RNA structural dynamics as captured by molecular simulations: a comprehensive overview
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 …
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 …
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
An improved dynamic programming algorithm is reported for RNA secondary structure
prediction by free energy minimization. Thermodynamic parameters for the stabilities of …
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 …
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 …
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 …
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 …
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 …
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 …
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 …
Biophysical methods are yielding low-resolution structures of the overall architecture of …