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 …

Noise in biology

LS Tsimring - Reports on Progress in Physics, 2014 - iopscience.iop.org
Noise permeates biology on all levels, from the most basic molecular, sub-cellular
processes to the dynamics of tissues, organs, organisms and populations. The functional …

[图书][B] Stochastic processes in cell biology

PC Bressloff - 2014 - Springer
One of the major challenges in modern biology is to understand how the molecular
components of a living cell operate in a highly noisy environment. What are the specific …

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

DA Silva, DR Weiss, F Pardo Avila… - Proceedings of the …, 2014 - National Acad Sciences
Transcription is a central step in gene expression, in which the DNA template is processively
read by RNA polymerase II (Pol II), synthesizing a complementary messenger RNA …

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

M Dangkulwanich, T Ishibashi, S Liu, ML Kireeva… - Elife, 2013 - elifesciences.org
During transcription elongation, RNA polymerase has been assumed to attain equilibrium
between pre-and post-translocated states rapidly relative to the subsequent catalysis. Under …

The mechanisms of substrate selection, catalysis, and translocation by the elongating RNA polymerase

GA Belogurov, I Artsimovitch - Journal of molecular biology, 2019 - Elsevier
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs,
ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has …

The elemental mechanism of transcriptional pausing

J Saba, XY Chua, TV Mishanina, D Nayak… - Elife, 2019 - elifesciences.org
Transcriptional pausing underlies regulation of cellular RNA biogenesis. A consensus
pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts …

An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron

C Zhao, F Liu, AM Pyle - Rna, 2018 - rnajournal.cshlp.org
Group II introns and non-LTR retrotransposons encode a phylogenetically related family of
highly processive reverse transcriptases (RTs) that are essential for mobility and persistence …

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

B Zamft, L Bintu, T Ishibashi… - Proceedings of the …, 2012 - National Acad Sciences
RNA polymerase pausing represents an important mechanism of transcriptional regulation.
In this study, we use a single-molecule transcription assay to investigate the effect of …

Studying genomic processes at the single-molecule level: introducing the tools and applications

D Dulin, J Lipfert, MC Moolman, NH Dekker - Nature Reviews Genetics, 2013 - nature.com
To understand genomic processes such as transcription, translation or splicing, we need to
be able to study their spatial and temporal organization at the molecular level. Single …