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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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Shen P, Liu Y, Qu X, Zhu M, Huang T, Sun Q. An optical keypad lock with high resettability based on a quantum dot-porphyrin FRET nanodevice. NANOSCALE ADVANCES 2023; 5:2986-2993. [PMID: 37260500 PMCID: PMC10228340 DOI: 10.1039/d3na00030c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023]
Abstract
Due to their appealing properties, nanomaterials have become ideal candidates for the implementation of computing systems. Herein, an optical keypad lock based on a Förster resonance energy transfer (FRET) nanodevice is developed. The nanodevice is composed of a green-emission quantum dot with a thick silica shell (gQD@SiO2) and peripheric blue-emission quantum dots with ultrathin silica spacer (bQD@SiO2), on which 5,10,15,20-tetrakis(4-sulfophenyl)porphyrin (TSPP) is covalently linked. The nanodevice outputs dual emission-based ratiometric fluorescence, depending on the FRET efficiency of bQD-porphyrin pairs, which is highly sensitive to the metalation of TSPP: values are 59.7%, 44.8%, and 10.1% for bQD-Zn(ii)TSPP, bQD-TSPP, and bQD-Fe(iii)TSPP pairs, respectively. As such, by using the competitive chelation-induced transmetalation of TSPP, the nanodevice is capable of implementing a 3-input keypad lock that is unlocked only by the correct input order of Zn(ii) chelator, iron ions, and UV light. Interestingly, the reversible transmetalation of TSPP permits the reset (lock) operation of the keypad lock with the correct input order of ascorbic acid, Zn(ii), and UV light. Application of the nanodevice is exemplified by the construction of paper and cellular keypad locks, respectively, both of which feature signal readability and/or high resettability, showing high potential for personal information identification and bio-encryption applications.
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Affiliation(s)
- Peng Shen
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Yuqian Liu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Joint International Research Lab of Lignocellulosic Functional Materials, College of Light Industry and Food Engineering, Nanjing Forestry University Nanjing 210037 China
| | - Xiaojun Qu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Mingsong Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Ting Huang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
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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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Hottechamps J, Noblet T, Méthivier C, Boujday S, Dreesen L. All-quantum dot based Förster resonant energy transfer: key parameters for high-efficiency biosensing. NANOSCALE 2023; 15:2614-2623. [PMID: 36648212 DOI: 10.1039/d2nr06161a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
While colloidal quantum dots (QDs) are commonly used as fluorescent donors within biosensors based on Förster resonant energy transfer (FRET), they are hesitantly employed as acceptors. On the sole basis of Förster theory and the well-known behaviour of organic dyes, it is often argued that the QD absorption band over the UV-visible range is too wide. Discarding these preconceptions inherited from classical fluorophores, we experimentally examine the FRET process occurring between donor and acceptor CdTe QDs and provide a mathematical description of it. We evidence that the specific features of QDs unexpectedly lead to the enhancement of acceptors' emission (up to +400%), and are thus suitable for the design of highly efficient all-QD based FRET sensors. Our model enables us to identify the critical parameters maximizing the contrast between positive and negative biosensing readouts: the concentrations of donors and acceptors, their spectral overlap, the densities of their excitonic states, their dissipative coupling with the medium and the statistics of QD-QD chemical pairing emerge as subtle and determinant parameters. We relate them quantitatively to the measured QD-QD FRET efficiency and discuss how they must be optimized for biosensing applications.
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Affiliation(s)
- Julie Hottechamps
- GRASP-Biophotonics, CESAM, University of Liege, Institute of Physics, Allée du 6 Août 17, 4000 Liège, Belgium.
| | - Thomas Noblet
- GRASP-Biophotonics, CESAM, University of Liege, Institute of Physics, Allée du 6 Août 17, 4000 Liège, Belgium.
| | - Christophe Méthivier
- Sorbonne Universités, UPMC Univ. Paris 6, UMR CNRS 7197 Laboratoire de Réactivité de Surface, F75005 Paris, France
| | - Souhir Boujday
- Sorbonne Universités, UPMC Univ. Paris 6, UMR CNRS 7197 Laboratoire de Réactivité de Surface, F75005 Paris, France
| | - Laurent Dreesen
- GRASP-Biophotonics, CESAM, University of Liege, Institute of Physics, Allée du 6 Août 17, 4000 Liège, Belgium.
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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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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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Parrino F, D'Arienzo M, Mostoni S, Dirè S, Ceccato R, Bellardita M, Palmisano L. Electron and Energy Transfer Mechanisms: The Double Nature of TiO 2 Heterogeneous Photocatalysis. Top Curr Chem (Cham) 2021; 380:2. [PMID: 34786587 DOI: 10.1007/s41061-021-00358-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
Photocatalytic chemical transformations in the presence of irradiated TiO2 are generally considered in terms of interfacial electron transfer. However, more elusive energy-transfer-driven reactions have been also hypothesized to occur, mainly on the basis of the indirect evidence of detected reaction products whose existence could not be justified simply by electron transfer. Unlike in homogeneous and colloidal systems, where energy transfer mechanisms have been investigated deeply for several organic syntheses, understanding of similar processes in heterogeneous systems is at only a nascent level. However, this gap of knowledge can be filled by considering the important achievements of synthetic heterogeneous photocatalysis, which bring the field closer to industrial exploitation. The present manuscript summarizes the main findings of previous literature reports and, also on the basis of some novel experimental evidences, tentatively proposes that the energy transfer in TiO2 photocatalysis could possess a Förster-like nature.
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Affiliation(s)
- Francesco Parrino
- Department of Industrial Engineering (DII), University of Trento, Via Sommarive 9, 38123, Trento, Italy.
| | - Massimiliano D'Arienzo
- Department of Materials Science (INSTM), University of Milano-Bicocca, Via R. Cozzi 55, 20125, Milano, Italy
| | - Silvia Mostoni
- Department of Materials Science (INSTM), University of Milano-Bicocca, Via R. Cozzi 55, 20125, Milano, Italy
| | - Sandra Dirè
- Department of Industrial Engineering (DII), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Riccardo Ceccato
- Department of Industrial Engineering (DII), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Marianna Bellardita
- Department of Engineering, University of Palermo, Viale delle Scienze ed. 6, 90128, Palermo, Italy
| | - Leonardo Palmisano
- Department of Engineering, University of Palermo, Viale delle Scienze ed. 6, 90128, Palermo, Italy
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Léger C, Yahia-Ammar A, Susumu K, Medintz IL, Urvoas A, Valerio-Lepiniec M, Minard P, Hildebrandt N. Picomolar Biosensing and Conformational Analysis Using Artificial Bidomain Proteins and Terbium-to-Quantum Dot Förster Resonance Energy Transfer. ACS NANO 2020; 14:5956-5967. [PMID: 32216328 DOI: 10.1021/acsnano.0c01410] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although antibodies remain a primary recognition element in all forms of biosensing, functional limitations arising from their size, stability, and structure have motivated the development and production of many different artificial scaffold proteins for biological recognition. However, implementing such artificial binders into functional high-performance biosensors remains a challenging task. Here, we present the design and application of Förster resonance energy transfer (FRET) nanoprobes comprising small artificial proteins (αRep bidomains) labeled with a Tb complex (Tb) donor on the C-terminus and a semiconductor quantum dot (QD) acceptor on the N-terminus. Specific binding of one or two protein targets to the αReps induced a conformational change that could be detected by time-resolved Tb-to-QD FRET. These single-probe FRET switches were used in a separation-free solution-phase assay to quantify different protein targets at sub-nanomolar concentrations and to measure the conformational changes with sub-nanometer resolution. Probing ligand-receptor binding under physiological conditions at very low concentrations in solution is a special feature of FRET that can be efficiently combined with other structural characterization methods to develop, understand, and optimize artificial biosensors. Our results suggest that the αRep FRET nanoprobes have a strong potential for their application in advanced diagnostics and intracellular live-cell imaging of ligand-receptor interactions.
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Affiliation(s)
- Corentin Léger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Akram Yahia-Ammar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | - Agathe Urvoas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie Valerio-Lepiniec
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Minard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Niko Hildebrandt
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France
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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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11
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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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Detection of Co2+ via fluorescence resonance energy transfer between synthesized nitrogen-doped carbon quantum dots and Rhodamine 6G. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s13738-020-01891-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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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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A FRET-based fluorescent probe for hydrogen peroxide based on the use of carbon quantum dots conjugated to gold nanoclusters. Mikrochim Acta 2019; 186:294. [DOI: 10.1007/s00604-019-3398-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/01/2019] [Indexed: 02/04/2023]
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15
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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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16
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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17
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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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18
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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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19
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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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20
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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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21
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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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22
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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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23
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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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24
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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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25
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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: 21] [Impact Index Per Article: 3.0] [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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26
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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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27
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Martynenko IV, Litvin AP, Purcell-Milton F, Baranov AV, Fedorov AV, Gun'ko YK. Application of semiconductor quantum dots in bioimaging and biosensing. J Mater Chem B 2017; 5:6701-6727. [DOI: 10.1039/c7tb01425b] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this review we present new concepts and recent progress in the application of semiconductor quantum dots (QD) as labels in two important areas of biology, bioimaging and biosensing.
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Affiliation(s)
- I. V. Martynenko
- BAM Federal Institute for Materials Research and Testing
- 12489 Berlin
- Germany
- ITMO University
- St. Petersburg
| | | | | | | | | | - Y. K. Gun'ko
- ITMO University
- St. Petersburg
- Russia
- School of Chemistry and CRANN
- Trinity College Dublin
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28
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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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29
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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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30
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Harris RD, Bettis Homan S, Kodaimati M, He C, Nepomnyashchii AB, Swenson NK, Lian S, Calzada R, Weiss EA. Electronic Processes within Quantum Dot-Molecule Complexes. Chem Rev 2016; 116:12865-12919. [PMID: 27499491 DOI: 10.1021/acs.chemrev.6b00102] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The subject of this review is the colloidal quantum dot (QD) and specifically the interaction of the QD with proximate molecules. It covers various functions of these molecules, including (i) ligands for the QDs, coupled electronically or vibrationally to localized surface states or to the delocalized states of the QD core, (ii) energy or electron donors or acceptors for the QDs, and (iii) structural components of QD assemblies that dictate QD-QD or QD-molecule interactions. Research on interactions of ligands with colloidal QDs has revealed that ligands determine not only the excited state dynamics of the QD but also, in some cases, its ground state electronic structure. Specifically, the article discusses (i) measurement of the electronic structure of colloidal QDs and the influence of their surface chemistry, in particular, dipolar ligands and exciton-delocalizing ligands, on their electronic energies; (ii) the role of molecules in interfacial electron and energy transfer processes involving QDs, including electron-to-vibrational energy transfer and the use of the ligand shell of a QD as a semipermeable membrane that gates its redox activity; and (iii) a particular application of colloidal QDs, photoredox catalysis, which exploits the combination of the electronic structure of the QD core and the chemistry at its surface to use the energy of the QD excited state to drive chemical reactions.
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Affiliation(s)
- Rachel D Harris
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Stephanie Bettis Homan
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Mohamad Kodaimati
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Chen He
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | | | - Nathaniel K Swenson
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Shichen Lian
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Raul Calzada
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Emily A Weiss
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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31
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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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32
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Palomo V, Díaz SA, Stewart MH, Susumu K, Medintz IL, Dawson PE. 3,4-Dihydroxyphenylalanine Peptides as Nonperturbative Quantum Dot Sensors of Aminopeptidase. ACS NANO 2016; 10:6090-9. [PMID: 27206058 PMCID: PMC4968404 DOI: 10.1021/acsnano.6b01682] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fluorescence-based assays for hydrolases that cleave within the substrate (endopeptidases) are common, while developing substrates for proteases that selectively cleave from peptide termini (exopeptidases) is more challenging, since the termini are specifically recognized by the enzyme and cannot be modified to facilitate a Förster resonance energy transfer (FRET)-based approach. The development of a robust system that enables the quenching of fluorescent particles by simple amino acid side chains would find broad utility for peptide sensors and would be advantageous for exopeptidases. Here we describe a quantum dot (QD)-based electron transfer (ET) sensor that is able to allow direct, quantitative monitoring of both exopeptidase and endopeptidase activity. The incorporation of 3,4-dihydroxyphenylalanine (DOPA) into the sequence of a peptide allows for the quenching of QD photoluminescence through an ET mechanism. DOPA is a nonproteinogenic amino acid that can replace a phenylalanine or tyrosine residue in a peptide sequence without severely altering structural properties, allowing for its introduction at multiple positions within a biologically active peptide substrate. Consequently, the quenching system presented here is ideally suited for incorporation into diverse peptide substrates for enzyme recognition, digestion, and activity sensing. Our findings suggest a broad utility of a small ET-capable amino acid side chain in detecting enzyme activity through ET-mediated QD luminescence quenching.
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Affiliation(s)
- Valle Palomo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, 92037 (USA)
| | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Michael H. Stewart
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, 92037 (USA)
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33
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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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34
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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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35
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Samanta A, Medintz IL. Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology. NANOSCALE 2016; 8:9037-95. [PMID: 27080924 DOI: 10.1039/c5nr08465b] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.
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Affiliation(s)
- Anirban Samanta
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA. and College of Science, George Mason University, Fairfax, Virginia 22030, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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36
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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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37
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Díaz S, Breger J, Medintz I. Monitoring Enzymatic Proteolysis Using Either Enzyme- or Substrate-Bioconjugated Quantum Dots. Methods Enzymol 2016; 571:19-54. [DOI: 10.1016/bs.mie.2016.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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38
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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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39
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Feng Y, Liu L, Hu S, Liu Y, Ren Y, Zhang X. Förster resonance energy transfer properties of a new type of near-infrared excitation PDT photosensitizer: CuInS2/ZnS quantum dots-5-aminolevulinic acid conjugates. RSC Adv 2016. [DOI: 10.1039/c6ra06937a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recently, near-infrared (NIR) excitation has been suggested for PDT improvement and therapy of cancer.
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Affiliation(s)
- Yueshu Feng
- School of Science
- Changchun University of Science and Technology
- International Joint Research Center for Nanophotonics and Biophotonics
- Changchun 130000
- China
| | - Liwei Liu
- School of Science
- Changchun University of Science and Technology
- International Joint Research Center for Nanophotonics and Biophotonics
- Changchun 130000
- China
| | - Siyi Hu
- School of Science
- Changchun University of Science and Technology
- International Joint Research Center for Nanophotonics and Biophotonics
- Changchun 130000
- China
| | - Yingyi Liu
- School of Science
- Changchun University of Science and Technology
- International Joint Research Center for Nanophotonics and Biophotonics
- Changchun 130000
- China
| | - Yu Ren
- School of Science
- Changchun University of Science and Technology
- International Joint Research Center for Nanophotonics and Biophotonics
- Changchun 130000
- China
| | - Xihe Zhang
- School of Science
- Changchun University of Science and Technology
- International Joint Research Center for Nanophotonics and Biophotonics
- Changchun 130000
- China
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40
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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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41
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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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42
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Lu L, Chen C, Zhao D, Sun J, Yang X. Europium Luminescence Used for Logic Gate and Ions Sensing with Enoxacin As the Antenna. Anal Chem 2015; 88:1238-45. [DOI: 10.1021/acs.analchem.5b03593] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lixia Lu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanxia Chen
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Zhao
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Sun
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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43
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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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44
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Zhou J, Yang Y, Zhang CY. Toward Biocompatible Semiconductor Quantum Dots: From Biosynthesis and Bioconjugation to Biomedical Application. Chem Rev 2015; 115:11669-717. [DOI: 10.1021/acs.chemrev.5b00049] [Citation(s) in RCA: 472] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Juan Zhou
- State
Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yong Yang
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chun-yang Zhang
- College
of Chemistry, Chemical Engineering and Materials Science, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Key Laboratory of Molecular and Nano Probes,
Ministry of Education, Shandong Provincial Key Laboratory of Clean
Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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45
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One-pot green synthesis of oxygen-rich nitrogen-doped graphene quantum dots and their potential application in pH-sensitive photoluminescence and detection of mercury(II) ions. Talanta 2015; 142:131-9. [DOI: 10.1016/j.talanta.2015.04.059] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 12/26/2022]
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46
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Massey M, Wu M, Conroy EM, Algar WR. Mind your P's and Q's: the coming of age of semiconducting polymer dots and semiconductor quantum dots in biological applications. Curr Opin Biotechnol 2015; 34:30-40. [DOI: 10.1016/j.copbio.2014.11.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/06/2014] [Indexed: 01/15/2023]
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47
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Ding S, Cargill AA, Das SR, Medintz IL, Claussen JC. Biosensing with Förster Resonance Energy Transfer Coupling between Fluorophores and Nanocarbon Allotropes. SENSORS 2015; 15:14766-87. [PMID: 26110411 PMCID: PMC4507682 DOI: 10.3390/s150614766] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/01/2015] [Accepted: 06/05/2015] [Indexed: 01/10/2023]
Abstract
Nanocarbon allotropes (NCAs), including zero-dimensional carbon dots (CDs), one-dimensional carbon nanotubes (CNTs) and two-dimensional graphene, exhibit exceptional material properties, such as unique electrical/thermal conductivity, biocompatibility and high quenching efficiency, that make them well suited for both electrical/electrochemical and optical sensors/biosensors alike. In particular, these material properties have been exploited to significantly enhance the transduction of biorecognition events in fluorescence-based biosensing involving Förster resonant energy transfer (FRET). This review analyzes current advances in sensors and biosensors that utilize graphene, CNTs or CDs as the platform in optical sensors and biosensors. Widely utilized synthesis/fabrication techniques, intrinsic material properties and current research examples of such nanocarbon, FRET-based sensors/biosensors are illustrated. The future outlook and challenges for the research field are also detailed.
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Affiliation(s)
- Shaowei Ding
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Allison A Cargill
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Suprem R Das
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA.
| | - Jonathan C Claussen
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
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Chou KF, Dennis AM. Förster Resonance Energy Transfer between Quantum Dot Donors and Quantum Dot Acceptors. SENSORS 2015; 15:13288-325. [PMID: 26057041 PMCID: PMC4507609 DOI: 10.3390/s150613288] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 01/27/2023]
Abstract
Förster (or fluorescence) resonance energy transfer amongst semiconductor quantum dots (QDs) is reviewed, with particular interest in biosensing applications. The unique optical properties of QDs provide certain advantages and also specific challenges with regards to sensor design, compared to other FRET systems. The brightness and photostability of QDs make them attractive for highly sensitive sensing and long-term, repetitive imaging applications, respectively, but the overlapping donor and acceptor excitation signals that arise when QDs serve as both the donor and acceptor lead to high background signals from direct excitation of the acceptor. The fundamentals of FRET within a nominally homogeneous QD population as well as energy transfer between two distinct colors of QDs are discussed. Examples of successful sensors are highlighted, as is cascading FRET, which can be used for solar harvesting.
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Affiliation(s)
- Kenny F Chou
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | - Allison M Dennis
- Department of Biomedical Engineering and Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.
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Use of biomolecular scaffolds for assembling multistep light harvesting and energy transfer devices. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2015. [DOI: 10.1016/j.jphotochemrev.2014.12.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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50
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Ding S, Cargill AA, Medintz IL, Claussen JC. Increasing the activity of immobilized enzymes with nanoparticle conjugation. Curr Opin Biotechnol 2015; 34:242-50. [PMID: 25957941 DOI: 10.1016/j.copbio.2015.04.005] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/03/2015] [Accepted: 04/07/2015] [Indexed: 12/16/2022]
Abstract
The efficiency and selectivity of enzymatic catalysis is useful to a plethora of industrial and manufacturing processes. Many of these processes require the immobilization of enzymes onto surfaces, which has traditionally reduced enzyme activity. However, recent research has shown that the integration of nanoparticles into enzyme carrier schemes has maintained or even enhanced immobilized enzyme performance. The nanoparticle size and surface chemistry as well as the orientation and density of immobilized enzymes all contribute to the enhanced performance of enzyme-nanoparticle conjugates. These improvements are noted in specific nanoparticles including those comprising carbon (e.g., graphene and carbon nanotubes), metal/metal oxides and polymeric nanomaterials, as well as semiconductor nanocrystals or quantum dots.
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Affiliation(s)
- Shaowei Ding
- Department of Mechanical Engineering, 2104 Black Engineering, Ames, IA 50011, United States
| | - Allison A Cargill
- Department of Mechanical Engineering, 2104 Black Engineering, Ames, IA 50011, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Jonathan C Claussen
- Department of Mechanical Engineering, 2104 Black Engineering, Ames, IA 50011, United States.
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