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 …
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 …
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
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 …
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
G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex
processes. Characterization of G4 folding landscape contributes to comprehending G4 roles …
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 …
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 …
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 …
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
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 …
High mechanical stability and slow unfolding rates are prevalent in parallel-stranded DNA G-quadruplexes
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 …
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 …
its loops and flanking sequences critically determine which of the diverse GQ conformers is …