How does RNA fold dynamically?

DZ Bushhouse, EK Choi, LM Hertz, JB Lucks - Journal of molecular biology, 2022 - Elsevier
Recent advances in interrogating RNA folding dynamics have shown the classical model of
RNA folding to be incomplete. Here, we pose three prominent questions for the field that are …

A roadmap for rRNA folding and assembly during transcription

ML Rodgers, SA Woodson - Trends in biochemical sciences, 2021 - cell.com
Ribonucleoprotein (RNP) assembly typically begins during transcription when folding of the
newly synthesized RNA is coupled with the recruitment of RNA-binding proteins (RBPs) …

A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery

LM Wee, AB Tong, AJ Florez Ariza… - Cell, 2023 - cell.com
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called
coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well …

Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates

MY Angela, PM Gasper, L Cheng, LB Lai, S Kaur… - Molecular cell, 2021 - cell.com
The series of RNA folding events that occur during transcription can critically influence
cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a …

Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing

CE Szyjka, EJ Strobel - Nature Communications, 2023 - nature.com
RNA begins to fold as it is transcribed by an RNA polymerase. Consequently, RNA folding is
constrained by the direction and rate of transcription. Understanding how RNA folds into …

Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo

T Ha, C Kaiser, S Myong, B Wu, J Xiao - Molecular cell, 2022 - cell.com
Owing to their unique abilities to manipulate, label, and image individual molecules in vitro
and in cellulo, single-molecule techniques provide previously unattainable access to …

The development of single molecule force spectroscopy: from polymer biophysics to molecular machines

C Bustamante, S Yan - Quarterly Reviews of Biophysics, 2022 - cambridge.org
The advent of single-molecule force spectroscopy represents the introduction of forces,
torques, and displacements as controlled variables in biochemistry. These methods afford …

Determination of protein–protein interactions at the single-molecule level using optical tweezers

WN Sánchez, L Robeson, V Carrasco… - Quarterly Reviews of …, 2022 - cambridge.org
Biomolecular interactions are at the base of all physical processes within living organisms;
the study of these interactions has led to the development of a plethora of different methods …

Upstream flanking sequence assists folding of an RNA thermometer

EA Jolley, KM Bormes, PC Bevilacqua - Journal of molecular biology, 2022 - Elsevier
Many heat shock genes in bacteria are regulated through a class of temperature-sensitive
stem-loop (SL) RNAs called RNA thermometers (RNATs). One of the most widely studied …

Spatiotemporal kinetics of the SRP pathway in live E. coli cells

IL Volkov, E Lundin, K Kipper… - Proceedings of the …, 2022 - National Acad Sciences
Mechanistic details of the signal recognition particle (SRP)-mediated insertion of membrane
proteins have been described from decades of in vitro biochemical studies. However, the …