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Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis
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Torella, Joseph P., Holden, Séamus, Santoso, Yusdi, Hohlbein, Johannes and Kapanidis, Achillefs N. (2011) Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis. Biophysical Journal, 100 (6). pp. 1568-1577. doi:10.1016/j.bpj.2011.01.066 ISSN 0006-3495.
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Official URL: http://dx.doi.org/10.1016/j.bpj.2011.01.066
Abstract
Histograms of single-molecule Förster resonance energy transfer (FRET) efficiency are often used to study the structures of biomolecules and relate these structures to function. Methods like probability distribution analysis analyze FRET histograms to detect heterogeneities in molecular structure, but they cannot determine whether this heterogeneity arises from dynamic processes or from the coexistence of several static structures. To this end, we introduce burst variance analysis (BVA), a method that detects dynamics by comparing the standard deviation of FRET from individual molecules over time to that expected from theory. Both simulations and experiments on DNA hairpins show that BVA can distinguish between static and dynamic sources of heterogeneity in single-molecule FRET histograms and can test models of dynamics against the observed standard deviation information. Using BVA, we analyzed the fingers-closing transition in the Klenow fragment of Escherichia coli DNA polymerase I and identified substantial dynamics in polymerase complexes formed prior to nucleotide incorporation; these dynamics may be important for the fidelity of DNA synthesis. We expect BVA to be broadly applicable to single-molecule FRET studies of molecular structure and to complement approaches such as probability distribution analysis and fluorescence correlation spectroscopy in studying molecular dynamics.
Item Type: | Journal Article | ||||||
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||
Journal or Publication Title: | Biophysical Journal | ||||||
Publisher: | Biophysical Society | ||||||
ISSN: | 0006-3495 | ||||||
Official Date: | 16 March 2011 | ||||||
Dates: |
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Volume: | 100 | ||||||
Number: | 6 | ||||||
Page Range: | pp. 1568-1577 | ||||||
DOI: | 10.1016/j.bpj.2011.01.066 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Restricted or Subscription Access | ||||||
Copyright Holders: | © 2011 Biophysical Society. Published by Elsevier Inc. |
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