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 …
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 …
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 …
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 …
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 …
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?
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 …
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 …
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 …
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
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 …
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
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 …
triplexes have been proposed and demonstrated as intermediates in the folding of G …