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 …
Mass spectrometry of nucleic acid noncovalent complexes
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the
unveiling of new biological roles in regulation of gene expression, specific DNA and RNA …
unveiling of new biological roles in regulation of gene expression, specific DNA and RNA …
Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers
We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field,
where emphasis has been made on the correct representation of the α/γ concerted rotation …
where emphasis has been made on the correct representation of the α/γ concerted rotation …
Adding a new separation dimension to MS and LC–MS: what is the utility of ion mobility spectrometry?
Ion mobility spectrometry is an analytical technique known for more than 100 years, which
entails separating ions in the gas phase based on their size, shape, and charge. While ion …
entails separating ions in the gas phase based on their size, shape, and charge. While ion …
G-quadruplex DNA assemblies: loop length, cation identity, and multimer formation
G-rich DNA sequences are able to fold into structures called G-quadruplexes. To obtain
general trends in the influence of loop length on the structure and stability of G-quadruplex …
general trends in the influence of loop length on the structure and stability of G-quadruplex …
Infrared multiphoton dissociation spectroscopy with free‐electron lasers: On the road from small molecules to biomolecules
L Jašíková, J Roithová - Chemistry–A European Journal, 2018 - Wiley Online Library
Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the
structure of isolated, mass‐selected ions in the gas phase. This method has been widely …
structure of isolated, mass‐selected ions in the gas phase. This method has been widely …
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 …
Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure
Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's
rotationally averaged collision cross section ΩEXP. Molecular modelling is used to visualize …
rotationally averaged collision cross section ΩEXP. Molecular modelling is used to visualize …
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 …
Stabilization and structure of telomeric and c-myc region intramolecular G-quadruplexes: the role of central cations and small planar ligands
A promising approach for anticancer strategies is the stabilization of telomeric DNA into a G-
quadruplex structure. To explore the intrinsic stabilization of folded G-quadruplexes, we …
quadruplex structure. To explore the intrinsic stabilization of folded G-quadruplexes, we …