Quadruplex DNA: sequence, topology and structure
ABSTRACT G-quadruplexes are higher-order DNA and RNA structures formed from G-rich
sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential …
sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential …
Metal cations in G-quadruplex folding and stability
This review is focused on the structural and physicochemical aspects of metal cation
coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G …
coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G …
Sequence, stability, and structure of G‐quadruplexes and their interactions with drugs
Y Chen, D Yang - Current protocols in nucleic acid chemistry, 2012 - Wiley Online Library
Although DNA is most widely known for its ability to store and pass along genetic
information, the discovery of G‐quadruplex structures has illuminated a new role for DNA in …
information, the discovery of G‐quadruplex structures has illuminated a new role for DNA in …
Telomere structure and stability: covalency in hydrogen bonds, not resonance assistance, causes cooperativity in guanine quartets
We show that the cooperative reinforcement between hydrogen bonds in guanine quartets is
not caused by resonance‐assisted hydrogen bonding (RAHB). This follows from extensive …
not caused by resonance‐assisted hydrogen bonding (RAHB). This follows from extensive …
Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures
J Šponer, X Cang, TE Cheatham III - Methods, 2012 - Elsevier
The article reviews the application of biomolecular simulation methods to understand the
structure, dynamics and interactions of nucleic acids with a focus on explicit solvent …
structure, dynamics and interactions of nucleic acids with a focus on explicit solvent …
Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations
J Sponer, A Mladek, N Spackova, X Cang… - Journal of the …, 2013 - ACS Publications
We provide theoretical predictions of the intrinsic stability of different arrangements of
guanine quadruplex (G-DNA) stems. Most computational studies of nucleic acids have …
guanine quadruplex (G-DNA) stems. Most computational studies of nucleic acids have …
Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in π-stacking and hydrogen-bonding behavior
We have investigated the performance of the dispersion-corrected density functionals (BLYP-
D, BP86-D and PBE-D) and the widely used B3LYP functional for describing the hydrogen …
D, BP86-D and PBE-D) and the widely used B3LYP functional for describing the hydrogen …
15N NMR spectroscopy in structural analysis: an update (2001-2005)
R Marek, A Lycka, E Kolehmainen… - Current Organic …, 2007 - ingentaconnect.com
Since our previous review article (Curr. Org. Chem. 2002, 6, 35), significant improvements
and an array of 15N NMR applications in structural analysis have been published. This …
and an array of 15N NMR applications in structural analysis have been published. This …
Ion binding to quadruplex DNA stems. Comparison of MM and QM descriptions reveals sizable polarization effects not included in contemporary simulations
Molecular mechanical (MM) force fields are commonly employed for biomolecular
simulations. Despite their success, the nonpolarizable nature of contemporary additive force …
simulations. Despite their success, the nonpolarizable nature of contemporary additive force …
NMR spectroscopy: quantum‐chemical calculations
M Bühl, T van Mourik - Wiley Interdisciplinary Reviews …, 2011 - Wiley Online Library
The first‐principles computation of nuclear magnetic resonance parameters, in particular
chemical shift and spin–spin coupling tensors, is reviewed. After a brief nontechnical …
chemical shift and spin–spin coupling tensors, is reviewed. After a brief nontechnical …