Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment
J Šponer, JE Šponer, A Mládek, P Jurečka… - …, 2013 - Wiley Online Library
Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last
decades, base stacking has been extensively studied by experimental and theoretical …
decades, base stacking has been extensively studied by experimental and theoretical …
Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations
J Šponer, I Berger, N Špačková… - Journal of …, 2000 - Taylor & Francis
Aromatic stacking of nucleic acid bases is one of the key players in determining the structure
and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive …
and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive …
Nature and magnitude of aromatic stacking of nucleic acid bases
J Šponer, KE Riley, P Hobza - Physical Chemistry Chemical Physics, 2008 - pubs.rsc.org
This review summarises recent advances in quantum chemical calculations of base-stacking
forces in nucleic acids. We explain in detail the very complex relationship between the gas …
forces in nucleic acids. We explain in detail the very complex relationship between the gas …
On the importance and origin of aromatic interactions in chemistry and biodisciplines
KE Riley, P Hobza - Accounts of chemical research, 2013 - ACS Publications
Aromatic systems contain both σ-and π-electrons, which in turn constitute σ-and π-molecular
orbitals (MOs). In discussing the properties of these systems, researchers typically refer to …
orbitals (MOs). In discussing the properties of these systems, researchers typically refer to …
Extended weak bonding interactions in DNA: π-stacking (base− base), base− backbone, and backbone− backbone interactions
We report on several weak interactions in nucleic acids, which, collectively, can make a
nonnegligible contribution to the structure and stability of these molecules. Fragments of …
nonnegligible contribution to the structure and stability of these molecules. Fragments of …
Nature of nucleic acid− base stacking: nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H …
J Šponer, J Leszczyński, P Hobza - The Journal of Physical …, 1996 - ACS Publications
Ab initio (MP2/6-31G*(0.25)) interaction energies were calculated for almost 240 geometries
of 10 stacked nucleic acid− base pairs: A⊙⊙⊙ A, C⊙⊙⊙ C, G⊙⊙⊙ G, U⊙⊙⊙ U …
of 10 stacked nucleic acid− base pairs: A⊙⊙⊙ A, C⊙⊙⊙ C, G⊙⊙⊙ G, U⊙⊙⊙ U …
Significant structural deformation of nucleic acid bases in stacked base pairs: an ab initio study beyond Hartree–Fock
P Hobza, J Šponer - Chemical physics letters, 1998 - Elsevier
Stacked structures of the uracil, thiouracil and cytosine dimers, adenine–uracil and uracil–
cytosine pairs were investigated by gradient optimization at the ab initio second-order Møller …
cytosine pairs were investigated by gradient optimization at the ab initio second-order Møller …
Effects of the biological backbone on DNA–protein stacking interactions
CDM Churchill, L Navarro-Whyte… - Physical Chemistry …, 2009 - pubs.rsc.org
The π–π stacking (face-to-face) interactions between the five natural DNA or RNA
nucleobases and the four aromatic amino acids were compared using three different types …
nucleobases and the four aromatic amino acids were compared using three different types …
Quantum-mechanical analysis of the energetic contributions to π stacking in nucleic acids versus rise, twist, and slide
TM Parker, EG Hohenstein, RM Parrish… - Journal of the …, 2013 - ACS Publications
Symmetry-adapted perturbation theory (SAPT) is applied to pairs of hydrogen-bonded
nucleobases to obtain the energetic components of base stacking (electrostatic, exchange …
nucleobases to obtain the energetic components of base stacking (electrostatic, exchange …
The physical basis of nucleic acid base stacking in water
It has been argued that the stacking of adenyl groups in water must be driven primarily by
electrostatic interactions, based upon NMR data showing stacking for two adenyl groups …
electrostatic interactions, based upon NMR data showing stacking for two adenyl groups …