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 …
Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies
Abstract Background Guanine quadruplexes (GQs) play vital roles in many cellular
processes and are of much interest as drug targets. In contrast to the availability of many …
processes and are of much interest as drug targets. In contrast to the availability of many …
[HTML][HTML] Martini coarse-grained force field: extension to RNA
JJ Uusitalo, HI Ingólfsson, SJ Marrink, I Faustino - Biophysical journal, 2017 - cell.com
RNA has an important role not only as the messenger of genetic information but also as a
regulator of gene expression. Given its central role in cell biology, there is significant interest …
regulator of gene expression. Given its central role in cell biology, there is significant interest …
[HTML][HTML] Learning to model G-quadruplexes: current methods and perspectives
I Ortiz de Luzuriaga, X Lopez… - Annual Review of …, 2021 - annualreviews.org
G-quadruplexes have raised considerable interest during the past years for the development
of therapies against cancer. These noncanonical structures of DNA may be found in …
of therapies against cancer. These noncanonical structures of DNA may be found in …
Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes
P Stadlbauer, P Kührová, L Vicherek… - Nucleic acids …, 2019 - academic.oup.com
Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in
important genomic regions. Parallel-stranded G4 folds are the most abundant, but their …
important genomic regions. Parallel-stranded G4 folds are the most abundant, but their …
Understanding the role of reline, a natural DES, on Temperature-Induced conformational changes of C-Kit G-Quadruplex DNA: a molecular dynamics study
The noncanonical guanine-rich DNAs have drawn particular attention to the scientific world
due to their controllable diverse and polymorphic structures. Apart from biological and …
due to their controllable diverse and polymorphic structures. Apart from biological and …
Effect of monovalent ion parameters on molecular dynamics simulations of G-quadruplexes
M Havrila, P Stadlbauer, B Islam… - Journal of chemical …, 2017 - ACS Publications
G-quadruplexes (GQs) are key noncanonical DNA and RNA architectures stabilized by
desolvated monovalent cations present in their central channels. We analyze extended …
desolvated monovalent cations present in their central channels. We analyze extended …
Studying the dynamics of a complex G-Quadruplex system: Insights into the comparison of MD and NMR data
Molecular dynamics (MD) simulations are coming of age in the study of nucleic acids,
including specific tertiary structures such as G-quadruplexes. While being precious for …
including specific tertiary structures such as G-quadruplexes. While being precious for …
Structural transitions in the RNA 7SK 5′ hairpin and their effect on HEXIM binding
K Röder, G Stirnemann, AC Dock-Bregeon… - Nucleic acids …, 2020 - academic.oup.com
Abstract 7SK RNA, as part of the 7SK ribonucleoprotein complex, is crucial to the regulation
of transcription by RNA-polymerase II, via its interaction with the positive transcription …
of transcription by RNA-polymerase II, via its interaction with the positive transcription …
In silico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level
C Yang, M Kulkarni, M Lim, Y Pak - Nucleic acids research, 2017 - academic.oup.com
The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs)(TBA-15)
starting from fully unfolded states was demonstrated using a prolonged time scale (10–12 …
starting from fully unfolded states was demonstrated using a prolonged time scale (10–12 …