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Relevant bibliographies by topics / Single Molecule Fluorescence Resonance Energy Transfer (smFRET)

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Academic literature on the topic 'Single Molecule Fluorescence Resonance Energy Transfer (smFRET)'

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Published: 7 September 2023

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Journal articles on the topic "Single Molecule Fluorescence Resonance Energy Transfer (smFRET)"

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Yang, Ziyu, Haiqi Xu, Jiayu Wang, Wei Chen, and Meiping Zhao. "Single-Molecule Fluorescence Techniques for Membrane Protein Dynamics Analysis." Applied Spectroscopy 75, no. 5 (April 20, 2021): 491–505. http://dx.doi.org/10.1177/00037028211009973.

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Fluorescence-based single-molecule techniques, mainly including fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence resonance energy transfer (smFRET), are able to analyze the conformational dynamics and diversity of biological macromolecules. They have been applied to analysis of the dynamics of membrane proteins, such as membrane receptors and membrane transport proteins, due to their superior ability in resolving spatio-temporal heterogeneity and the demand of trace amounts of analytes. In this review, we first introduced the basic principle involved in FCS and smFRET. Then we summarized the labeling and immobilization strategies of membrane protein molecules, the confocal-based and TIRF-based instrumental configuration, and the data processing methods. The applications to membrane protein dynamics analysis are described in detail with the focus on how to select suitable fluorophores, labeling sites, experimental setup, and analysis methods. In the last part, the remaining challenges to be addressed and further development in this field are also briefly discussed.

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Sengupta, Bhaswati, and Mai Huynh. "Contribution of smFRET to Chromatin Research." Biophysica 3, no. 1 (February 8, 2023): 93–108. http://dx.doi.org/10.3390/biophysica3010007.

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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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LeBlanc, Sharonda, Prakash Kulkarni, and Keith Weninger. "Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins." Biomolecules 8, no. 4 (November 8, 2018): 140. http://dx.doi.org/10.3390/biom8040140.

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Intrinsically disordered proteins (IDPs) are often modeled using ideas from polymer physics that suggest they smoothly explore all corners of configuration space. Experimental verification of this random, dynamic behavior is difficult as random fluctuations of IDPs cannot be synchronized across an ensemble. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) is one of the few approaches that are sensitive to transient populations of sub-states within molecular ensembles. In some implementations, smFRET has sufficient time resolution to resolve transitions in IDP behaviors. Here we present experimental issues to consider when applying smFRET to study IDP configuration. We illustrate the power of applying smFRET to IDPs by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. The examples we discuss, PAGE4 and a disordered segment of the GluN2B subunit of the NMDA receptor, illustrate the great potential of smFRET to inform how IDP function can be regulated by controlling the detailed ensemble of disordered states within biological networks.

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Li, Maodong, Tanlin Sun, Fan Jin, Daqi Yu, and Zhirong Liu. "Dimension conversion and scaling of disordered protein chains." Molecular BioSystems 12, no. 9 (2016): 2932–40. http://dx.doi.org/10.1039/c6mb00415f.

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To extract protein dimension and energetics information from single-molecule fluorescence resonance energy transfer spectroscopy (smFRET) data, it is essential to establish the relationship between the distributions of the radius of gyration (R_g) and the end-to-end (donor-to-acceptor) distance (R_ee).

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Yukhnovets, Olessya, Henning Höfig, Nuno Bustorff, Alexandros Katranidis, and Jörg Fitter. "Impact of Molecule Concentration, Diffusion Rates and Surface Passivation on Single-Molecule Fluorescence Studies in Solution." Biomolecules 12, no. 3 (March 18, 2022): 468. http://dx.doi.org/10.3390/biom12030468.

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For single-molecule studies in solution, very small concentrations of dye-labelled molecules are employed in order to achieve single-molecule sensitivity. In typical studies with confocal microscopes, often concentrations in the pico-molar regime are required. For various applications that make use of single-molecule Förster resonance energy transfer (smFRET) or two-color coincidence detection (TCCD), the molecule concentration must be set explicitly to targeted values and furthermore needs to be stable over a period of several hours. As a consequence, specific demands must be imposed on the surface passivation of the cover slides during the measurements. The aim of having only one molecule in the detection volume at the time is not only affected by the absolute molecule concentration, but also by the rate of diffusion. Therefore, we discuss approaches to control and to measure absolute molecule concentrations. Furthermore, we introduce an approach to calculate the probability of chance coincidence events and demonstrate that measurements with challenging smFRET samples require a strict limit of maximal sample concentrations in order to produce meaningful results.

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Hu, Jinyong, Meiyan Wu, Li Jiang, Zhensheng Zhong, Zhangkai Zhou, Thitima Rujiralai, and Jie Ma. "Combining gold nanoparticle antennas with single-molecule fluorescence resonance energy transfer (smFRET) to study DNA hairpin dynamics." Nanoscale 10, no. 14 (2018): 6611–19. http://dx.doi.org/10.1039/c7nr08397a.

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Girodat, Dylan, Avik K. Pati, Daniel S. Terry, Scott C. Blanchard, and Karissa Y. Sanbonmatsu. "Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein." PLOS Computational Biology 16, no. 11 (November 5, 2020): e1008293. http://dx.doi.org/10.1371/journal.pcbi.1008293.

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Molecular Dynamics (MD) simulations seek to provide atomic-level insights into conformationally dynamic biological systems at experimentally relevant time resolutions, such as those afforded by single-molecule fluorescence measurements. However, limitations in the time scales of MD simulations and the time resolution of single-molecule measurements have challenged efforts to obtain overlapping temporal regimes required for close quantitative comparisons. Achieving such overlap has the potential to provide novel theories, hypotheses, and interpretations that can inform idealized experimental designs that maximize the detection of the desired reaction coordinate. Here, we report MD simulations at time scales overlapping with in vitro single-molecule Förster (fluorescence) resonance energy transfer (smFRET) measurements of the amino acid binding protein LIV-BPSS at sub-millisecond resolution. Computationally efficient all-atom structure-based simulations, calibrated against explicit solvent simulations, were employed for sampling multiple cycles of LIV-BPSS clamshell-like conformational changes on the time scale of seconds, examining the relationship between these events and those observed by smFRET. The MD simulations agree with the smFRET measurements and provide valuable information on local dynamics of fluorophores at their sites of attachment on LIV-BPSS and the correlations between fluorophore motions and large-scale conformational changes between LIV-BPSS domains. We further utilize the MD simulations to inform the interpretation of smFRET data, including Förster radius (R0) and fluorophore orientation factor (κ2) determinations. The approach we describe can be readily extended to distinct biochemical systems, allowing for the interpretation of any FRET system conjugated to protein or ribonucleoprotein complexes, including those with more conformational processes, as well as those implementing multi-color smFRET.

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Yang, Jie, Sarah Perrett, and Si Wu. "Single Molecule Characterization of Amyloid Oligomers." Molecules 26, no. 4 (February 11, 2021): 948. http://dx.doi.org/10.3390/molecules26040948.

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The misfolding and aggregation of polypeptide chains into β-sheet-rich amyloid fibrils is associated with a wide range of neurodegenerative diseases. Growing evidence indicates that the oligomeric intermediates populated in the early stages of amyloid formation rather than the mature fibrils are responsible for the cytotoxicity and pathology and are potentially therapeutic targets. However, due to the low-populated, transient, and heterogeneous nature of amyloid oligomers, they are hard to characterize by conventional bulk methods. The development of single molecule approaches provides a powerful toolkit for investigating these oligomeric intermediates as well as the complex process of amyloid aggregation at molecular resolution. In this review, we present an overview of recent progress in characterizing the oligomerization of amyloid proteins by single molecule fluorescence techniques, including single-molecule Förster resonance energy transfer (smFRET), fluorescence correlation spectroscopy (FCS), single-molecule photobleaching and super-resolution optical imaging. We discuss how these techniques have been applied to investigate the different aspects of amyloid oligomers and facilitate understanding of the mechanism of amyloid aggregation.

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Verma, Awadhesh Kumar, Ashab Noumani, Amit K. Yadav, and Pratima R. Solanki. "FRET Based Biosensor: Principle Applications Recent Advances and Challenges." Diagnostics 13, no. 8 (April 8, 2023): 1375. http://dx.doi.org/10.3390/diagnostics13081375.

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Förster resonance energy transfer (FRET)-based biosensors are being fabricated for specific detection of biomolecules or changes in the microenvironment. FRET is a non-radiative transfer of energy from an excited donor fluorophore molecule to a nearby acceptor fluorophore molecule. In a FRET-based biosensor, the donor and acceptor molecules are typically fluorescent proteins or fluorescent nanomaterials such as quantum dots (QDs) or small molecules that are engineered to be in close proximity to each other. When the biomolecule of interest is present, it can cause a change in the distance between the donor and acceptor, leading to a change in the efficiency of FRET and a corresponding change in the fluorescence intensity of the acceptor. This change in fluorescence can be used to detect and quantify the biomolecule of interest. FRET-based biosensors have a wide range of applications, including in the fields of biochemistry, cell biology, and drug discovery. This review article provides a substantial approach on the FRET-based biosensor, principle, applications such as point-of-need diagnosis, wearable, single molecular FRET (smFRET), hard water, ions, pH, tissue-based sensors, immunosensors, and aptasensor. Recent advances such as artificial intelligence (AI) and Internet of Things (IoT) are used for this type of sensor and challenges.

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Durham, Ryan J., Nabina Paudyal, Elisa Carrillo, Nidhi Kaur Bhatia, David M. Maclean, Vladimir Berka, Drew M. Dolino, Alemayehu A. Gorfe, and Vasanthi Jayaraman. "Conformational spread and dynamics in allostery of NMDA receptors." Proceedings of the National Academy of Sciences 117, no. 7 (February 3, 2020): 3839–47. http://dx.doi.org/10.1073/pnas.1910950117.

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Allostery can be manifested as a combination of repression and activation in multidomain proteins allowing for fine tuning of regulatory mechanisms. Here we have used single molecule fluorescence resonance energy transfer (smFRET) and molecular dynamics simulations to study the mechanism of allostery underlying negative cooperativity between the two agonists glutamate and glycine in the NMDA receptor. These data show that binding of one agonist leads to conformational flexibility and an increase in conformational spread at the second agonist site. Mutational and cross-linking studies show that the dimer–dimer interface at the agonist-binding domain mediates the allostery underlying the negative cooperativity. smFRET on the transmembrane segments shows that they are tightly coupled in the unliganded and single agonist-bound form and only upon binding both agonists the transmembrane domain explores looser packing which would facilitate activation.

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Dissertations / Theses on the topic "Single Molecule Fluorescence Resonance Energy Transfer (smFRET)"

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Wallace, Mark Ian. "A study of DNA conformational dynamics using single-molecule fluorescence resonance energy transfer." Thesis, University of Cambridge, 2001. https://www.repository.cam.ac.uk/handle/1810/251799.

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Schuler, Benjamin, Everett A. Lipman, Peter J. Steinbach, Michael Kumke, and William A. Eaton. "Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence." Universität Potsdam, 2005. http://opus.kobv.de/ubp/volltexte/2007/1222/.

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To determine whether Förster resonance energy transfer (FRET) measurements can provide quantitative distance information in single-molecule fluorescence experiments on polypeptides, we measured FRET efficiency distributions for donor and acceptor dyes attached to the ends of freely diffusing polyproline molecules of various lengths. The observed mean FRET efficiencies agree with those determined from ensemble lifetime measurements but differ considerably from the values expected from Förster theory, with polyproline treated as a rigid rod. At donor–acceptor distances much less than the Förster radius R0, the observed efficiencies are lower than predicted, whereas at distances comparable to and greater than R0, they are much higher. Two possible contributions to the former are incomplete orientational averaging during the donor lifetime and, because of the large size of the dyes, breakdown of the point-dipole approximation assumed in Förster theory. End-to-end distance distributions and correlation times obtained from Langevin molecular dynamics simulations suggest that the differences for the longer polyproline peptides can be explained by chain bending, which considerably shortens the donor–acceptor distances.

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Uphoff, Stephan. "Studying protein-DNA interactions in vitro and in vivo using single-molecule photoswitching." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:d0a52864-6d26-44a4-8fb7-5d12624a04ba.

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Protein-DNA interactions govern the fundamental cellular processes of DNA replication, transcription, repair, and chromosome organisation. Despite their importance, the detailed molecular mechanisms of protein-DNA interactions and their organisation in the cell remain elusive. The complexity of molecular biology demands new experimental concepts that resolve the structural and functional diversity of biomolecules. In this thesis, I describe fluorescence methods that give a direct view on protein-DNA interactions at the single-molecule level. These methods employ photoswitching to control the number of active fluorophores in the sample. Forster Resonance Energy Transfer (FRET) measures the distance between a donor and an acceptor fluorophore to report on biomolecular structure and dynamics in vitro. Because a single distance gives only limited structural information, I developed "switchable FRET" that employs photoswitching to sequentially probe multiple FRET pairs per molecule. Switchable FRET resolved two distances within static and dynamic DNA constructs and protein-DNA complexes. Towards application of switchable FRET, I investigated aspects of the nucleotide selection mechanism of DNA polymerase. I further explored application of single-molecule imaging in the complex environment of the living cell. Photoswitching was used to resolve the precise localisations of individual fluorophores. I constructed a super-resolution fluorescence microscope to image fixed cellular structures and track the movement of individual fluorescent fusion proteins in live bacteria. I applied the method to directly visualise DNA repair processes by DNA polymerase I and ligase, generating a quantitative account of their repair rates, search times, copy numbers, and spatial distribution in the cell. I validated the approach by tracking diffusion of replisome components and their association with the replication fork. Finally, super-resolution microscopy showed dense clusters of SMC (Structural Maintenance of Chromosomes) protein complexes in vivo that have previously been hidden by the limited resolution of conventional microscopy.

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Brehove, Matthew Steven. "Access to the Genome: A Study of Transcription Factor Binding Within Nucleosomes." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1480603783786784.

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Pérez, González Daniel Cibrán. "Single-molecule studies of nucleic acid folding and nucleic acid-protein interactions." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/12039.

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Nucleic acids and proteins, some of the building blocks of life, are not static structures but highly dynamic entities that need to interact with one another to meet cellular demands. The work presented in this thesis focuses on the application of highly sensitive fluorescence methods, both at ensemble and single-molecule level, to determine the dynamics and structure of specific biomolecular interactions with nanometer resolution and in temporal scales from nanoseconds to minutes, which includes most biologically relevant processes. The main aims of my PhD can be classified in three areas: i) exploring new fluorescent sensors with increased specificity for certain nucleic acid structures; ii) understanding how some of these nucleic acids sense the presence of small molecules in the cellular environment and trigger gene regulation by altering their structure; and iii) understanding how certain molecular machines, such as helicase proteins, are able to unwind the DNA double helix by using chemical energy in the form of ATP hydrolysis.

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Qureshi, Mohammad Haroon. "Replication Protein A Mediated G-Quadruplex Unfolding - A Single Molecule FRET Study." Kent State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=kent1385984615.

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Hwang, William Liang. "The Mechanism and Regulation of Chromatin Remodeling by ISWI Family Enzymes." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10947.

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Eukaryotic genomes are packaged as chromatin, which restricts access to the DNA by critical processes such as DNA replication, repair, and transcription. As a result, eukaryotic cells rely on ATP-dependent chromatin remodeling enzymes (remodelers) to alter the position, structure, and composition of nucleosomes. Understanding the mechanism and regulation of remodeling requires detailed information about transient intermediates of the remodeling process--a challenge ideally suited for single-molecule approaches. In particular, we use single-molecule fluorescence resonance energy transfer (smFRET) to measure nanometer-scale distance changes between strategically placed donor and acceptor dyes to monitor nucleosome translocation in real-time. The mechanism(s) by which remodelers use the free energy of ATP hydrolysis to disrupt histone-DNA contacts and reposition nucleosomes are not well understood. Using smFRET, we show that remodeling by ISWI enzymes begins with a 7 base-pair (bp) step followed by subsequent 3 bp steps toward the exit-side of the nucleosome. These multi-bp steps are actually compound steps composed of 1 bp elementary steps. We discover that DNA movement on the entry side lags behind exit side translocation, which is contrary to previously proposed models. Based on our results, we propose a new integrated mechanism for nucleosome translocation by ISWI enzymes. In the physiological context, remodelers are highly regulated. We study the regulation of human ACF, a prototypical ISWI complex, by critical features of the nucleosomal substrate. First, we dissect how the nucleosome translocation cycle is affected by the linker DNA length and histone H4 tail. Next, we introduce mutations/deletions into conserved enzyme domains to determine the mechanism by which linker length information sensed by the Acfl accessory subunit is allosterically transmitted to the Snf2h catalytic subunit. Interestingly, we find that Acfl modulates the activity of Snf2h indirectly by interacting with the H4 tail in a linker-length dependent fashion. While the majority of our experiments focus on observing changes in nucleosome position, we also develop strategies for site-specific labeling of ISWI enzymes and demonstrate their use in the study of dynamic enzyme-substrate interactions and enzyme conformational changes.

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Piguet, Joachim. "Advanced Fluorescence Microscopy to Study Plasma Membrane Protein Dynamics." Doctoral thesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-178147.

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Membrane protein dynamics is of great importance for living organisms. The precise localization of proteins composing a synapse on the membrane facing a nerve terminus is essential for proper functioning of the nervous system. In muscle fibers, the nicotinic acetylcholine is densely packed under the motor nerve termini. A receptor associated protein, rapsyn, acts as a linker between the receptor and the other components of the synaptic suramolecular assembly. Advances in fluorescence microscopy have allowed to measure the behavior of a single receptor in the cell membrane. In this work single-molecule microscopy was used to track the motion of ionotropic acetylcholine (nAChR) and serotonin (5HT3R) receptors in the plasma membrane of cells. We present methods for measuring single-molecule diffusion and their analysis. Single molecule tracking has shown a high dependence of acetylcholine receptors diffusion on its associated protein rapsyn. Comparing muscle cells that either express rapsyn or are devoid of it, we found that rapsyn plays an important role on receptor immobilization. A three-fold increase of receptor mobility was observed in muscle cells devoid of rapsyn. However, in these cells, a certain fraction of immobilized receptors was also found immobile. Furthermore, nAChR were strongly confined in membrane domains of few tens of nanometers. This showed that membrane composition and membrane associated proteins influence on receptor localization. During muscle cell differentiation, the fraction of immobile nAChR diminished along with the decreasing nAChR and stable rapsyn expression levels. The importance of rapsyn in nAChR immobilization has been further confirmed by measurements in HEK 293 cells, where co-expression of rapsyn increased immobilization of the receptor. nAChR is a ligand-gated ion-channel of the Cys-loop family. In mammals, members of this receptor family share general structural and functional features. They are homo- or hetero-pentamers and form a membrane-spanning ion channel. Subunits have three major regions, an extracellular ligand binding domain, a transmembrane channel and a large intracellular loop. 5HT3R was used as a model to study the effect of this loop on receptor mobility. Single-molecule tracking experiments on receptors with progressively larger deletions in the intracellular loop did not show a dependence of the size of the loop on the diffusion coefficient of mobile receptors. However, two regions were identified to play a role in receptor mobility by changing the fractions of immobile and directed receptors. Interestingly, a prokaryotic homologue of cys-loop receptors, ELIC, devoid of a large cytoplasmic loop was found to be immobile or to show directed diffusion similar as the wild-type 5HT3R. The scaffolding protein rapsyn stabilizes nAChR clusters in a concentration dependent manner. We have measured the density and self-interactions of rapsyn using FRET microscopy. Point-mutations of rapsyn, known to provoke myopathies, destabilized rapsyn self-interactions. Rapsyn-N88K, and R91L were found at high concentration in the cytoplasm suggesting that this modification disturbs membrane association of rapsyn. A25V was found to accumulate in the endoplasmic reticulum. Fluorescent tools to measure intracellular concentration of calcium ions are of great value to study the function of neurons. Rapsyn is highly abundant at the neuromuscular junction and thus is a genuine synaptic marker. A fusion protein of rapsyn with a genetically encoded ratiometric calcium sensor has been made to probe synapse activity. This thesis has shown that the combined use of biologically relevant system and modern fluorescence microscopy techniques deliver important information on pLGIC behaviour in the cell membrane.

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Valeri, Alessandro [Verfasser]. "Fluorescence resonance energy transfer between multiple chromophores studied by single-molecule spectroscopy / Alessandro Valeri." 2010. http://d-nb.info/1000132781/34.

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Huang, Yun-Tzu, and 黃蘊慈. "Distance Variations between Active Sites of H+-pyrophosphatase Determined by Single Molecule Fluorescence Resonance Energy Transfer." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/86183766690838245647.

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博士
國立清華大學
生物資訊與結構生物研究所
98
Homodimeric H+-pyrophosphatase (H+-PPase; EC 3.6.1.1) is a unique enzyme playing a pivotal physiological role in pH homeostasis of organisms. This novel enzyme supplies energy at expense of hydrolyzing metabolic byproduct, pyrophosphate (PPi), for H+ translocation across membrane. The functional unit of a monomer suffices for enzymatic reaction of H+-PPase, while that for the translocation is homodimer. Its active site on each subunit consists of PPi binding motif, Acidic I and II motifs, and several essential residues. In this investigation, structural mapping of these vital regions was primarily determined utilizing single molecule fluorescence resonance energy transfer. Distances between two C termini and also two N termini on homodimeric subunits of H+-PPase are 49.3 ± 4.0 Å and 67.2 ± 5.7 Å, respectively. Furthermore, putative PPi binding motifs on individual subunits are found to be relatively far away from each other (70.8 ± 4.8 Å), while binding of potassium and substrate analogue led them to closer proximity (56.6 ± 4.1 Å). Moreover, substrate analogue but not potassium elicits significantly distance variations between two Acidic I motifs and two H622 residues on homodimeric subunits. Taken together, this study provides the first quantitative measurements of distances between various essential motifs, residues and putative active sites on homodimeric subunits of H+-PPase. A working model is accordingly proposed elucidating the distance variations of dimeric H+-PPase upon substrate binding.

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Books on the topic "Single Molecule Fluorescence Resonance Energy Transfer (smFRET)"

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service), ScienceDirect (Online, ed. Single molecule tools: Super-resolution, particle tracking, multiparameter and force based methods. San Diego, CA: Academic Press/Elsevier, 2010.

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Book chapters on the topic "Single Molecule Fluorescence Resonance Energy Transfer (smFRET)"

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Johnson-Buck, Alexander E., Mario R. Blanco, and Nils G. Walter. "Single-Molecule Fluorescence Resonance Energy Transfer." In Encyclopedia of Biophysics, 1–9. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-642-35943-9_492-1.

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Johnson-Buck, Alexander E., Mario R. Blanco, and Nils G. Walter. "Single-Molecule Fluorescence Resonance Energy Transfer." In Encyclopedia of Biophysics, 2329–35. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_492.

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Lu, Ying, Jianbing Ma, and Ming Li. "Single-Molecule Biosensing by Fluorescence Resonance Energy Transfer." In Single-Molecule Tools for Bioanalysis, 79–120. Boca Raton: Jenny Stanford Publishing, 2022. http://dx.doi.org/10.1201/9781003189138-3.

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Spenkuch, Felix, Olwen Domingo, Gerald Hinze, Thomas Basché, and Mark Helm. "Studying RNA Using Single Molecule Fluorescence Resonance Energy Transfer." In Handbook of RNA Biochemistry, 499–526. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2014. http://dx.doi.org/10.1002/9783527647064.ch24.

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Fagerburg, Matt V., and Sanford H. Leuba. "Optimal Practices for Surface-Tethered Single Molecule Total Internal Reflection Fluorescence Resonance Energy Transfer Analysis." In DNA Nanotechnology, 273–89. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-142-0_19.

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MacDougall, Daniel D., and Ruben L. Gonzalez. "Exploring the structural dynamics of the translational machinery using single-molecule fluorescence resonance energy transfer." In Ribosomes, 273–93. Vienna: Springer Vienna, 2011. http://dx.doi.org/10.1007/978-3-7091-0215-2_22.

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Choi, Ucheor B., Keith R. Weninger, and Mark E. Bowen. "Immobilization of Proteins for Single-Molecule Fluorescence Resonance Energy Transfer Measurements of Conformation and Dynamics." In Intrinsically Disordered Protein Analysis, 3–20. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-3704-8_1.

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Andreou, Alexandra Z., and Dagmar Klostermeier. "Conformational Changes of DEAD-Box Helicases Monitored by Single Molecule Fluorescence Resonance Energy Transfer." In Methods in Enzymology, 75–109. Elsevier, 2012. http://dx.doi.org/10.1016/b978-0-12-396546-2.00004-8.

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Han, Jun, Erwen Mei, Mei-Ping Kung, Hank F. Kung, Jian-Min Yuan, and Hai-Lung Dai. "Single-Molecule Fluorescence Resonance Energy Transfer Studies of β-Amyloid Clusters in Physiological Solutions." In Biophysics and Biochemistry of Protein Aggregation, 297–311. World Scientific, 2017. http://dx.doi.org/10.1142/9789813202382_0008.

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Greenfeld, Max, and Daniel Herschlag. "Measuring the Energetic Coupling of Tertiary Contacts in RNA Folding using Single Molecule Fluorescence Resonance Energy Transfer." In Methods in Enzymology, 205–20. Elsevier, 2010. http://dx.doi.org/10.1016/s0076-6879(10)72009-7.

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Conference papers on the topic "Single Molecule Fluorescence Resonance Energy Transfer (smFRET)"

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Ernst, S., B. Verhalen, N. Zarrabi, S. Wilkens, and M. Börsch. "Drug transport mechanism of P-glycoprotein monitored by single molecule fluorescence resonance energy transfer." In SPIE BiOS, edited by Ammasi Periasamy, Karsten König, and Peter T. C. So. SPIE, 2011. http://dx.doi.org/10.1117/12.872989.

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Cotlet, Mircea, Tom Vosch, Sadahiro Masuo, Marcus Sauer, Klaus Muellen, Johan Hofkens, and Frans De Schryver. "Single-molecule spectroscopy to probe competitive fluorescence resonance energy transfer pathways in bichromophoric synthetic systems." In Biomedical Optics 2004, edited by Dan V. Nicolau, Joerg Enderlein, Robert C. Leif, and Daniel L. Farkas. SPIE, 2004. http://dx.doi.org/10.1117/12.531322.

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Fore, Samantha, Thomas Huser, Yin Yuen, and Lambertus Hesselink. "Single Molecule Pulsed Interleaved Excitation Fluorescence Resonance Energy Transfer (PIE-FRET) inside Nanometer-scale Apertures at Biologically Relevant Concentration." In CLEO 2007. IEEE, 2007. http://dx.doi.org/10.1109/cleo.2007.4453191.

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Yeh, Hsin-Chih, Christopher M. Puleo, Yi-Ping Ho, and Tza-Huei Wang. "Towards Single-Molecule Diagnostics Using Microfluidic Manipulation and Quantum Dot Nanosensors." In ASME 2007 5th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2007. http://dx.doi.org/10.1115/icnmm2007-30213.

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Abstract:

In this report, we review several single-molecule detection (SMD) methods and newly developed nanocrystal-mediated single-fluorophore strategies for ultrasensitive and specific analysis of genomic sequences. These include techniques, such as quantum dot (QD)-mediated fluorescence resonance energy transfer (FRET) technology and dual-color fluorescence coincidence and colocalization analysis, which allow separation-free detection of low-abundance DNA sequences and mutational analysis of oncogenes. Microfluidic approaches developed for use with single-molecule detection to achieve rapid, low-volume, and quantitative analysis of nucleic acids, such as electrokinetic manipulation of single molecules and confinement of sub-nanoliter samples using microfluidic networks integrated with valves, are also discussed.

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Tsourkas, Andrew, Jason Xu, and Gang Bao. "Hybridization Dynamics and Kinetics of Fret-Enhanced Molecular Beacons." In ASME 2001 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2001. http://dx.doi.org/10.1115/imece2001/bed-23163.

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Abstract:

Abstract Many human diseases start with a defect in the genome. Cancer, for example, is a genetic disease that arises from a single cell that behaves abnormally, dividing uncontrollably and leading, eventually, to the development of a tumor. A critical step in diagnosing and treating cancer is to detect cancer cells that result from the mutated genes. In spite of the extensive biomedical research efforts during the last few decades, it is still difficult to detect cancer at its early stages — when a cancer is diagnosed it is often too late to cure. A novel way of achieving early detection of cancer is to detect mRNA transcripts that arise from mutated genes in living cells [1]. We have developed a FRET-enhanced molecular beacons methodology which, combined with the state-of-the-art fluorescence imaging techniques, has the potential to detect cancer cells. FRET (Fluorescence resonance energy transfer) refers to the non-radiative transfer of energy from a donor molecule to an acceptor molecule through dipole-dipole coupling. As shown schematically in Figure 1, molecular beacons are dual labeled antisense oligonucleotides (ODNs) with a fluorophore (A or D) at one end and a quencher (Q) at the other; they are designed to form a hairpin structure in the absence of a complimentary target such that fluorescence of the fluorophore is quenched. Upon hybridization with the target mRNA, the molecular beacon opens up, leading to fluorescence [2,3].

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