive EuIII
/TbIII
Cyclen Complexes as Luminescent Logic Gate Mimics. Chemphyschem 2017; 18:1746-1751. [DOI: 10.1002/cphc.201700440] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Laura K. Truman
- School of Chemistry and Trinity Biomedical Sciences Institute; Trinity College Dublin; 152-160 Pearse Street Dublin, Dublin 2 Ireland
| | - Samuel J. Bradberry
- School of Chemistry and Trinity Biomedical Sciences Institute; Trinity College Dublin; 152-160 Pearse Street Dublin, Dublin 2 Ireland
| | - Steve Comby
- School of Chemistry and Trinity Biomedical Sciences Institute; Trinity College Dublin; 152-160 Pearse Street Dublin, Dublin 2 Ireland
| | - Oxana Kotova
- School of Chemistry and Trinity Biomedical Sciences Institute; Trinity College Dublin; 152-160 Pearse Street Dublin, Dublin 2 Ireland
| | - Thorfinnur Gunnlaugsson
- School of Chemistry and Trinity Biomedical Sciences Institute; Trinity College Dublin; 152-160 Pearse Street Dublin, Dublin 2 Ireland
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32
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Gao RR, Yao TM, Lv XY, Zhu YY, Zhang YW, Shi S. Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing. Chem Sci 2017; 8:4211-4222. [PMID: 28626564 PMCID: PMC5469004 DOI: 10.1039/c7sc00361g] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/05/2017] [Indexed: 11/30/2022] Open
Abstract
To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2 : 1 multiplexer, and a 1 : 2 demultiplexer. Moreover, a parity checker which is capable of identifying odd and even numbers from natural numbers is constructed conceptually. Finally, a multi-valued logic gate (ternary inhibit gate) is readily achieved by taking this DNA/Ag NC system as a universal platform. All of the above logic circuits share the same building blocks, indicating the great prospects of the assembly of nanomaterials and DNA for biochemical logic devices. Considering its biocompatibility, the novel prototypes developed here may have potential applications in the fields of biological computers and medical diagnosis and serve as a promising proof of principle in the not-too-distant future.
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Affiliation(s)
- Ru-Ru Gao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Tian-Ming Yao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Xiao-Yan Lv
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Yan-Yan Zhu
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Yi-Wei Zhang
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Shuo Shi
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
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Díaz SA, Lasarte Aragonés G, Buckhout-White S, Qiu X, Oh E, Susumu K, Melinger JS, Huston AL, Hildebrandt N, Medintz IL. Bridging Lanthanide to Quantum Dot Energy Transfer with a Short-Lifetime Organic Dye. J Phys Chem Lett 2017; 8:2182-2188. [PMID: 28467088 DOI: 10.1021/acs.jpclett.7b00584] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Semiconductor nanocrystals or quantum dots (QDs) should act as excellent Förster resonance energy transfer (FRET) acceptors due to their large absorption cross section, tunable emission, and high quantum yields. Engaging this type of FRET can be complicated due to direct excitation of the QD acceptor along with its longer excited-state lifetime. Many cases of QDs acting as energy transfer acceptors are within time-gated FRET from long-lifetime lanthanides, which allow the QDs to decay before observing FRET. Efficient QD sensitization requires the lanthanide to be in close proximity to the QD. To overcome the lifetime mismatch issues and limited transfer range, we utilized a Cy3 dye to bridge the energy transfer from an extremely long lived terbium emitter to the QD. We demonstrated that short-lifetime dyes can be used as energy transfer relays between extended lifetime components and in this way increased the distance of terbium-QD FRET to ∼14 nm.
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Affiliation(s)
| | | | | | - Xue Qiu
- NanoBioPhotonics, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA , 91400 Orsay, France
| | - Eunkeu Oh
- Sotera Defense Solutions , Columbia, Maryland 21046, United States
| | - Kimihiro Susumu
- Sotera Defense Solutions , Columbia, Maryland 21046, United States
| | | | | | - Niko Hildebrandt
- NanoBioPhotonics, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA , 91400 Orsay, France
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34
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Enzyme‐Based Logic Gates and Networks with Output Signals Analyzed by Various Methods. Chemphyschem 2017; 18:1688-1713. [DOI: 10.1002/cphc.201601402] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Indexed: 01/16/2023]
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35
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Brown CW, Buckhout-White S, Díaz SA, Melinger JS, Ancona MG, Goldman ER, Medintz IL. Evaluating Dye-Labeled DNA Dendrimers for Potential Applications in Molecular Biosensing. ACS Sens 2017; 2:401-410. [PMID: 28723206 DOI: 10.1021/acssensors.6b00778] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA nanostructures provide a reliable and predictable scaffold for precisely positioning fluorescent dyes to form energy transfer cascades. Furthermore, these structures and their attendant dye networks can be dynamically manipulated by biochemical inputs, with the changes reflected in the spectral response. However, the complexity of DNA structures that have undergone such types of manipulation for direct biosensing applications is quite limited. Here, we investigate four different modification strategies to effect such dynamic manipulations using a DNA dendrimer scaffold as a testbed, and with applications to biosensing in mind. The dendrimer has a 2:1 branching ratio that organizes the dyes into a FRET-based antenna in which excitonic energy generated on multiple initial Cy3 dyes displayed at the periphery is then transferred inward through Cy3.5 and/or Cy5 relay dyes to a Cy5.5 final acceptor at the focus. Advantages of this design included good transfer efficiency, large spectral separation between the initial donor and final acceptor emissions for signal transduction, and an inherent tolerance to defects. Of the approaches to structural rearrangement, the first two mechanisms we consider employed either toehold-mediated strand displacement or strand replacement and their impact was mainly via direct transfer efficiency, while the other two were more global in their effect using either a belting mechanism or an 8-arm star nanostructure to compress the nanostructure and thereby modulate its spectral response through an enhancement in parallelism. The performance of these mechanisms, their ability to reset, and how they might be utilized in biosensing applications are discussed.
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Affiliation(s)
- Carl W. Brown
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | | | - Sebastián A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
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36
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Algar WR, Khachatrian A, Melinger JS, Huston AL, Stewart MH, Susumu K, Blanco-Canosa JB, Oh E, Dawson PE, Medintz IL. Concurrent Modulation of Quantum Dot Photoluminescence Using a Combination of Charge Transfer and Förster Resonance Energy Transfer: Competitive Quenching and Multiplexed Biosensing Modality. J Am Chem Soc 2016; 139:363-372. [DOI: 10.1021/jacs.6b11042] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- W. Russ Algar
- Department
of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Ani Khachatrian
- Sotera Defense Solutions, Columbia, Maryland 21046, United States
| | | | | | | | - Kimihiro Susumu
- Sotera Defense Solutions, Columbia, Maryland 21046, United States
| | - Juan B. Blanco-Canosa
- Departments
of Chemistry and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Eunkeu Oh
- Sotera Defense Solutions, Columbia, Maryland 21046, United States
| | - Philip E. Dawson
- Departments
of Chemistry and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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37
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Yu X, Li M, Li T, Zhou S, Liu H. A resettable and reprogrammable biomolecular keypad lock with dual outputs based on glucose oxidase-Au nanoclusters-Prussian blue nanocomposite films on an electrode surface. NANOSCALE 2016; 8:20027-20036. [PMID: 27883152 DOI: 10.1039/c6nr07344a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this work, electrochromic Prussian blue (PB) films were electrodeposited on the surface of indium tin oxide (ITO) electrodes, and a dispersion mixture of glucose oxidase (GOD), chitosan (CS) and gold nanoclusters (AuNCs) was then cast on the PB surface to form CS-AuNC-GOD/PB nanocomposite film electrodes. The blue PB component in the films could be changed into its colourless reduced form of Prussian white (PW) upon application of -0.2 V. The addition of glucose to the solution would produce H2O2 with the help of GOD in the films and oxygen in the solution, which could oxidize PW back to PB. In the meantime, the fluorescence emission signal of the AuNCs in the films was greatly influenced by the form of PB/PW. Based on these properties, the amperometric current, fluorescence intensity and UV-vis absorbance of the film electrodes demonstrated potential- and glucose-sensitive ON-OFF behaviors. Thus, a 2-input/3-output biomolecular logic gate system with 3 different types of output signals and a 2-to-1 encoder were developed. Furthermore, a resettable and reprogrammable 3-input biomolecular keypad lock was established with fluorescence intensity and UV-vis absorbance as dual outputs, which greatly enhanced the security level of the keypad lock. This work reported for the first time an enzyme-based keypad lock with dual outputs, which might open a new avenue to design more complicated biomolecular keypad lock systems.
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Affiliation(s)
- Xue Yu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
| | - Menglu Li
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
| | - Tianrui Li
- Beijing No. 55 High School, Beijing 100027, P. R. China
| | - Shuo Zhou
- Beijing No. 55 High School, Beijing 100027, P. R. China
| | - Hongyun Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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38
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Recent developments in lanthanide-to-quantum dot FRET using time-gated fluorescence detection and photon upconversion. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.03.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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39
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Fratto BE, Guz N, Fallon TT, Katz E. An Enzyme-based 1:2 Demultiplexer Interfaced with an Electrochemical Actuator. Chemphyschem 2016; 18:1721-1725. [PMID: 27481283 DOI: 10.1002/cphc.201600799] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Indexed: 12/26/2022]
Abstract
An enzyme-based 1:2 demultiplexer is designed in a flow system composed of three cells where each one is modified with a different enzyme: hexokinase, glucose dehydrogenase and glucose-6-phosphate dehydrogenase. The Input signal activating the biocatalytic cascade is represented by glucose, while the Address signal represented by ATP is responsible for directing the Input signal to one of the output channels, depending on the logic value of the Address. The biomolecular 1:2 demultiplexer is extended to include two electrochemical actuators releasing entrapped DNA molecules in the active output channel. The modular design of the system allows for easy exchange and extension of the functional elements. The present demultiplexer can be easily integrated in various biomolecular logic systems, including different logic gates based on the enzyme- or DNA-based reactions, as well as containing different chemical actuators, for example, with a biomolecular release function.
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Affiliation(s)
- Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Nataliia Guz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Tyler T Fallon
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
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40
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Verma A, Fratto BE, Privman V, Katz E. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications. SENSORS 2016; 16:s16071042. [PMID: 27399702 PMCID: PMC4969838 DOI: 10.3390/s16071042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 02/07/2023]
Abstract
We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.
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Affiliation(s)
- Arjun Verma
- Department of Physics, Clarkson University, Potsdam, NY 13699, USA.
| | - Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
| | - Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, NY 13699, USA.
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
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41
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Hildebrandt N, Spillmann CM, Algar WR, Pons T, Stewart MH, Oh E, Susumu K, Díaz SA, Delehanty JB, Medintz IL. Energy Transfer with Semiconductor Quantum Dot Bioconjugates: A Versatile Platform for Biosensing, Energy Harvesting, and Other Developing Applications. Chem Rev 2016; 117:536-711. [DOI: 10.1021/acs.chemrev.6b00030] [Citation(s) in RCA: 457] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Niko Hildebrandt
- NanoBioPhotonics
Institut d’Electronique Fondamentale (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, 91400 Orsay, France
| | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Thomas Pons
- LPEM;
ESPCI Paris, PSL Research University; CNRS; Sorbonne Universités, UPMC, F-75005 Paris, France
| | | | - Eunkeu Oh
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Kimihiro Susumu
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Sebastian A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
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42
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Mattera L, Bhuckory S, Wegner KD, Qiu X, Agnese F, Lincheneau C, Senden T, Djurado D, Charbonnière LJ, Hildebrandt N, Reiss P. Compact quantum dot-antibody conjugates for FRET immunoassays with subnanomolar detection limits. NANOSCALE 2016; 8:11275-83. [PMID: 27188210 DOI: 10.1039/c6nr03261c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A novel two-step approach for quantum dot (QD) functionalization and bioconjugation is presented, which yields ultra-compact, stable, and highly luminescent antibody-QD conjugates suitable for use in FRET immunoassays. Hydrophobic InPZnS/ZnSe/ZnS (emission wavelength: 530 nm), CdSe/ZnS (605 nm), and CdSeTe/ZnS (705 nm) QDs were surface functionalized with zwitterionic penicillamine, enabling aqueous phase transfer under conservation of the photoluminescence properties. Post-functionalization with a heterobifunctional crosslinker, containing a lipoic acid group and a maleimide function, enabled the subsequent coupling to sulfhydryl groups of proteins. This was demonstrated by QD conjugation with fragmented antibodies (F(ab)). The obtained F(ab)-QD conjugates range among the smallest antibody-functionalized nanoprobes ever reported, with a hydrodynamic diameter <13 nm, PL quantum yield up to 66% at 705 nm, and colloidal stability of several months in various buffers. They were applied as FRET acceptors in homogeneous, time-gated immunoassays using Tb-antibodies as FRET donors, both coupled by an immunological sandwich complex between the two antibodies and a PSA (prostate specific antigen) biomarker. The advantages of the compact surface coating for FRET could be demonstrated by an 6.2 and 2.5 fold improvement of the limit of detection (LOD) for PSA compared to commercially available hydrophilic QDs emitting at 605 and 705 nm, respectively. While the commercial QDs contain identical inorganic cores responsible for their fluorescence, they are coated with a comparably thick amphiphilic polymer layer leading to much larger hydrodynamic diameters (>26 nm without biomolecules). The LODs of 0.8 and 3.7 ng mL(-1) obtained in 50 μL serum samples are below the clinical cut-off level of PSA (4 ng mL(-1)) and demonstrate their direct applicability in clinical diagnostics.
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Affiliation(s)
- Lucia Mattera
- Univ. Grenoble Alpes, INAC-SyMMES, F-38054 Grenoble Cedex 9, France
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43
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Dennis AM, Delehanty JB, Medintz IL. Emerging Physicochemical Phenomena along with New Opportunities at the Biomolecular-Nanoparticle Interface. J Phys Chem Lett 2016; 7:2139-50. [PMID: 27219278 DOI: 10.1021/acs.jpclett.6b00570] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Efforts to create new nanoparticle-biomolecule hybrids for diverse applications including biosensing, theranostics, drug delivery, and even biocomputation continue to grow at an unprecedented rate. As the composite designs become more sophisticated, new and unanticipated physicochemical phenomena are emerging at the nanomaterial-biological interface. These phenomena arise from two interrelated factors, namely, the novel architecture of nanoparticle bioconjugates and the unique physicochemical properties of their interfacial environment. Here we examine how the augmented functionality imparted by such hybrid structures, including accessing concentric energy transfer, enhanced enzymatic activity, and sensitivity to electric fields, is leading to new applications. We discuss some lesser-understood phenomena that arise at the nanoparticle interface, such as the complex and confounding issue of protein corona formation, along with their unexpected benefits. Overall, understanding these complex phenomena will improve the design of composite materials while uncovering new opportunities for their application.
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Affiliation(s)
- Allison M Dennis
- Department of Biomedical Engineering, Boston University , 44 Cummington Mall, Boston, Massachusetts 02215, United States
| | - James B Delehanty
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory , 4555 Overlook Avenue, Southwest, Washington, District of Columbia 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory , 4555 Overlook Avenue, Southwest, Washington, District of Columbia 20375, United States
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44
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Afsari HS, Cardoso Dos Santos M, Lindén S, Chen T, Qiu X, van Bergen en Henegouwen PMP, Jennings TL, Susumu K, Medintz IL, Hildebrandt N, Miller LW. Time-gated FRET nanoassemblies for rapid and sensitive intra- and extracellular fluorescence imaging. SCIENCE ADVANCES 2016; 2:e1600265. [PMID: 27386579 PMCID: PMC4928903 DOI: 10.1126/sciadv.1600265] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/19/2016] [Indexed: 05/20/2023]
Abstract
Time-gated Förster resonance energy transfer (FRET) using the unique material combination of long-lifetime terbium complexes (Tb) and semiconductor quantum dots (QDs) provides many advantages for highly sensitive and multiplexed biosensing. Although time-gated detection can efficiently suppress sample autofluorescence and background fluorescence from directly excited FRET acceptors, Tb-to-QD FRET has rarely been exploited for biomolecular imaging. We demonstrate Tb-to-QD time-gated FRET nanoassemblies that can be applied for intra- and extracellular imaging. Immunostaining of different epitopes of the epidermal growth factor receptor (EGFR) with Tb- and QD-conjugated antibodies and nanobodies allowed for efficient Tb-to-QD FRET on A431 cell membranes. The broad usability of Tb-to-QD FRET was further demonstrated by intracellular Tb-to-QD FRET and Tb-to-QD-to-dye FRET using microinjection as well as cell-penetrating peptide-mediated endocytosis with HeLa cells. Effective brightness enhancement by FRET from several Tb to the same QD, the use of low nanomolar concentrations, and the quick and sensitive detection void of FRET acceptor background fluorescence are important advantages for advanced intra- and extracellular imaging of biomolecular interactions.
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Affiliation(s)
- Hamid Samareh Afsari
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607–7061, USA
| | - Marcelina Cardoso Dos Santos
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | - Stina Lindén
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | - Ting Chen
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607–7061, USA
| | - Xue Qiu
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | | | | | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Sotera Defense Solutions, Columbia, MD 21046, USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Niko Hildebrandt
- NanoBioPhotonics (www.nanofret.com), Institut d’Electronique Fondamentale, Université Paris-Saclay, Université Paris-Sud, CNRS, 91405 Orsay Cedex, France
| | - Lawrence W. Miller
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607–7061, USA
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45
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Recent developments in Förster resonance energy transfer (FRET) diagnostics using quantum dots. Anal Bioanal Chem 2016; 408:4475-83. [DOI: 10.1007/s00216-016-9434-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/14/2016] [Accepted: 02/18/2016] [Indexed: 12/21/2022]
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46
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Sy M, Nonat A, Hildebrandt N, Charbonnière LJ. Lanthanide-based luminescence biolabelling. Chem Commun (Camb) 2016; 52:5080-95. [DOI: 10.1039/c6cc00922k] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multiplexing, time-resolution, FRET…lanthanide-based biolabels reveal exceptional spectroscopic properties for bioanalytical applications.
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Affiliation(s)
- Mohamadou Sy
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse
- IPHC
- UMR 7178 CNRS
- Université de Strasbourg
- ECPM
| | - Aline Nonat
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse
- IPHC
- UMR 7178 CNRS
- Université de Strasbourg
- ECPM
| | - Niko Hildebrandt
- NanoBioPhotonics, Institut d'Electronique Fondamentale
- Université Paris-Saclay
- Université Paris-Sud
- CNRS
- Orsay
| | - Loïc J. Charbonnière
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse
- IPHC
- UMR 7178 CNRS
- Université de Strasbourg
- ECPM
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47
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Li JJ, Algar WR. A long-wavelength quantum dot-concentric FRET configuration: characterization and application in a multiplexed hybridization assay. Analyst 2016; 141:3636-47. [DOI: 10.1039/c6an00492j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum dot-based concentric Förster resonance energy transfer (cFRET) is a promising modality for the development of multifunctional fluorescent probes for bioanalysis and bioimaging. A new long-wavelength configuration and multiplexed hybridization assay format expands the scope of cFRET.
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Affiliation(s)
- Jia Jun Li
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - W. Russ Algar
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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48
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Buckhout-White S, Brown III CW, Hastman DA, Ancona MG, Melinger JS, Goldman ER, Medintz IL. Expanding molecular logic capabilities in DNA-scaffolded multiFRET triads. RSC Adv 2016. [DOI: 10.1039/c6ra23079b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Dynamic rearrangement of DNA nanostructures provides a straightforward yet powerful mechanism for sequence-specific sensing and potential signaling of such interactions.
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Affiliation(s)
- Susan Buckhout-White
- Center for Bio/Molecular Science and Engineering, Code 6900
- U.S. Naval Research Laboratory
- Washington
- USA
| | - Carl W. Brown III
- Center for Bio/Molecular Science and Engineering, Code 6900
- U.S. Naval Research Laboratory
- Washington
- USA
- College of Science
| | - David A. Hastman
- Center for Bio/Molecular Science and Engineering, Code 6900
- U.S. Naval Research Laboratory
- Washington
- USA
| | - Mario G. Ancona
- Electronics Science and Technology Division, Code 6876
- U.S. Naval Research Laboratory
- Washington
- USA
| | - Joseph S. Melinger
- Electronics Science and Technology Division, Code 6876
- U.S. Naval Research Laboratory
- Washington
- USA
| | - Ellen R. Goldman
- Center for Bio/Molecular Science and Engineering, Code 6900
- U.S. Naval Research Laboratory
- Washington
- USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900
- U.S. Naval Research Laboratory
- Washington
- USA
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Zhang S, Wang K, Huang C, Sun T. Reconfigurable and resettable arithmetic logic units based on magnetic beads and DNA. NANOSCALE 2015; 7:20749-20756. [PMID: 26602962 DOI: 10.1039/c5nr06733b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Based on the characteristics of magnetic beads and DNA, a simple and universal platform was developed for the integration of multiple logic gates to achieve resettable half adder and half subtractor functions. The signal reporter was composed of a split G-quadruplex DNAzyme and AuNP-surface immobilized molecular beacon molecule. The novel feature of the designed system is that the inputs (split G-quadruplexes) can interact with hairpin-modified Au NPs linked to magnetic particles. Another novel feature is that the logic operations can be reset by heating the output system and by using the magnetic separation of the computing modules. Moreover, the developed half adder and half subtractor are realized on a simple DNA/magnetic bead platform in an enzyme-free system and share a constant threshold setpoint. Due to the diversity and design flexibility of DNA, these investigations may provide a new method for the development of resettable DNA-based arithmetic operations.
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Affiliation(s)
- Siqi Zhang
- College of Sciences, Northeastern University, Shenyang, 110819, China.
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Spillmann CM, Stewart MH, Susumu K, Medintz IL. Combining semiconductor quantum dots and bioscaffolds into nanoscale energy transfer devices. APPLIED OPTICS 2015; 54:F85-F95. [PMID: 26560627 DOI: 10.1364/ao.54.000f85] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Significant advances have been made in the development of nanoscale devices capable of exciton transport via Förster resonance energy transfer. Several requirements must be met for effective operation, including a reliable energy-harvesting source along with highly organized, precisely placed energy relay elements. For the latter, biological scaffolds such as DNA provide a customizable, symmetric, and stable structure that can be site-specifically modified with organic fluorophores. Here, advancements in nanoscale energy transfer devices incorporating semiconductor nanocrystals and bioscaffolds are reviewed with discussion of biofunctionalization, linker chemistries, design considerations, and concluding with applications in light harvesting, multiplexed biosensing, and optical logic.
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