DNA mechanics and its biological impact

Aakash Basu; Dmitriy G Bobrovnikov; Taekjip Ha

doi:10.1016/j.jmb.2021.166861

DNA mechanics and its biological impact

J Mol Biol. 2021 Mar 19;433(6):166861. doi: 10.1016/j.jmb.2021.166861. Epub 2021 Feb 1.

Authors

Aakash Basu¹, Dmitriy G Bobrovnikov², Taekjip Ha³

Affiliations

¹ Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: abasu10@jhmi.edu.
² Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
³ Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.

PMID: 33539885
DOI: 10.1016/j.jmb.2021.166861

Abstract

Almost all nucleoprotein interactions and DNA manipulation events involve mechanical deformations of DNA. Extraordinary progresses in single-molecule, structural, and computational methods have characterized the average mechanical properties of DNA, such as bendability and torsional rigidity, in high resolution. Further, the advent of sequencing technology has permitted measuring, in high-throughput, how such mechanical properties vary with sequence and epigenetic modifications along genomes. We review these recent technological advancements, and discuss how they have contributed to the emerging idea that variations in the mechanical properties of DNA play a fundamental role in regulating, genome-wide, diverse processes involved in chromatin organization.

Keywords: DNA physics; chromatin biophysics; genomics; mechanobiology of DNA; singlemolecule biophysics.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Base Sequence
Biomechanical Phenomena*
Cryoelectron Microscopy
DNA, Superhelical / chemistry*
DNA, Superhelical / genetics
DNA, Superhelical / metabolism
Epigenesis, Genetic
Escherichia coli / genetics
Escherichia coli / metabolism
Genome*
High-Throughput Nucleotide Sequencing
Histones / chemistry*
Histones / genetics
Histones / metabolism
Humans
Nucleic Acid Conformation
Nucleosomes / chemistry
Nucleosomes / metabolism
Nucleosomes / ultrastructure*
Pliability
Protein Multimerization
Single Molecule Imaging
Torsion, Mechanical

Substances

DNA, Superhelical
Histones
Nucleosomes

Grants and funding

HHMI/Howard Hughes Medical Institute/United States