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A Two-Step Method for smFRET Data Analysis
Journal of Physical Chemistry B, 2016 We demonstrate a two-step data analysis method to increase the accuracy of single-molecule Förster Resonance Energy Transfer (smFRET) experiments. Most current smFRET studies are at a time resolution on the millisecond level. When the system also contains molecular dynamics on the millisecond level, simulations show that large errors are present (e.g.,
Anatoly B Kolomeisky +2 more
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Metal Ion Induced Heterogeneity in RNA Folding Studied by smFRET [PDF]
Coordination Chemistry Reviews, 2016 More than two decades of investigating nucleic acids and ribonucleic acids (RNA) using single molecule Förster resonance energy transfer (smFRET) have passed. It turned out that sample heterogeneity in structure and function of RNA molecules as well as folding intermediates, kinetic subpopulations, and interconversion rates of conformational states of ...
Richard Börner +2 more
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Riboswitch Structure and Dynamics by smFRET Microscopy [PDF]
Methods in Enzymology, 2014 Riboswitches are structured noncoding RNA elements that control the expression of their embedding messenger RNAs by sensing the intracellular concentration of diverse metabolites. As the name suggests, riboswitches are dynamic in nature so that studying their inherent conformational dynamics and ligand-mediated folding is important for understanding ...
Nils G. Walter, Krishna C Suddala
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Learning continuous potentials from smFRET
Biophysical Journal, 2022ABSTRACT Potential energy landscapes are useful models in describing events such as protein folding and binding. While single molecule fluorescence resonance energy transfer (smFRET) experiments encode information on continuous potentials for the system probed, including rarely visited barriers between putative potential minima, this ...
J. Shepard Bryan, Steve Pressé
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Preparation of Ribosomes for smFRET Studies: A Simplified Approach [PDF]
Archives of Biochemistry and Biophysics, 2016 During the past decade, single-molecule studies of the ribosome have significantly advanced our understanding of protein synthesis. The broadest application of these methods has been towards the investigation of ribosome conformational dynamics using single-molecule Förster resonance energy transfer (smFRET).
Donald H Burke +2 more
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Extraction of Rapid Kinetics From smFRET Measurements Using Integrative Detectors
Cell Reports Physical Science, 2021 Hidden Markov models (HMMs) are used to learn single-molecule kinetics across a range of experimental techniques. By their construction, HMMs assume that single-molecule events occur on slower timescales than those of data acquisition. To move beyond that HMM limitation and allow for single-molecule events to occur on any timescale, we must treat ...
Kunihiko Ishii +2 more
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Ribosome Structure and Dynamics by smFRET Microscopy
Methods in Enzymology, 2014Composed of both RNA and protein components, the ribosome is one of the largest macromolecular machines in life responsible for the production of all protein. Interestingly, the major catalytic center of the ribosome (the peptidyl transferase center) and much of the binding regions for both mRNA and tRNA are composed of RNA making the ribosome one of ...
Peter V Cornish, Bassem Shebl
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High-Throughput smFRET Analysis of Freely Diffusing Nucleic Acid Molecules and Associated Proteins [PDF]
Methods, 2019 Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for nanometer-scale studies of single molecules. Solution-based smFRET, in particular, can be used to study equilibrium intra- and intermolecular conformations, binding ...
Xavier Michalet +2 more
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8-Spot smFRET Analysis Using Two 8-Pixel SPAD Arrays
Proceedings of SPIE, 2013 Single-molecule Förster resonance energy transfer (smFRET) techniques are now widely used to address outstanding problems in biology and biophysics. In order to study freely diffusing molecules, current approaches consist in exciting a low concentration
Xavier Michalet +2 more
exaly +2 more sources