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 …

Folding and misfolding pathways of G-quadruplex DNA

A Marchand, V Gabelica - Nucleic acids research, 2016 - academic.oup.com
G-quadruplexes adopt various folding topologies, but information on their folding pathways
remains scarce. Here, we used electrospray mass spectrometry to detect and quantify the …

[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 …

Insights into the Competition between K+ and Pb2+ Binding to a G-Quadruplex and Discovery of a Novel K+–Pb2+–Quadruplex Intermediate

Z Yu, W Zhou, G Ma, Y Li, L Fan, X Li… - The Journal of Physical …, 2018 - ACS Publications
Numerous studies have reported cation-dependent stability and topological changes of G-
quadruplexes (G4s), but competitions between cations at different concentrations for binding …

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 …

Conformational plasticity of parallel G-quadruplex─ implications on duplex–Quadruplex motifs

RKR Sannapureddi, MK Mohanty… - Journal of the …, 2023 - ACS Publications
DNA G-quadruplexes are essential motifs in molecular biology performing a wide range of
functions enabled by their unique and diverse structures. In this study, we focus on the …

Sequence and solvent effects on telomeric DNA bimolecular G-quadruplex folding kinetics

A Marchand, R Ferreira… - The Journal of …, 2013 - ACS Publications
Telomeric DNA sequences are particularly polymorphic: the adopted structure is exquisitely
sensitive to the sequence and to the chemical environment, for example, solvation …

Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops

CM Olsen, HT Lee, LA Marky - The Journal of Physical Chemistry …, 2009 - ACS Publications
G-quadruplexes are a highly studied DNA motif with a potential role in a variety of cellular
processes and more recently are considered novel targets for drug therapy in aging and …

A General Framework to Interpret Hydrogen–Deuterium Exchange Native Mass Spectrometry of G-Quadruplex DNA

E Largy, M Ranz, V Gabelica - Journal of the American Chemical …, 2023 - ACS Publications
G-quadruplexes (G4s) are secondary structures formed by guanine-rich oligonucleotides
involved in various biological processes. However, characterizing G4s is challenging …

Tracing effects of fluorine substitutions on G-quadruplex conformational changes

J Dickerhoff, L Haase, W Langel… - ACS Chemical Biology, 2017 - ACS Publications
A human telomere sequence that folds into an intramolecular (3+ 1)-hybrid G-quadruplex
was modified by the incorporation of 2′-fluoro-2′-deoxyriboguanosines (FG) into syn …