Energetics of Twisted DNA Topologies

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2021 May 11

PMID 33974883

Citations 1

Authors

Wenxuan Xu

David Dunlap

Laura Finzi

Affiliations

Soon will be listed here.

Abstract

Our goal is to review the main theoretical models used to calculate free energy changes associated with common, torsion-induced conformational changes in DNA and provide the resulting equations hoping to facilitate quantitative analysis of both in vitro and in vivo studies. This review begins with a summary of work regarding the energy change of the negative supercoiling-induced B- to L-DNA transition, followed by a discussion of the energetics associated with the transition to Z-form DNA. Finally, it describes the energy changes associated with the formation of DNA curls and plectonemes, which can regulate DNA-protein interactions and promote cross talk between distant DNA elements, respectively. The salient formulas and parameters for each scenario are summarized in table format to facilitate comparison and provide a concise, user-friendly resource.

Citing Articles

Single-molecule visualization of twin-supercoiled domains generated during transcription.

Janissen R, Barth R, Polinder M, van der Torre J, Dekker C Nucleic Acids Res. 2023; 52(4):1677-1687.

PMID: 38084930 PMC: 10899792. DOI: 10.1093/nar/gkad1181.

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