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 …
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 …
supercoiling, and how DNA supercoiling, in turn, plays an important role in regulating gene …
Transcription under torsion
J Ma, L Bai, MD Wang - Science, 2013 - science.org
In cells, RNA polymerase (RNAP) must transcribe supercoiled DNA, whose torsional state is
constantly changing, but how RNAP deals with DNA supercoiling remains elusive. We report …
constantly changing, but how RNAP deals with DNA supercoiling remains elusive. We report …
DNA topology regulates PAM-Cas9 interaction and DNA unwinding to enable near-PAMless cleavage by thermophilic Cas9
YJ Shi, M Duan, JM Ding, FQ Wang, LL Bi, CX Zhang… - Molecular Cell, 2022 - cell.com
CRISPR-Cas9-mediated genome editing depends on PAM recognition to initiate DNA
unwinding. PAM mutations can abolish Cas9 binding and prohibit editing. Here, we …
unwinding. PAM mutations can abolish Cas9 binding and prohibit editing. Here, we …
Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA
RNA plays myriad roles in the transmission and regulation of genetic information that are
fundamentally constrained by its mechanical properties, including the elasticity and …
fundamentally constrained by its mechanical properties, including the elasticity and …
Storage of mechanical energy in DNA nanorobotics using molecular torsion springs
M Vogt, M Langecker, M Gouder, E Kopperger… - Nature Physics, 2023 - nature.com
DNA nanostructures are increasingly used for the realization of mechanically active
nanodevices and DNA-based nanorobots. A fundamental challenge in this context is the …
nanodevices and DNA-based nanorobots. A fundamental challenge in this context is the …
Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry
Double-stranded DNA (dsDNA) unconstrained by torsion undergoes an overstretching
transition at about 65 pN, elongating the DNA to about 1.7-fold. Three possible structural …
transition at about 65 pN, elongating the DNA to about 1.7-fold. Three possible structural …
Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss
The nucleosome, the fundamental packing unit of chromatin, has a distinct chirality: 147 bp
of DNA are wrapped around the core histones in a left-handed, negative superhelix. It has …
of DNA are wrapped around the core histones in a left-handed, negative superhelix. It has …
Chromatinization modulates topoisomerase II processivity
Type IIA topoisomerases are essential DNA processing enzymes that must robustly and
reliably relax DNA torsional stress. While cellular processes constantly create varying …
reliably relax DNA torsional stress. While cellular processes constantly create varying …
Torsional stiffness of extended and plectonemic DNA
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 …
regulation of motor protein progression. However, direct measurements of these parameters …