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 …
quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen …
Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes
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 …
producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs …
Mechanical stability and unfolding pathways of parallel tetrameric G-quadruplexes probed by pulling simulations
Z Zhang, V Mlynsky, M Krepl, J Sponer… - Journal of Chemical …, 2024 - ACS Publications
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich
DNA and RNA sequences. Folding of GQs is a complex process, where several aspects …
DNA and RNA sequences. Folding of GQs is a complex process, where several aspects …
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 …
which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 …
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 …
G-hairpins. Telomeric GQs influence genome stability and telomerase activity, making …
Conformations of human telomeric G-quadruplex studied using a nucleotide-independent nitroxide label
X Zhang, CX Xu, R Di Felice, J Sponer, B Islam… - Biochemistry, 2016 - ACS Publications
Guanine-rich oligonucleotides can form a unique G-quadruplex (GQ) structure with stacking
units of four guanine bases organized in a plane through Hoogsteen bonding. GQ structures …
units of four guanine bases organized in a plane through Hoogsteen bonding. GQ structures …
Stability of two-quartet G-quadruplexes and their dimers in atomistic simulations
B Islam, P Stadlbauer, M Vorlickova… - Journal of Chemical …, 2020 - ACS Publications
G-quadruplexes (GQs) are four-stranded noncanonical DNA and RNA architectures that can
be formed by guanine-rich sequences. The stability of GQs increases with the number of G …
be formed by guanine-rich sequences. The stability of GQs increases with the number of G …
Computational and experimental characterization of rDNA and rRNA G-quadruplexes
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 …
studied for their role in controlling the growth of cancer cells. G-quadruplexes have been …
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 …
Origin of ion specificity of telomeric DNA G-quadruplexes investigated by free-energy simulations
T Siebenmorgen, M Zacharias - Biophysical journal, 2017 - cell.com
Telomeric DNA consists of tandem repeats of the sequence d (TTAGGG) that form G-
quadruplex structures made of stacked guanines with monovalent cations bound at a central …
quadruplex structures made of stacked guanines with monovalent cations bound at a central …