Modeling and analysis of single-molecule experiments by Witkoskie, James B

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Looking back on 28 years of cryogenic single-molecule experiments by Orrit Michel

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Interconvertible lac repressor-DNA loops revealed by single-molecule experiments. by Oi Kwan Wong, Martin Guthold, Dorothy A Erie, Jeff Gelles

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Polymers through pores: single-molecule experiments with nucleic acids, polypeptides and polysaccharides by Bayley, H

A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments by Miranda Molina, Lindsey E. Way, Zhongqing Ren, Qin Liao, Bianca Guerra, Brandon Shields, Xindan Wang, HyeongJun Kim

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Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning by Yasuhiro Matsunaga, Yuji Sugita

Subjects: “…single-molecule experiment…”
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Slow proton transfer coupled to unfolding explains the puzzling results of single-molecule experiments on BBL, a paradigmatic downhill folding protein. by Michele Cerminara, Luis A Campos, Ravishankar Ramanathan, Victor Muñoz

“…We then show that a simple theoretical model of protein folding coupled to proton transfer explains quantitatively all these results as well as the two sets of single-molecule experiments, including their more puzzling features. …”
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Beta-Barrel Channel Response to High Electric Fields: Functional Gating or Reversible Denaturation? by Ekaterina M. Nestorovich, Sergey M. Bezrukov

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Looping and reconfiguration dynamics of a flexible chain with internal friction by Nairhita Samanta, Jayanta Ghosh, Rajarshi Chakrabarti

“…In a nutshell, bypassing expensive simulations we show how simple models like that of Rouse and Zimm can support the single molecule experiment and computer simulation results on intra-chain diffusion coefficients, looping time and even can predict the effects of tail length on the looping time.…”
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Measurement of hindered diffusion in complex geometries for high-speed studies of single-molecule forces by Tobias F. Bartsch, Camila M. Villasante, Felicitas E. Hengel, Ahmed Touré, Daniel M. Firester, Aaron Oswald, A. J. Hudspeth

“…Abstract In a high-speed single-molecule experiment with a force probe, a protein is tethered between two substrates that are manipulated to exert force on the system. …”
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Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding by Xu, Xinliang, Ge, Hao, Gu, Chan, Gao, Yi Qin, Wang, Siyuan S., Thio, Beng Joo Reginald, Hynes, James T., Xie, X. Sunney, Cao, Jianshu

“…This length scale is in agreement with that reported from the single-molecule experiment. Our model can be reduced to the worm-like chain form at length scales larger than lP but is able to explain DNA’s mechanical properties on shorter length scales, in particular, the DNA allostery of protein–DNA interactions.…”
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Single-molecule chemistry studied using the protein pore -α-hemolysin by Choi, LS

“…However, due to the ‘slow’ reaction rate of the Diels-Alder reaction (rate constant ~10⁻¹ M⁻¹s⁻) relative to the time-scale of the single-molecule experiment, we failed to observed chemical conversion at the single-molecule level. …”

Overcoming chromatin barriers by Babette E de Jong, John van Noort

“…Single-molecule experiments reveal the dynamics of transcription through a nucleosome with single-base-pair accuracy.…”
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On the move by Robert A Forties, Jie Ma, Michelle D Wang

“…Single-molecule experiments have shed new light on the mechanisms responsible for the movement of RNA polymerase along DNA during transcription.…”
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High-throughput single-molecule quantification of individual base stacking energies in nucleic acids by Jibin Abraham Punnoose, Kevin J. Thomas, Arun Richard Chandrasekaran, Javier Vilcapoma, Andrew Hayden, Kacey Kilpatrick, Sweta Vangaveti, Alan Chen, Thomas Banco, Ken Halvorsen

“…In this work, the authors use a centrifuge force microscope for high-throughput single-molecule experiments to elucidate stacking energies between individual bases of DNA.…”
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Temperature-Dependent Activity of Motor Proteins: Energetics and Their Implications for Collective Behavior by Saumya Yadav, Ambarish Kunwar

“…Transport properties of these motors such as processivity, velocity, and their load dependence have been well established through single-molecule experiments. Temperature dependent biophysical properties of molecular motors are now being probed using single-molecule experiments. …”
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Shining the spotlight on functional molecular complexes: The new science of single-molecule cell biology. by Leake, M

“…What has emerged recently is the technical ability to now perform key single-molecule experiments whilst retaining the native biological context-namely to do single-molecule experiments on functional living cells. …”

Single-molecule biophysics experiments in silico: Toward a physical model of a replisome by Christopher Maffeo, Han-Yi Chou, Aleksei Aksimentiev

“…Summary: The interpretation of single-molecule experiments is frequently aided by computational modeling of biomolecular dynamics. …”
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Hyperstretching DNA by Koen Schakenraad, Andreas S. Biebricher, Maarten Sebregts, Brian ten Bensel, Erwin J. G. Peterman, Gijs J. L. Wuite, Iddo Heller, Cornelis Storm, Paul van der Schoot

“…Here the authors combine theory and single-molecule experiments to show that intercalator binding stabilises a new structural state of DNA: hyperstretched DNA.…”
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Resonator nanophotonic standing-wave array trap for single-molecule manipulation and measurement by Fan Ye, James T. Inman, Yifeng Hong, Porter M. Hall, Michelle D. Wang

“…Here, the authors present enhanced force generation in a nanophotonic standing-wave array trap by integrating a critically-coupled resonator design and demonstrate common single-molecule experiments.…”
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