How Nanopore Translocation Experiments Can Measure RNA Unfolding.
| Autor: | Bandarkar P; Department of Physics, Northeastern University, Boston, Massachusetts., Yang H; Department of Physics, Northeastern University, Boston, Massachusetts., Henley RY; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California., Wanunu M; Department of Physics, Northeastern University, Boston, Massachusetts. Electronic address: m.wanunu@northeastern.edu., Whitford PC; Department of Physics, Northeastern University, Boston, Massachusetts. Electronic address: p.whitford@neu.edu. |
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| Jazyk: | angličtina |
| Zdroj: | Biophysical journal [Biophys J] 2020 Apr 07; Vol. 118 (7), pp. 1612-1620. Date of Electronic Publication: 2020 Feb 04. |
| DOI: | 10.1016/j.bpj.2020.01.030 |
| Abstrakt: | Electrokinetic translocation of biomolecules through solid-state nanopores represents a label-free single-molecule technique that may be used to measure biomolecular structure and dynamics. Recent investigations have attempted to distinguish individual transfer RNA (tRNA) species based on the associated pore translocation times, ion-current noise, and blockage currents. By manufacturing sufficiently smaller pores, each tRNA is required to undergo a deformation to translocate. Accordingly, differences in nanopore translocation times and distributions may be used to infer the mechanical properties of individual tRNA molecules. To bridge our understanding of tRNA structural dynamics and nanopore measurements, we apply molecular dynamics simulations using a simplified "structure-based" energetic model. Calculating the free-energy landscape for distinct tRNA species implicates transient unfolding of the terminal RNA helix during nanopore translocation. This provides a structural and energetic framework for interpreting current experiments, which can aid the design of methods for identifying macromolecules using nanopores. (Copyright © 2020 Biophysical Society. Published by Elsevier Inc. All rights reserved.) |
| Databáze: | MEDLINE |
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