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 …

Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for …

YB Göç, J Poziemski, W Smolińska, D Suwała… - International Journal of …, 2022 - mdpi.com
The initial aim of this work was to elucidate the mutual influence of different single-stranded
segments (loops and caps) on the thermodynamic stability of RNA G-quadruplexes. To this …

Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes

AE Bergues-Pupo, JR Arias-Gonzalez… - Nucleic acids …, 2015 - academic.oup.com
Cations are known to mediate diverse interactions in nucleic acids duplexes but they are
critical in the arrangement of four-stranded structures. Here, we use all-atom molecular …

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 …

Kinetic and Thermodynamic Control of G-Quadruplex Polymorphism by Na+ and K+ Cations

DA Nicholson, DJ Nesbitt - The Journal of Physical Chemistry B, 2023 - ACS Publications
G-Quadruplexes (G4s) are ubiquitous nucleic acid folding motifs that exhibit structural
diversity that is dependent on cationic conditions. In this work, we exploit temperature …

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 …

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 …

Modelling the DNA topology: the effect of the loop bending on G-quadruplex stability

AE Bergues-Pupo, F Falo… - Journal of Statistical …, 2019 - iopscience.iop.org
The guanine quadruplexes are DNA/RNA guanine-rich sequences assembled into four-
stranded helical structures having important roles in gene regulation and chromosome …

Computational insights into the stability and folding pathways of human telomeric DNA G-quadruplexes

D Luo, Y Mu - The Journal of Physical Chemistry B, 2016 - ACS Publications
G-quadruplex is a noncanonical yet crucial secondary structure of nucleic acids, which has
proven its importance in cell aging, anticancer therapies, gene expression, and genome …

Direct measurement of sequential folding pathway and energy landscape of human telomeric G-quadruplex structures

W Li, XM Hou, PY Wang, XG Xi, M Li - Journal of the American …, 2013 - ACS Publications
Single-stranded guanine-rich sequences fold into compact G-quadruplexes. Although G-
triplexes have been proposed and demonstrated as intermediates in the folding of G …