Optical tweezers in single-molecule biophysics

CJ Bustamante, YR Chemla, S Liu… - Nature Reviews Methods …, 2021 - nature.com
Optical tweezers have become the method of choice in single-molecule manipulation
studies. In this Primer, we first review the physical principles of optical tweezers and the …

DNA supercoiling during transcription

J Ma, MD Wang - Biophysical reviews, 2016 - Springer
The twin-supercoiled-domain model describes how transcription can drive DNA
supercoiling, and how DNA supercoiling, in turn, plays an important role in regulating gene …

Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments

J Lipfert, JWJ Kerssemakers, T Jager, NH Dekker - Nature methods, 2010 - nature.com
We introduce magnetic torque tweezers, which enable direct single-molecule
measurements of torque. Our measurements of the effective torsional stiffness C of dsDNA …

Quantifying how DNA stretches, melts and changes twist under tension

P Gross, N Laurens, LB Oddershede, U Bockelmann… - Nature Physics, 2011 - nature.com
In cells, DNA is constantly twisted, bent and stretched by numerous proteins mediating
genome transactions. Understanding these essential biological processes requires in-depth …

Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA

J Lipfert, GM Skinner, JM Keegstra… - Proceedings of the …, 2014 - National Acad Sciences
RNA plays myriad roles in the transmission and regulation of genetic information that are
fundamentally constrained by its mechanical properties, including the elasticity and …

Chromatinization modulates topoisomerase II processivity

J Lee, M Wu, JT Inman, G Singh, SH Park… - Nature …, 2023 - nature.com
Type IIA topoisomerases are essential DNA processing enzymes that must robustly and
reliably relax DNA torsional stress. While cellular processes constantly create varying …

Torsional stiffness of extended and plectonemic DNA

X Gao, Y Hong, F Ye, JT Inman, MD Wang - Physical review letters, 2021 - APS
DNA torsional elastic properties play a crucial role in DNA structure, topology, and the
regulation of motor protein progression. However, direct measurements of these parameters …

Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers

F Kriegel, N Ermann, J Lipfert - Journal of structural biology, 2017 - Elsevier
Nucleic acids are central to the storage and transmission of genetic information. Mechanical
properties, along with their sequence, both enable and fundamentally constrain the …

Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics

A Marin-Gonzalez, JG Vilhena… - Proceedings of the …, 2017 - National Acad Sciences
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces
induce local changes in the molecule structure, inhibiting or promoting the binding of …

Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors

MY Sheinin, S Forth, JF Marko, MD Wang - Physical review letters, 2011 - APS
DNA melting under torsion plays an important role in a wide variety of cellular processes. In
the present Letter, we have investigated DNA melting at the single-molecule level using an …