Mechanistic insights into the ligand-induced unfolding of an RNA G-quadruplex

S Haldar, Y Zhang, Y Xia, B Islam, S Liu… - Journal of the …, 2022 - ACS Publications
The cationic porphyrin TMPyP4 is a well-established DNA G-quadruplex (G4) binding ligand
that can stabilize different topologies via multiple binding modes. However, TMPyP4 can …

Manipulating DNA G‐Quadruplex Structures by Using Guanosine Analogues

L Haase, B Karg, K Weisz - ChemBioChem, 2019 - Wiley Online Library
The ability to control the folding topology of DNA G‐quadruplexes allows for rational design
of quadruplex‐based scaffolds for potential use in various therapeutic and technological …

[引用][C] Energetics, kinetics and dynamics of quadruplex folding

JL Mergny, J Gros, A De Cian, A Bourdoncle… - Quadruplex Nucleic …, 2006 - books.rsc.org
The inclination of guanosine monophosphate (GMP) or guanine-rich poly-and
oligonucleotides to self-assemble has been recognized for several decades. 1–4 G …

A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology

AYQ Zhang, A Bugaut, S Balasubramanian - Biochemistry, 2011 - ACS Publications
G-Quadruplexes are noncanonical nucleic acid secondary structures based on guanine
association that are readily adopted by G-rich RNA and DNA sequences. Naturally occurring …

The Transition from Unfolded to Folded G-Quadruplex DNA Analyzed and Interpreted by Two-Dimensional Infrared Spectroscopy

AL Soenarjo, Z Lan, IV Sazanovich… - Journal of the …, 2023 - ACS Publications
A class of DNA folds/structures known collectively as G-quadruplexes (G4) commonly forms
in guanine-rich areas of genomes. G4-DNA is thought to have a functional role in the …

Direct and single‐molecule visualization of the solution‐state structures of G‐hairpin and G‐triplex intermediates

A Rajendran, M Endo, K Hidaka… - Angewandte …, 2014 - Wiley Online Library
We present the direct and single‐molecule visualization of the in‐pathway intermediates of
the G‐quadruplex folding that have been inaccessible by any experimental method …

Isothermal folding of G-quadruplexes

RD Gray, JB Chaires - Methods, 2012 - Elsevier
Thermodynamic studies of G-quadruplex stability are an essential complement to structures
obtained by NMR or X-ray crystallography. An understanding of the energetics of …

Molecular dynamics simulations of G-quadruplexes: the basic principles and their application to folding and ligand binding

J Šponer, B Islam, P Stadlbauer, S Haider - Annual Reports in Medicinal …, 2020 - Elsevier
Current state-of-the art explicit-solvent atomistic molecular dynamics (MD) simulations are
reviewed. We describe the basic principles and limitations of MD methodology. We also …

Monitoring G-quadruplex formation with DNA carriers and solid-state nanopores

F Boskovic, J Zhu, K Chen, UF Keyser - Nano Letters, 2019 - ACS Publications
G-quadruplexes (Gqs) are guanine-rich DNA structures formed by single-stranded DNA.
They are of paramount significance to gene expression regulation, but also drug targets for …

Basket-type G-quadruplex with two tetrads in the presence of TMAO and urea: A molecular dynamics study

EA Oprzeska-Zingrebe, J Smiatek - Journal of Molecular Structure, 2023 - Elsevier
DNA G-quadruplexes are non-canonical DNA structures, which have been proved to play an
important role in key biological processes, such as gene expression, replication, regulation …