Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes

MD Polêto, JA Lemkul - Journal of Chemical Information and …, 2023 - ACS Publications
The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA,
producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs …

Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

JA Lemkul - Nucleic Acids Research, 2020 - academic.oup.com
DNA and RNA sequences rich in guanine can fold into noncanonical structures called G-
quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen …

Molecular Dynamics Simulations of the c-kit1 Promoter G-Quadruplex: Importance of Electronic Polarization on Stability and Cooperative Ion Binding

AM Salsbury, JA Lemkul - The Journal of Physical Chemistry B, 2018 - ACS Publications
G-quadruplexes (GQs) are guanine-rich, noncanonical nucleic acid structures that play
fundamental roles in genomic stability and the regulation of gene expression. GQs are …

Ion Binding Properties and Dynamics of the bcl-2 G-Quadruplex Using a Polarizable Force Field

BD Ratnasinghe, AM Salsbury… - Journal of chemical …, 2020 - ACS Publications
G-quadruplexes (GQs) are topologically diverse, highly thermostable noncanonical nucleic
acid structures that form in guanine-rich sequences in DNA and RNA. GQs are implicated in …

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 …

Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li+, Na+, K+, and Rb+ Series. Assessment of the Accuracy of the SIBFA …

N Gresh, S Naseem-Khan, L Lagardère… - The Journal of …, 2017 - ACS Publications
Stacking of guanine quartets (GQs) can trigger the formation of DNA or RNA quadruple
helices, which play numerous biochemical roles. The GQs are stabilized by alkali cations …

Computational and experimental characterization of rDNA and rRNA G-quadruplexes

AT Green, AJ Pickard, R Li… - The Journal of …, 2022 - ACS Publications
DNA G-quadruplexes in human telomeres and gene promoters are being extensively
studied for their role in controlling the growth of cancer cells. G-quadruplexes have been …

Electron-hole transfer in G-quadruplexes with different tetrad stacking geometries: a combined QM and MD study

CJ Lech, AT Phan, ME Michel-Beyerle… - The Journal of …, 2013 - ACS Publications
G-quadruplex nucleic acids represent a unique avenue for the building of electrically
conductive wires. These four-stranded structures are formed through the stacking of multiple …

Why Are Left-Handed G-Quadruplexes Scarce?

M Jurkowski, M Kogut, S Sappati… - The Journal of Physical …, 2024 - ACS Publications
G-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene
expression and genome maintenance. While they hold promise as nanodevice components …

Ion-Dependent Conformational Plasticity of Telomeric G-Hairpins and G-Quadruplexes

AM Salsbury, HM Michel, JA Lemkul - ACS omega, 2022 - ACS Publications
Telomeric DNA is guanine-rich and can adopt structures such as G-quadruplexes (GQs) and
G-hairpins. Telomeric GQs influence genome stability and telomerase activity, making …