1
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Algama CH, Basir J, Wijesinghe KM, Dhakal S. Fluorescence-Based Multimodal DNA Logic Gates. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:1185. [PMID: 39057862 PMCID: PMC11280116 DOI: 10.3390/nano14141185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024]
Abstract
The use of DNA structures in creating multimodal logic gates bears high potential for building molecular devices and computation systems. However, due to the complex designs or complicated working principles, the implementation of DNA logic gates within molecular devices and circuits is still quite limited. Here, we designed simple four-way DNA logic gates that can serve as multimodal platforms for simple to complex operations. Using the proximity quenching of the fluorophore-quencher pair in combination with the toehold-mediated strand displacement (TMSD) strategy, we have successfully demonstrated that the fluorescence output, which is a result of gate opening, solely relies on the oligonucleotide(s) input. We further demonstrated that this strategy can be used to create multimodal (tunable displacement initiation sites on the four-way platform) logic gates including YES, AND, OR, and the combinations thereof. The four-way DNA logic gates developed here bear high promise for building biological computers and next-generation smart molecular circuits with biosensing capabilities.
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Affiliation(s)
| | | | | | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
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2
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Sethi S, Wijesinghe KM, Dhakal S. Single-Molecule FRET-Based Multiplexed Detection. Methods Mol Biol 2024; 2744:183-195. [PMID: 38683319 DOI: 10.1007/978-1-0716-3581-0_11] [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: 05/01/2024]
Abstract
Single-molecule multiplexed detection is a high-promise toolkit for the expanding field of biosensing and molecular diagnostics. Among many single-molecule techniques available today for biomarker sensing including fluorescence, force, electrochemical, spectroscopic, barcoding, and other techniques, fluorescence-based approaches are arguably the most widely used methods due to their high sensitivity, selectivity, and readily available fluorophore-labeling schemes for a wide variety of biomolecules. However, multiplexed imaging using fluorescence techniques has proven to be challenging due to the sophisticated labeling schemes often requiring multiple FRET (fluorescence resonance energy transfer) pairs and/or excitation sources, which lead to overlapping signals and complicate data analysis. Here, we describe a single-molecule FRET method that enables multiplexed analysis while still using only one FRET pair, and thus the described approach is a significant step forward from conventional FRET methods.
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Affiliation(s)
- Srishty Sethi
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA.
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3
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Sabbih GO, Wijesinghe KM, Algama C, Dhakal S, Danquah MK. Computational generation and characterization of IsdA-binding aptamers with single-molecule FRET analysis. Biotechnol J 2023; 18:e2300076. [PMID: 37593983 DOI: 10.1002/biot.202300076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Staphylococcus aureus is a major foodborne bacterial pathogen. Early detection of S. aureus is crucial to prevent infections and ensure food quality. The iron-regulated surface determinant protein A (IsdA) of S. aureus is a unique surface protein necessary for sourcing vital iron from host cells for the survival and colonization of the bacteria. The function, structure, and location of the IsdA protein make it an important protein for biosensing applications relating to the pathogen. Here, we report an in-silico approach to develop and validate high-affinity binding aptamers for the IsdA protein detection using custom-designed in-silico tools and single-molecule Fluorescence Resonance Energy Transfer (smFRET) measurements. We utilized in-silico oligonucleotide screening methods and metadynamics-based methods to generate 10 aptamer candidates and characterized them based on the Dissociation Free Energy (DFE) of the IsdA-aptamer complexes. Three of the aptamer candidates were shortlisted for smFRET experimental analysis of binding properties. Limits of detection in the low picomolar range were observed for the aptamers, and the results correlated well with the DFE calculations, indicating the potential of the in-silico approach to support aptamer discovery. This study showcases a computational SELEX method in combination with single-molecule binding studies deciphering effective aptamers against S. aureus IsdA, protein. The established approach demonstrates the ability to expedite aptamer discovery that has the potential to cut costs and predict binding efficacy. The application can be extended to designing aptamers for various protein targets, enhancing molecular recognition, and facilitating the development of high-affinity aptamers for multiple uses.
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Affiliation(s)
| | | | - Chamika Algama
- Virginia Commonwealth University, Richmond, Virginia, USA
| | - Soma Dhakal
- Virginia Commonwealth University, Richmond, Virginia, USA
| | - Michael K Danquah
- University of Tennessee, Chattanooga, Tennessee, USA
- University of Tennessee, Knoxville, Tennessee, USA
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4
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Wijesinghe KM, Sabbih G, Algama CH, Syed R, Danquah MK, Dhakal S. FRET-Based Single-Molecule Detection of Pathogen Protein IsdA Using Computationally Selected Aptamers. Anal Chem 2023. [PMID: 37327207 DOI: 10.1021/acs.analchem.3c00717] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Iron-regulated surface determinant protein A (IsdA) is a key surface protein found in the foodborne bacteria─Staphylococcus aureus (S. aureus)─which is known to be critical for bacterial survival and colonization. S. aureus is pathogenic and has been linked to foodborne diseases; thus, early detection is critical to prevent diseases caused by this bacterium. Despite IsdA being a specific marker for S. aureus and several detection methods have been developed for sensitive detection of this bacteria such as cell culture, nucleic acids amplification, and other colorimetric and electrochemical methods, the detection of S. aureus through IsdA is underdeveloped. Here, by combining computational generation of target-guided aptamers and fluorescence resonance energy transfer (FRET)-based single-molecule analysis, we presented a widely applicable and robust detection method for IsdA. Three different RNA aptamers specific to the IsdA protein were identified and their ability to switch a FRET construct to a high-FRET state in the presence of protein was verified. The presented approach demonstrated the detection of IsdA down to picomolar levels (×10-12 M, equivalent to ∼1.1 femtomoles IsdA) with a dynamic range extending to ∼40 nM. The FRET-based single-molecule technique that we reported here is capable of detecting the foodborne pathogen protein IsdA with high sensitivity and specificity and has a broader application in the food industry and aptamer-based sensing field by enabling quantitative detection of a wide range of pathogen proteins.
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Affiliation(s)
- Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Godfred Sabbih
- Department of Chemical Engineering, University of Tennessee, Chattanooga, Tennessee 37403, United States
| | - Chamika Harshani Algama
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Rida Syed
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga, Tennessee 37403, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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5
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Darwish GH, Massey M, Daudet G, Alde LG, Algar WR. Tetrameric Antibody Complexes and Affinity Tag Peptides for the Selective Immobilization and Imaging of Single Quantum Dots. Bioconjug Chem 2023. [PMID: 37243625 DOI: 10.1021/acs.bioconjchem.3c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Colloidal semiconductor quantum dots (QDs) are of widespread interest as fluorescent labels for bioanalysis and imaging applications. Single-particle measurements have proven to be a very powerful tool for better understanding the fundamental properties and behaviors of QDs and their bioconjugates; however, a recurring challenge is the immobilization of QDs in a solution-like environment that minimizes interactions with a bulk surface. Immobilization strategies for QD-peptide conjugates are particularly underdeveloped within this context. Here, we present a novel strategy for the selective immobilization of single QD-peptide conjugates using a combination of tetrameric antibody complexes (TACs) and affinity tag peptides. A glass substrate is modified with an adsorbed layer of concanavalin A (ConA) that binds a subsequent layer of dextran that minimizes nonspecific binding. A TAC with anti-dextran and anti-affinity tag antibodies binds to the dextran-coated glass surface and to the affinity tag sequence of QD-peptide conjugates. The result is spontaneous and sequence-selective immobilization of single QDs without any chemical activation or cross-linking. Controlled immobilization of multiple colors of QDs is possible using multiple affinity tag sequences. Experiments confirmed that this approach positions the QD away from the bulk surface. The method supports real-time imaging of binding and dissociation, measurements of Förster resonance energy transfer (FRET), tracking of dye photobleaching, and detection of proteolytic activity. We anticipate that this immobilization strategy will be useful for studies of QD-associated photophysics, biomolecular interactions and processes, and digital assays.
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Affiliation(s)
- Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Melissa Massey
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Gabrielle Daudet
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Luis G Alde
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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6
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Contribution of smFRET to Chromatin Research. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Chromatins are structural components of chromosomes and consist of DNA and histone proteins. The structure, dynamics, and function of chromatins are important in regulating genetic processes. Several different experimental and theoretical tools have been employed to understand chromatins better. In this review, we will focus on the literatures engrossed in understanding of chromatins using single-molecule Förster resonance energy transfer (smFRET). smFRET is a single-molecule fluorescence microscopic technique that can furnish information regarding the distance between two points in space. This has been utilized to efficiently unveil the structural details of chromatins.
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7
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Kaur A, Mahmoud R, Megalathan A, Pettit S, Dhakal S. Multiplexed smFRET Nucleic Acid Sensing Using DNA Nanotweezers. BIOSENSORS 2023; 13:119. [PMID: 36671954 PMCID: PMC9856376 DOI: 10.3390/bios13010119] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
The multiplexed detection of disease biomarkers is part of an ongoing effort toward improving the quality of diagnostic testing, reducing the cost of analysis, and accelerating the treatment processes. Although significant efforts have been made to develop more sensitive and rapid multiplexed screening methods, such as microarrays and electrochemical sensors, their limitations include their intricate sensing designs and semi-quantitative detection capabilities. Alternatively, fluorescence resonance energy transfer (FRET)-based single-molecule counting offers great potential for both the sensitive and quantitative detection of various biomarkers. However, current FRET-based multiplexed sensing typically requires the use of multiple excitation sources and/or FRET pairs, which complicates labeling schemes and the post-analysis of data. We present a nanotweezer (NT)-based sensing strategy that employs a single FRET pair and is capable of detecting multiple targets. Using DNA mimics of miRNA biomarkers specific to triple-negative breast cancer (TNBC), we demonstrated that the developed sensors are sensitive down to the low picomolar range (≤10 pM) and can discriminate between targets with a single-base mismatch. These simple hybridization-based sensors hold great promise for the sensitive detection of a wider spectrum of nucleic acid biomarkers.
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8
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Ghimire ML, Gibbs DR, Mahmoud R, Dhakal S, Reiner JE. Nanopore Analysis as a Tool for Studying Rapid Holliday Junction Dynamics and Analyte Binding. Anal Chem 2022; 94:10027-10034. [PMID: 35786863 DOI: 10.1021/acs.analchem.2c00342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Holliday junctions (HJs) are an important class of nucleic acid structure utilized in DNA break repair processes. As such, these structures have great importance as therapeutic targets and for understanding the onset and development of various diseases. Single-molecule fluorescence resonance energy transfer (smFRET) has been used to study HJ structure-fluctuation kinetics, but given the rapid time scales associated with these kinetics (approximately sub-milliseconds) and the limited bandwidth of smFRET, these studies typically require one to slow down the structure fluctuations using divalent ions (e.g., Mg2+). This modification limits the ability to understand and model the underlying kinetics associated with HJ fluctuations. We address this here by utilizing nanopore sensing in a gating configuration to monitor DNA structure fluctuations without divalent ions. A nanopore analysis shows that HJ fluctuations occur on the order of 0.1-10 ms and that the HJ remains locked in a single conformation with short-lived transitions to a second conformation. It is not clear what role the nanopore plays in affecting these kinetics, but the time scales observed indicate that HJs are capable of undergoing rapid transitions that are not detectable with lower bandwidth measurement techniques. In addition to monitoring rapid HJ fluctuations, we also report on the use of nanopore sensing to develop a highly selective sensor capable of clear and rapid detection of short oligo DNA strands that bind to various HJ targets.
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Affiliation(s)
- Madhav L Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Dalton R Gibbs
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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9
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Wijesinghe KM, Kanak MA, Harrell JC, Dhakal S. Single-Molecule Sensor for High-Confidence Detection of miRNA. ACS Sens 2022; 7:1086-1094. [PMID: 35312280 PMCID: PMC9112324 DOI: 10.1021/acssensors.1c02748] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) play a crucial role in regulating gene expression and have been linked to many diseases. Therefore, sensitive and accurate detection of disease-linked miRNAs is vital to the emerging revolution in early diagnosis of diseases. While the detection of miRNAs is a challenge due to their intrinsic properties such as small size, high sequence similarity among miRNAs and low abundance in biological fluids, the majority of miRNA-detection strategies involve either target/signal amplification or involve complex sensing designs. In this study, we have developed and tested a DNA-based fluorescence resonance energy transfer (FRET) sensor that enables ultrasensitive detection of a miRNA biomarker (miRNA-342-3p) expressed by triple-negative breast cancer (TNBC) cells. The sensor shows a relatively low FRET state in the absence of a target but it undergoes continuous FRET transitions between low- and high-FRET states in the presence of the target. The sensor is highly specific, has a detection limit down to low femtomolar (fM) without having to amplify the target, and has a large dynamic range (3 orders of magnitude) extending to 300 000 fM. Using this strategy, we demonstrated that the sensor allows detection of miRNA-342-3p in the miRNA-extracts from cancer cell lines and TNBC patient-derived xenografts. Given the simple-to-design hybridization-based detection, the sensing platform developed here can be used to detect a wide range of miRNAs enabling early diagnosis and screening of other genetic disorders.
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Affiliation(s)
- Kalani M. Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Mazhar A. Kanak
- Division of Transplant Surgery, Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298, United States
| | - J. Chuck Harrell
- Department of Pathology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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10
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Rodríguez-Sevilla P, Thompson SA, Jaque D. Multichannel Fluorescence Microscopy: Advantages of Going beyond a Single Emission. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Paloma Rodríguez-Sevilla
- Nanomaterials for Bioimaging Group (NanoBIG) Departamento de Física de Materiales Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 Madrid 28049 Spain
| | - Sebastian A. Thompson
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanociencia) C/Faraday 9 Madrid 28049 Spain
- Nanobiotechnology Unit Associated to the National Center for Biotechnology (CNB-CSIC-IMDEA) Madrid 28049 Spain
| | - Daniel Jaque
- Nanomaterials for Bioimaging Group (NanoBIG) Departamento de Física de Materiales Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 Madrid 28049 Spain
- Instituto Ramón y Cajal de Investigación Sanitaria Hospital Ramón y Cajal Ctra. Colmenar km. 9,100 Madrid 28034 Spain
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11
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Current clinical testing approach of COVID. SENSING TOOLS AND TECHNIQUES FOR COVID-19 2022. [PMCID: PMC9334984 DOI: 10.1016/b978-0-323-90280-9.00003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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Liu Y, Sun X, Yuan H, Liu B, Zhou B, Chen X, Li X, Xue Q. Sensitive detection of p53 DNA based on spatially confined fluorescence resonance energy transfer and multivalent assembly of branched DNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4314-4319. [PMID: 34476425 DOI: 10.1039/d1ay01110c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A key challenge for the discrete distribution-based Förster resonance energy transfer system (D-FRET) is the reduced intensity and stability of signal probes in complex biological matrices. Here, we present a spatially confined FRET (SC-FRET) probe with a stable structure and strong signal output. It consists of multivalent FRET pairs labeled with FAM or TAMRA. In this assay, p53 DNA was chosen as a model hairpin probe (HP), and two kinds of branched DNA probes (ssDNA-FAM, ssDNA-TAMRA) were involved. Under the action of p53 DNA, the unfolded HP acts as a primer to initiate polymerization extension of KFP polymerase and cleavage of Nb.BbvCI endonuclease, which produces plenty of ssDNA (primer-DNA). The branched DNA is designed to have the same binding core and different sticky ends, the core part of which can self-assemble to form X-shaped branched DNA (X-FAM or X-TAMRA), and the sticky ends of which are complementary to the primer-DNA. Therefore, the primer-DNAs released during the polymerization cleavage process will combine a large number of X-FAM and X-TAMRA in a limited space through complementary base pairing. Fluorescence was transferred from FAM to TAMRA, and a strong FRET response was generated by the locational effects. The proposed SC-FRET system based on the multivalent assembly of branched DNA exhibited a strong FRET response with an LOD of 0.01394 pM. Importantly, it also showed a high-contrast and stable FRET response in HeLa cells. Its superior biological stability is attributed to the large steric hindrance of the compact and rigid frame of the SC-FRET probe, which helps prevent intracellular degradation and provides a powerful tool for biomedical research.
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Affiliation(s)
- Yeling Liu
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Xia Sun
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Hui Yuan
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Bingxin Liu
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Bingqian Zhou
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Xuening Chen
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, China
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Qingwang Xue
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
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13
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Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021; 8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
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14
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Kaur A, Ellison M, Dhakal S. MASH-FRET: A Simplified Approach for Single-Molecule Multiplexing Using FRET. Anal Chem 2021; 93:8856-8863. [PMID: 34124890 DOI: 10.1021/acs.analchem.1c00848] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Multiplexed detection has been a big motivation in biomarker analysis as it not only saves cost and labor but also improves the reliability of diagnosis. Among the many approaches for multiplexed detection, fluorescence resonance energy transfer (FRET)-based multiplexing is gaining popularity particularly due to its low background and quantitative nature. Although several FRET-based approaches have been developed for multiplexing, they require either multiple FRET pairs in combination with multiple excitation sources or complicated algorithms to accurately assign signals for individual FRET pairs. Therefore, the need for multiple FRET pairs and multiple excitation sources not only complicates the experimental design but also increases the cost and labor. In this regard, multiplexed sensing by tuning the interdye distance of a single FRET pair could be an ideal solution if identification of multiple FRET efficiencies in a single imaging is possible. Here, implementing a program called MASH-FRET, we evaluated the rigor and capability of this program in identifying seemingly overlapped FRET populations obtained from a multiplexed detection experiment using a single FRET pair. Through MASH-FRET-enabled bootstrap-based analysis of FRET data (also called BOBA-FRET), we demonstrated that the resolution and statistical confidence of the poorly resolved or even unresolved FRET populations can be readily determined. Using simulated FRET data, we further demonstrated that the program can easily identify FRET populations separated by ∼0.1 in mean FRET values, indicating an upper limit of ∼9-fold multiplexing without the need for complicated labeling schemes and multiexcitation sources. Therefore, this paper presents a data analysis approach on an existing platform that has a great potential to simplify the technological needs for multiplexing and to broaden the scope of FRET-based single-molecule analyses.
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Affiliation(s)
- Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Mischa Ellison
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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15
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Abstract
Selective and sensitive detection of nucleic acid biomarkers is of great significance in early-stage diagnosis and targeted therapy. Therefore, the development of diagnostic methods capable of detecting diseases at the molecular level in biological fluids is vital to the emerging revolution in the early diagnosis of diseases. However, the vast majority of the currently available ultrasensitive detection strategies involve either target/signal amplification or involve complex designs. Here, using a p53 tumor suppressor gene whose mutation has been implicated in more than 50% of human cancers, we show a background-free ultrasensitive detection of this gene on a simple platform. The sensor exhibits a relatively static mid-FRET state in the absence of a target that can be attributed to the time-averaged fluorescence intensity of fast transitions among multiple states, but it undergoes continuous dynamic switching between a low- and a high-FRET state in the presence of a target, allowing a high-confidence detection. In addition to its simple design, the sensor has a detection limit down to low femtomolar (fM) concentration without the need for target amplification. We also show that this sensor is highly effective in discriminating against single-nucleotide polymorphisms (SNPs). Given the generic hybridization-based detection platform, the sensing strategy developed here can be used to detect a wide range of nucleic acid sequences enabling early diagnosis of diseases and screening genetic disorders.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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16
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Megalathan A, Wijesinghe KM, Ranson L, Dhakal S. Single-Molecule Analysis of Nanocircle-Embedded I-Motifs under Crowding. J Phys Chem B 2021; 125:2193-2201. [PMID: 33629846 DOI: 10.1021/acs.jpcb.0c09640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytosine (C)-rich regions of single-stranded DNA or RNA can fold into a tetraplex structure called i-motifs, which are typically stable under acidic pHs due to the need for protons to stabilize C-C interactions. While new studies have shown evidence for the formation of i-motifs at neutral and even physiological pH, it is not clear whether i-motifs can stably form in cells where DNA experiences topological constraint and crowding. Similarly, several studies have shown that a molecularly crowded environment promotes the formation of i-motifs at physiological pH; however, whether the intracellular crowding counteracts the topological destabilization of i-motifs is yet to be investigated. In this manuscript, using fluorescence resonance energy transfer (FRET)-based single-molecule analyses of human telomeric (hTel) i-motifs embedded in nanocircles as a proof-of-concept platform, we investigated the overall effects of crowding and topological constraint on the i-motif behavior. The smFRET analysis of the nanoassembly showed that the i-motif remains folded at pH 5.5 but unfolds at higher pHs. However, in the presence of a crowder (30% PEG 6000), i-motifs are formed at physiological pH overcoming the topological constraint imposed by the DNA nanocircles. Analysis of FRET-time traces show that the hTel sequence primarily assumes the folded state at pH ≤7.0 under crowding, but it undergoes slow conformational transitions between the folded and unfolded states at physiological pH. Our demonstration that the i-motif can form under cell-mimic crowding and topologically constrained environments may provide new insights into the potential biological roles of i-motifs and also into the design and development of i-motif-based biosensors, therapy, and other nanotechnological applications.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Leslie Ranson
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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17
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An all-graphene quantum dot Förster resonance energy transfer (FRET) probe for ratiometric detection of HE4 ovarian cancer biomarker. Colloids Surf B Biointerfaces 2021; 198:111458. [DOI: 10.1016/j.colsurfb.2020.111458] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/20/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022]
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18
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Liu L, Zhang L, Liang Y. Visual sensing of multiple proteins based on three kinds of metal nanoparticles as sensor receptors. Colloids Surf B Biointerfaces 2021; 200:111574. [PMID: 33476955 DOI: 10.1016/j.colsurfb.2021.111574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/18/2020] [Accepted: 01/08/2021] [Indexed: 12/28/2022]
Abstract
We propose a colorimetric sensing array consisting of 4-aminothiophenol (p-ATP)-modified gold nanoparticles (Au NPs), silver nanoparticles (Ag NPs), and core-shell Au@Ag nanocubes (Au@Ag NCs) as sensing elements to identify multiple proteins according to the diverse colorimetric response patterns. In the absence of proteins, the sensor element solution itself did not agglomerate. After interacting with six proteins (lysozyme (LZM), hemoglobin (HGB), peroxidase from horseradish (HRP), bovine liver from peroxidase (CAT), trypsin from bovin pancreas (TRY), and pepsin (PEP)), due to the different binding ability between the sensing elements and various proteins, the sensing array exhibits a unique pattern of colorimetric variations, linear discrimination analysis (LDA) was applied to analyze the pattern and produced a clustering map for a clearer differentiation of these proteins.
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Affiliation(s)
- Lei Liu
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Liguo Zhang
- School of Environment, South China Normal University, Guangdong Provincial Engineering Technology Research Center for Wastewater Management and Treatment, Guangzhou, 510006, China.
| | - Yong Liang
- School of Chemistry and Environment, South China Normal University, Guangzhou, 510631, China.
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19
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Abstract
The COVID-19 pandemic has created huge damage to society and brought panic around the world. Such panic can be ascribed to the seemingly deceptive features of COVID-19: Compared to other deadly viral outbreaks, it has medium transmission and mortality rates. As a result, the severity of the causative coronavirus, SARS-CoV-2, was deeply underestimated by society at the beginning of the COVID-19 outbreak. Based on this, in this review, we define the viruses with features similar to those of SARS-CoV-2 as the Panic Zone viruses. To contain those viruses, accurate and fast diagnosis followed by effective isolation and treatment of patients are pivotal at the early stage of virus breakouts. This is especially true when there is no cure or vaccine available for a transmissible disease, which is the case for the current COVID-19 pandemic. As of July 2020, more than 100 kits for COVID-19 diagnosis on the market have been surveyed in this review, while emerging sensing techniques for SARS-CoV-2 are also discussed. It is of critical importance to rationally use these kits for efficient management and control of the Panic Zone viruses. Therefore, we discuss guidelines to select diagnostic kits at different outbreak stages of the Panic Zone viruses, SARS-CoV-2 in particular. While it is of utmost importance to use nucleic acid based detection kits with low false negativity (high sensitivity) at the early stage of an outbreak, the low false positivity (high specificity) gains importance at later stages of the outbreak. When society is set to reopen from the lockdown stage of the COVID-19 pandemic, it becomes critical to have immunoassay based kits with high specificity to identify people who can safely return to society after their recovery from SARS-CoV-2 infections. Finally, since a massive attack from a viral pandemic requires a massive defense from the whole society, we urge both government and the private sector to research and develop affordable and reliable point-of-care testing (POCT) kits, which can be used massively by the general public (and therefore called massive POCT) to contain Panic Zone viruses in the future.
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Affiliation(s)
| | | | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA (44240)
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20
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Yuan X, Yang C, He Q, Chen J, Yu D, Li J, Zhai S, Qin Z, Du K, Chu Z, Qin P. Current and Perspective Diagnostic Techniques for COVID-19. ACS Infect Dis 2020; 6:1998-2016. [PMID: 32677821 PMCID: PMC7409380 DOI: 10.1021/acsinfecdis.0c00365] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 02/08/2023]
Abstract
Since late December 2019, the coronavirus pandemic (COVID-19; previously known as 2019-nCoV) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been surging rapidly around the world. With more than 1,700,000 confirmed cases, the world faces an unprecedented economic, social, and health impact. The early, rapid, sensitive, and accurate diagnosis of viral infection provides rapid responses for public health surveillance, prevention, and control of contagious diffusion. More than 30% of the confirmed cases are asymptomatic, and the high false-negative rate (FNR) of a single assay requires the development of novel diagnostic techniques, combinative approaches, sampling from different locations, and consecutive detection. The recurrence of discharged patients indicates the need for long-term monitoring and tracking. Diagnostic and therapeutic methods are evolving with a deeper understanding of virus pathology and the potential for relapse. In this Review, a comprehensive summary and comparison of different SARS-CoV-2 diagnostic methods are provided for researchers and clinicians to develop appropriate strategies for the timely and effective detection of SARS-CoV-2. The survey of current biosensors and diagnostic devices for viral nucleic acids, proteins, and particles and chest tomography will provide insight into the development of novel perspective techniques for the diagnosis of COVID-19.
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Affiliation(s)
- Xi Yuan
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
| | - Chengming Yang
- Southern
University of Science and Technology Hospital, Shenzhen, Guangdong 518055, China
| | - Qian He
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
| | - Junhu Chen
- National
Institute of Parasitic Diseases, Chinese
Center for Disease Control and Prevention, Shanghai 200025, China
| | - Dongmei Yu
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
- Department
of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jie Li
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
- Kunming
Dog Base of Police Security, Ministry of Public Security, Kunming, Yunnan 650204, China
| | - Shiyao Zhai
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
| | - Zhifeng Qin
- Animal &
Plant Inspection and Quarantine Technology Center, Shenzhen Customs District People’s Republic of China, Shenzhen, Guangdong 518045, China
| | - Ke Du
- Department
of Mechanical Engineering, Rochester Institute
of Technology, Rochester, New York 14623, United States
| | - Zhenhai Chu
- Southern
University of Science and Technology Hospital, Shenzhen, Guangdong 518055, China
| | - Peiwu Qin
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
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21
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Deng Y, Ma L, Han Q, Yu C, Johnson-Buck A, Su X. DNA-Templated Timer Probes for Multiplexed Sensing. NANO LETTERS 2020; 20:2688-2694. [PMID: 32119561 DOI: 10.1021/acs.nanolett.0c00313] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Simultaneous analysis based on encoded fluorophores suffers from potential crosstalk between fluorophores and the limited number of colors that can be practically resolved. Inspired by nontrivial temporal patterns in living organisms, we developed a DNA-templated probe by utilizing DNA polymerase (DNAP) for multiplexed detection of nucleic acids. These probes use differential delay times of signaling by a DNAP-mediated extension to distinguish different targets, which serve as the primers. Taking advantage of the high processivity and the controllable kinetics of DNAP, we find that multiplexed detection can be achieved in homogeneous solution using a single fluorophore. As a proof of concept, we developed assays for genomic DNA from four different bacteria. In addition, we designed and implemented probes to undergo a single oscillation in signal as an alternative way for multiplexing. We anticipate this approach will find broad applications not only in sensing but also in synthetic DNA nanosystems.
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Affiliation(s)
- Yingnan Deng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Liang Ma
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Qianqian Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Alexander Johnson-Buck
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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22
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Single-molecule analysis of nucleic acid biomarkers - A review. Anal Chim Acta 2020; 1115:61-85. [PMID: 32370870 DOI: 10.1016/j.aca.2020.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.
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FRET-Based Aptasensor for the Selective and Sensitive Detection of Lysozyme. SENSORS 2020; 20:s20030914. [PMID: 32050422 PMCID: PMC7038949 DOI: 10.3390/s20030914] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
Lysozyme is a conserved antimicrobial enzyme and has been cited for its role in immune modulation. Increase in lysozyme concentration in body fluids is also regarded as an early warning of some diseases such as Alzheimer’s, sarcoidosis, Crohn’s disease, and breast cancer. Therefore, a method for a sensitive and selective detection of lysozyme can benefit many different areas of research. In this regard, several aptamers that are specific to lysozyme have been developed, but there is still a lack of a detection method that is sensitive, specific, and quantitative. In this work, we demonstrated a single-molecule fluorescence resonance energy transfer (smFRET)-based detection of lysozyme using an aptamer sensor (also called aptasensor) in which the binding of lysozyme triggers its conformational switch from a low-FRET to high-FRET state. Using this strategy, we demonstrated that the aptasensor is sensitive down to 2.3 picomoles (30 nM) of lysozyme with a dynamic range extending to ~2 µM and has little to no interference from similar biomolecules. The smFRET approach used here requires a dramatically small amount of aptasensor (~3000-fold less as compared to typical bulk fluorescence methods), and it is cost effective compared to enzymatic and antibody-based approaches. Additionally, the aptasensor can be readily regenerated in situ via a process called toehold mediated strand displacement (TMSD). The FRET-based aptasensing of lysozyme that we developed here could be implemented to detect other protein biomarkers by incorporating protein-specific aptamers without the need for changing fluorophore-labeled DNA strands.
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25
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Fang Z, Liu L, Wang Y, Xi D, Zhang S. Unambiguous Discrimination of Multiple Protein Biomarkers by Nanopore Sensing with Double-Stranded DNA-Based Probes. Anal Chem 2019; 92:1730-1737. [DOI: 10.1021/acs.analchem.9b02965] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhen Fang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P.R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Liping Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P.R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
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26
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Single-Step FRET-Based Detection of Femtomoles DNA. SENSORS 2019; 19:s19163495. [PMID: 31405068 PMCID: PMC6719117 DOI: 10.3390/s19163495] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022]
Abstract
Sensitive detection of nucleic acids and identification of single nucleotide polymorphism (SNP) is crucial in diagnosis of genetic diseases. Many strategies have been developed for detection and analysis of DNA, including fluorescence, electrical, optical, and mechanical methods. Recent advances in fluorescence resonance energy transfer (FRET)-based sensing have provided a new avenue for sensitive and quantitative detection of various types of biomolecules in simple, rapid, and recyclable platforms. Here, we report single-step FRET-based DNA sensors designed to work via a toehold-mediated strand displacement (TMSD) process, leading to a distinct change in the FRET efficiency upon target binding. Using single-molecule FRET (smFRET), we show that these sensors can be regenerated in situ, and they allow detection of femtomoles DNA without the need for target amplification while still using a dramatically small sample size (fewer than three orders of magnitude compared to the typical sample size of bulk fluorescence). In addition, these single-molecule sensors exhibit a dynamic range of approximately two orders of magnitude. Using one of the sensors, we demonstrate that the single-base mismatch sequence can be discriminated from a fully matched DNA target, showing a high specificity of the method. These sensors with simple and recyclable design, sensitive detection of DNA, and the ability to discriminate single-base mismatch sequences may find applications in quantitative analysis of nucleic acid biomarkers.
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