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 …

Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies

J Šponer, G Bussi, P Stadlbauer, P Kührová… - … et Biophysica Acta (BBA …, 2017 - Elsevier
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 …

[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 …

[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 …

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 …

Understanding the role of reline, a natural DES, on Temperature-Induced conformational changes of C-Kit G-Quadruplex DNA: a molecular dynamics study

S Pal, S Paul - The Journal of Physical Chemistry B, 2020 - ACS Publications
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 …

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 …

Studying the dynamics of a complex G-Quadruplex system: Insights into the comparison of MD and NMR data

M Castelli, F Doria, M Freccero… - Journal of Chemical …, 2022 - ACS Publications
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 …

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 …

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 …