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 …

Guiding the folding of G-quadruplexes through loop residue interactions

J Jana, YM Vianney, N Schröder… - Nucleic Acids …, 2022 - academic.oup.com
A G-rich sequence was designed to allow folding into either a stable parallel or hybrid-type
topology. With the parent sequence featuring coexisting species, various related sequences …

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 …

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 …

Conformational dynamics of strand register shifts in DNA G-quadruplexes

JT Grün, C Hennecker, DP Klötzner… - Journal of the …, 2019 - ACS Publications
The complex folding energy landscape of DNA G-quadruplexes leads to numerous
conformations for this functionally important class of noncanonical DNA structures. A new …

Folding dynamics of parallel and antiparallel G-triplexes under the influence of proximal DNA

XM Lu, H Li, J You, W Li, PY Wang, M Li… - The Journal of …, 2018 - ACS Publications
The G-triplex is a kind of DNA structure formed by G-rich sequences. Previous studies have
shown that it is an intermediate for the folding of G-quadruplex and has an antiparallel …

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 …

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 …

High mechanical stability and slow unfolding rates are prevalent in parallel-stranded DNA G-quadruplexes

Y Cheng, Y Zhang, Z Gong, X Zhang, Y Li… - The Journal of …, 2020 - ACS Publications
Guanine-rich repeat sequences are known to adopt diverse G-quadruplex (G4) topologies.
Determining the unfolding rates of individual G4 species is challenging due to the …

Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure

S Takahashi, N Sugimoto - Biophysical Chemistry, 2017 - Elsevier
DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by
guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and …