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 …

An overview of the molecular mechanisms of recombinational DNA repair

SC Kowalczykowski - Cold Spring Harbor Perspectives …, 2015 - cshperspectives.cshlp.org
Recombinational DNA repair is a universal aspect of DNA metabolism and is essential for
genomic integrity. It is a template-directed process that uses a second chromosomal copy …

Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion

Z Zhao, J Fu, S Dhakal, A Johnson-Buck, M Liu… - Nature …, 2016 - nature.com
Cells routinely compartmentalize enzymes for enhanced efficiency of their metabolic
pathways. Here we report a general approach to construct DNA nanocaged enzymes for …

[PDF][PDF] Independent and stochastic action of DNA polymerases in the replisome

JE Graham, KJ Marians, SC Kowalczykowski - Cell, 2017 - cell.com
It has been assumed that DNA synthesis by the leading-and lagging-strand polymerases in
the replisome must be coordinated to avoid the formation of significant gaps in the nascent …

Rotation tracking of genome-processing enzymes using DNA origami rotors

P Kosuri, BD Altheimer, M Dai, P Yin, X Zhuang - Nature, 2019 - nature.com
Many genome-processing reactions, including transcription, replication and repair, generate
DNA rotation. Methods that directly measure DNA rotation, such as rotor bead tracking …

Single-molecule analysis and engineering of DNA motors

S Mohapatra, CT Lin, XA Feng, A Basu, T Ha - Chemical reviews, 2019 - ACS Publications
Molecular motors are diverse enzymes that transduce chemical energy into mechanical
work and, in doing so, perform critical cellular functions such as DNA replication and …

Restart could optimize the probability of success in a Bernoulli trial

S Belan - Physical review letters, 2018 - APS
The recently noticed ability of restart to reduce the expected completion time of first-passage
processes allows appealing opportunities for performance improvement in a variety of …

Theoretical perspectives on biological machines

ML Mugnai, C Hyeon, M Hinczewski… - Reviews of Modern Physics, 2020 - APS
Many biological functions are executed by molecular machines, which like man-made
motors are powered by chemical energy, released by adenosine triphosphate hydrolysis …

Colloquium: Random first order transition theory concepts in biology and physics

TR Kirkpatrick, D Thirumalai - Reviews of Modern Physics, 2015 - APS
The routine transformation of a liquid, as it is rapidly cooled, resulting in glass formation, is
remarkably complex. A theoretical explanation of the dynamics associated with this process …

Activities of gyrase and topoisomerase IV on positively supercoiled DNA

RE Ashley, A Dittmore, SA McPherson… - Nucleic acids …, 2017 - academic.oup.com
Although bacterial gyrase and topoisomerase IV have critical interactions with positively
supercoiled DNA, little is known about the actions of these enzymes on overwound …