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Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins

Sanders, Joshua C.
; 
Holmstrom, Erik D.
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Abstract
The conformations of biological macromolecules are intimately related to their cellular functions. Conveniently, the well-characterized dipole–dipole distance-dependence of Förster resonance energy transfer (FRET) makes it possible to measure and monitor the nanoscale spatial dimensions of these conformations using fluorescence spectroscopy. For this reason, FRET is often used in conjunction with single-molecule detection to study a wide range of conformationally dynamic biochemical processes. Written for those not yet familiar with the subject, this review aims to introduce biochemists to the methodology associated with single-molecule FRET, with a particular emphasis on how it can be combined with biomolecular simulations to study diverse interactions between nucleic acids and proteins. In the first section, we highlight several conceptual and practical considerations related to this integrative approach. In the second section, we review a few recent research efforts wherein various combinations of single-molecule FRET and biomolecular simulations were used to study the structural and dynamic properties of biochemical systems involving different types of nucleic acids (e.g., DNA and RNA) and proteins (e.g., folded and disordered).
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Date
2021-04-16
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Portland Press
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Chemistry Scholarly Works
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Sanders_2021.pdf
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Keywords
Conformational Dynamics, FRET, Nucleic Acids, Proteins, Simulations, Single-Molecule
Citation
Dominika Gruszka, Joshua C. Sanders, Erik D. Holmstrom; Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins. Essays Biochem 16 April 2021; 65 (1): 37–49. doi: https://doi.org/10.1042/EBC20200022
URI
https://hdl.handle.net/1808/32426
DOI
10.1042/EBC20200022
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