RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Chemical nucleases

DS Sigman, A Mazumder, DM Perrin - Chemical Reviews, 1993 - ACS Publications
The first-order rate constants for the hydrolysis of a phosphodiester bond under
physiological conditions have been estimated to be 6 X 10-9 and 6 X 10-10 min-1 for single …

[HTML][HTML] Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

DH Mathews, J Sabina, M Zuker, DH Turner - Journal of molecular biology, 1999 - Elsevier
An improved dynamic programming algorithm is reported for RNA secondary structure
prediction by free energy minimization. Thermodynamic parameters for the stabilities of …

Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage

S Riesenberg, N Helmbrecht, P Kanis, T Maricic… - Nature …, 2022 - nature.com
The first step in CRISPR-Cas9-mediated genome editing is the cleavage of target DNA
sequences that are complementary to so-called spacer sequences in CRISPR guide RNAs …

Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins

TEIII Cheatham, JL Miller, T Fox… - Journal of the …, 1995 - ACS Publications
This communication presents results from molecular dynamics (MD) simulations with
AMBER 4.11 and the Cornell et al? force field of three different, fully solvated, fully charged …

The non‐Watson–Crick base pairs and their associated isostericity matrices

NB Leontis, J Stombaugh, E Westhof - Nucleic acids research, 2002 - academic.oup.com
RNA molecules exhibit complex structures in which a large fraction of the bases engage in
non‐Watson–Crick base pairing, forming motifs that mediate long‐range RNA–RNA …

Targeting RNA with small molecules

JR Thomas, PJ Hergenrother - Chemical reviews, 2008 - ACS Publications
The recently discovered functions of RNA dramatically expand the cellular roles for this
macromolecule. RNA can no longer be viewed as a passive element, working simply as an …

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective

RR Gutell, N Larsen, CR Woese - Microbiological reviews, 1994 - Am Soc Microbiol
The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now
quite refined. The models presented here differ from their immediate predecessors only in …

Relationship between internucleotide linkage geometry and the stability of RNA

GA Soukup, RR Breaker - Rna, 1999 - cambridge.org
The inherent chemical instability of RNA under physiological conditions is primarily due to
the spontaneous cleavage of phosphodiester linkages via intramolecular transesterification …

Ribosomes and translation

R Green, HF Noller - Annual review of biochemistry, 1997 - annualreviews.org
The ribosome is a large multifunctional complex composed of both RNA and proteins.
Biophysical methods are yielding low-resolution structures of the overall architecture of …