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 …
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 …
A direct view of the complex multi-pathway folding of telomeric G-quadruplexes
M Aznauryan, S Søndergaard, SL Noer… - Nucleic Acids …, 2016 - academic.oup.com
Abstract G-quadruplexes (G4s) are DNA secondary structures that are capable of forming
and function in vivo. The propensity of G4s to exhibit extreme polymorphism and complex …
and function in vivo. The propensity of G4s to exhibit extreme polymorphism and complex …
Coarse-grained simulations complemented by atomistic molecular dynamics provide new insights into folding and unfolding of human telomeric G-quadruplexes
P Stadlbauer, L Mazzanti, T Cragnolini… - Journal of Chemical …, 2016 - ACS Publications
G-quadruplexes are the most important noncanonical DNA architectures. Many quadruplex-
forming sequences, including the human telomeric sequence d (GGGTTA) n, have been …
forming sequences, including the human telomeric sequence d (GGGTTA) n, have been …
Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations
DNA G-hairpins are potential key structures participating in folding of human telomeric
guanine quadruplexes (GQ). We examined their properties by standard MD simulations …
guanine quadruplexes (GQ). We examined their properties by standard MD simulations …
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 …
Can we execute reliable MM-PBSA free energy computations of relative stabilities of different guanine quadruplex folds?
The self-assembly and stability of DNA G-quadruplexes (GQs) are affected by the intrinsic
stability of different GpG base steps embedded in their G-quartet stems. We have carried out …
stability of different GpG base steps embedded in their G-quartet stems. We have carried out …
Structural dynamics of propeller loop: towards folding of RNA G-quadruplex
We have carried out an extended set of standard and enhanced-sampling MD simulations
(for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the …
(for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the …
G-register exchange dynamics in guanine quadruplexes
RW Harkness, AK Mittermaier - Nucleic Acids Research, 2016 - academic.oup.com
Abstract G-quadruplexes (GQs) are 4-stranded DNA structures formed by tracts of stacked,
Hoogsteen-hydrogen bonded guanosines. GQs are found in gene promoters and telomeres …
Hoogsteen-hydrogen bonded guanosines. GQs are found in gene promoters and telomeres …
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
P Stadlbauer, M Krepl, TE Cheatham… - Nucleic acids …, 2013 - academic.oup.com
Explicit solvent molecular dynamics simulations have been used to complement preceding
experimental and computational studies of folding of guanine quadruplexes (G-DNA). We …
experimental and computational studies of folding of guanine quadruplexes (G-DNA). We …