Mechanical stability and unfolding pathways of parallel tetrameric G-quadruplexes probed by pulling simulations

Z Zhang, V Mlynsky, M Krepl, J Sponer… - Journal of Chemical …, 2024 - ACS Publications
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich
DNA and RNA sequences. Folding of GQs is a complex process, where several aspects …

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations

P Stadlbauer, V Mlýnský, M Krepl… - Journal of Chemical …, 2023 - ACS Publications
Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many
biological processes. GQs formed in single-stranded regions often need to be unwound by …

[HTML][HTML] Molecular dynamics simulations reveal the parallel stranded d (GGGA) 3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble

P Pokorná, V Mlýnský, G Bussi, J Šponer… - International Journal of …, 2024 - Elsevier
Abstract G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through
complex processes. Characterization of the G4 folding landscape may help to elucidate …

Parallel G-quadruplex folds via multiple paths involving G-tract stacking and structuring from coil ensemble

P Pokorna, V Mlynsky, G Bussi, J Sponer, P Stadlbauer - bioRxiv, 2023 - biorxiv.org
G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex
processes. Characterization of G4 folding landscape contributes to comprehending G4 roles …

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 …

Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

JA Lemkul - Nucleic Acids Research, 2020 - academic.oup.com
DNA and RNA sequences rich in guanine can fold into noncanonical structures called G-
quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen …

Folding kinetics of G-quadruplexes: Duplex stem loops drive and accelerate G-quadruplex folding

TQN Nguyen, KW Lim, AT Phan - The Journal of Physical …, 2020 - ACS Publications
The folding kinetics is an important parameter affecting the relevance of DNA and RNA G-
quadruplex (G4) structures in biological processes. Previous studies of the G4 folding …

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 …

High mechanical stability and slow unfolding rates are prevalent in parallel-stranded DNA G-quadruplexes

Y Cheng, Y Zhang, Z Gong, X Zhang, Y Li… - The Journal of …, 2020 - ACS Publications
Guanine-rich repeat sequences are known to adopt diverse G-quadruplex (G4) topologies.
Determining the unfolding rates of individual G4 species is challenging due to the …

Improving all-atom force field to accurately describe DNA G-quadruplex loops

H Kim, Y Pak - The Journal of Physical Chemistry B, 2022 - ACS Publications
The DNA G-quadruplex (GQ) displays structural polymorphisms, and interactions between
its loops and flanking sequences critically determine which of the diverse GQ conformers is …