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 …

Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives

M Solayman, T Litfin, J Singh, K Paliwal… - Briefings in …, 2022 - academic.oup.com
Characterizing RNA structures and functions have mostly been focused on 2D, secondary
and 3D, tertiary structures. Recent advances in experimental and computational techniques …

Comparative study of single-stranded oligonucleotides secondary structure prediction tools

T Binet, S Padiolleau-Lefèvre, S Octave, B Avalle… - BMC …, 2023 - Springer
Background Single-stranded nucleic acids (ssNAs) have important biological roles and a
high biotechnological potential linked to their ability to bind to numerous molecular targets …

The role of structure in regulatory RNA elements

JN Tants, A Schlundt - Bioscience reports, 2024 - portlandpress.com
Regulatory RNA elements fulfill functions such as translational regulation, control of
transcript levels, and regulation of viral genome replication. Trans-acting factors (ie, RNA …

Regulation of bacterial gene expression by non-coding RNA: It is all about time!

A Chauvier, NG Walter - Cell Chemical Biology, 2024 - cell.com
Commensal and pathogenic bacteria continuously evolve to survive in diverse ecological
niches by efficiently coordinating gene expression levels in their ever-changing …

The Escherichia coli ribB riboswitch senses flavin mononucleotide within a defined transcriptional window

SH Eschbach, EDM Hien, T Ghosh, AM Lamontagne… - RNA, 2024 - rnajournal.cshlp.org
Riboswitches are metabolite-binding RNA regulators that modulate gene expression at the
levels of transcription and translation. One of the hallmarks of riboswitch regulation is that …

Riboswitch-mediated regulation of riboflavin biosynthesis genes in prokaryotes

Vikram, V Mishra, A Rana, JJ Ahire - 3 Biotech, 2022 - Springer
Prokaryotic organisms frequently use riboswitches to quantify intracellular metabolite
concentration via high-affinity metabolite receptors. Riboswitches possess a metabolite …

Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats

MH D'Souza, T Mrozowich, MD Badmalia… - Nucleic acids …, 2022 - academic.oup.com
Abstract Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory
noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also …

c‐di‐GMP regulates activity of the PlzA RNA chaperone from the Lyme disease spirochete

T Van Gundy, D Patel, BE Bowler… - Molecular …, 2023 - Wiley Online Library
PlzA is ac‐di‐GMP‐binding protein crucial for adaptation of the Lyme disease spirochete
Borrelia (Borreliella) burgdorferi during its enzootic life cycle. Unliganded apo‐PlzA is …

Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes

F Qi, J Chen, Y Chen, J Sun, Y Lin… - Genomics …, 2024 - academic.oup.com
Accurate identification of the correct, biologically relevant RNA structures is critical to
understanding various aspects of RNA biology since proper folding represents the key to …