Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA

M Kogut, C Kleist, J Czub - Nucleic acids research, 2016 - academic.oup.com
Abstract G-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in
which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 …

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 …

[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 …

G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triad·water complex and implication for small-molecule binding

B Heddi, N Martín-Pintado, Z Serimbetov… - Nucleic acids …, 2016 - academic.oup.com
G-quadruplexes are non-canonical structures of nucleic acids, in which guanine bases form
planar G-tetrads (G· G· G· G) that stack on each other in the core of the structure. G …

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 …

Can we execute reliable MM-PBSA free energy computations of relative stabilities of different guanine quadruplex folds?

B Islam, P Stadlbauer, S Neidle, S Haider… - The Journal of …, 2016 - ACS Publications
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 …

G‐Quadruplex Formation by DNA Sequences Deficient in Guanines: Two Tetrad Parallel Quadruplexes Do Not Fold Intramolecularly

I Kejnovská, P Stadlbauer, L Trantírek… - … A European Journal, 2021 - Wiley Online Library
Guanine quadruplexes (G4s) are noncanonical forms of nucleic acids that are frequently
found in genomes. The stability of G4s depends, among other factors, on the number of G …

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 …

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 …

Guanine base stacking in G-quadruplex nucleic acids

CJ Lech, B Heddi, AT Phan - Nucleic acids research, 2013 - academic.oup.com
G-quadruplexes constitute a class of nucleic acid structures defined by stacked guanine
tetrads (or G-tetrads) with guanine bases from neighboring tetrads stacking with one another …