[HTML][HTML] 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 …

On the importance of cotranscriptional RNA structure formation

D Lai, JR Proctor, IM Meyer - Rna, 2013 - rnajournal.cshlp.org
The expression of genes, both coding and noncoding, can be significantly influenced by
RNA structural features of their corresponding transcripts. There is by now mounting …

[HTML][HTML] 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 …

Thermal adaptation of mRNA secondary structure: stability versus lability

M Liao, Y Dong, GN Somero - Proceedings of the National …, 2021 - National Acad Sciences
Macromolecular function commonly involves rapidly reversible alterations in three-
dimensional structure (conformation). To allow these essential conformational changes …

Viroid research and its significance for RNA technology and basic biochemistry

G Steger, D Riesner - Nucleic Acids Research, 2018 - academic.oup.com
Viroids were described 47 years ago as the smallest RNA molecules capable of infecting
plants and autonomously self-replicating without an encoded protein. Work on viroids …

Regulatory effects of cotranscriptional RNA structure formation and transitions

SR Liu, CG Hu, JZ Zhang - Wiley Interdisciplinary Reviews …, 2016 - Wiley Online Library
RNAs, which play significant roles in many fundamental biological processes of life, fold into
sophisticated and precise structures. RNA folding is a dynamic and intricate process, which …

[HTML][HTML] How to find RNA thermometers

F Righetti, F Narberhaus - Frontiers in cellular and infection …, 2014 - frontiersin.org
Temperature is one of the decisive signals that a mammalian pathogen has entered its warm-
blooded host. Among the many ways to register temperature changes, bacteria often use …

[HTML][HTML] Fixed-parameter tractable sampling for RNA design with multiple target structures

S Hammer, W Wang, S Will, Y Ponty - BMC bioinformatics, 2019 - Springer
Background The design of multi-stable RNA molecules has important applications in
biology, medicine, and biotechnology. Synthetic design approaches profit strongly from …

IRIS: A method for predicting in vivo RNA secondary structures using PARIS data

J Zhou, P Li, W Zeng, W Ma, Z Lu, R Jiang… - Quantitative …, 2020 - Wiley Online Library
Background RNA secondary structures play a pivotal role in posttranscriptional regulation
and the functions of non‐coding RNAs, yet in vivo RNA secondary structures remain …

RNA‐mediated signal perception in pathogenic bacteria

D Ignatov, J Johansson - Wiley Interdisciplinary Reviews: RNA, 2017 - Wiley Online Library
Bacterial pathogens encounter several different environments during an infection, many of
them possibly being detrimental. In order to sense its surroundings and adjust the gene …