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 …
Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis
X Cang, J Sponer, TE Cheatham, III - Journal of the American …, 2011 - ACS Publications
The lengths of G-tracts and their connecting loop sequences determine G-quadruplex
folding and stability. Complete understanding of the sequence–structure relationships …
folding and stability. Complete understanding of the sequence–structure relationships …
[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 …
Toward a full structural characterization of G-quadruplex DNA in aqueous solution: Molecular dynamics simulations of four G-quadruplex molecules
A systematic study on guanine (G) quadruplex DNA flexibility was performed by using
extended explicit molecular dynamics (MD) simulations on four quadruplex molecules …
extended explicit molecular dynamics (MD) simulations on four quadruplex molecules …
Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields
E Fadrná, N Špačková, J Sarzynska… - Journal of chemical …, 2009 - ACS Publications
We have carried out a set of explicit solvent molecular dynamics (MD) simulations on two
DNA quadruplex (G-DNA) molecules, namely the antiparallel d (G4T4G4) 2 dimeric …
DNA quadruplex (G-DNA) molecules, namely the antiparallel d (G4T4G4) 2 dimeric …
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 …
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 …
Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail
M Kogut, C Kleist, J Czub - PLoS computational biology, 2019 - journals.plos.org
G-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid
sequences and shown to exist in living cells where they participate in regulation of gene …
sequences and shown to exist in living cells where they participate in regulation of gene …
G-quadruplex DNA: a longer story
RC Monsen, JO Trent, JB Chaires - Accounts of chemical …, 2022 - ACS Publications
Conspectus G-quadruplexes (G4s) are distinctive four-stranded DNA or RNA structures
found within cells that are thought to play functional roles in gene regulation and …
found within cells that are thought to play functional roles in gene regulation and …
Stability of two-quartet G-quadruplexes and their dimers in atomistic simulations
B Islam, P Stadlbauer, M Vorlickova… - Journal of Chemical …, 2020 - ACS Publications
G-quadruplexes (GQs) are four-stranded noncanonical DNA and RNA architectures that can
be formed by guanine-rich sequences. The stability of GQs increases with the number of G …
be formed by guanine-rich sequences. The stability of GQs increases with the number of G …