An ab initio molecular orbital study on the sequence-dependency of DNA conformation: an evaluation of intra-and inter-strand stacking interaction energy

M Aida - Journal of theoretical biology, 1988 - Elsevier
The various nearest neighbor stacking interaction energies of stacked base pairs in the DNA
double helix are calculated for both A-and B-type conformations using an ab initio molecular …

The molecular structure of the left-handed Z-DNA double helix at 1.0-Å atomic resolution: Geometry, conformation, and ionic interactions of d (CGCGCG)

RV Gessner, CA Frederick, GJ Quigley, A Rich… - Journal of Biological …, 1989 - Elsevier
The structure of d (CGCGCG) crystallized in the presence of magnesium and sodium ions
alone is compared to that of the spermine form of the molecule. The very high resolution …

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

J Šponer, J Leszczynski… - … : Original Research on …, 2001 - Wiley Online Library
This review summarizes results concerning molecular interactions of nucleic acid bases as
revealed by advanced ab initio quantum chemical (QM) calculations published in last few …

Z‐DNA crystallography

PS Ho, BHM Mooers - Biopolymers: Original Research on …, 1997 - Wiley Online Library
We review the effect of sequence on the structure of left‐handed Z‐DNA in single crystals.
The various substituent groups that define a nucleotide base as guanine, cytosine, thymine …

GT wobble base‐pairing in Z‐DNA at 1.0 A atomic resolution: the crystal structure of d (CGCGTG).

PS Ho, CA Frederick, GJ Quigley… - The EMBO …, 1985 - embopress.org
The DNA oligomer d (CGCGTG) crystallizes as a Z‐DNA double helix containing two
guanine‐thymine base pair mismatches of the wobble type. The crystal diffracts to 1 A …

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 …

Sequence-dependent DNA condensation and the electrostatic zipper

JC Sitko, EM Mateescu, HG Hansma - Biophysical Journal, 2003 - cell.com
Sequence-dependent configuration changes and condensation of double-stranded poly (dG-
dC)·(dG-dC)(GC-DNA) and ds poly (dA-dT)·(dA-dT)(AT-DNA) were observed by atomic force …

[引用][C] The transition between b-DNA and z-DNA

TM Jovin, DM Soumpasis… - Annual Review of Physical …, 1987 - annualreviews.org
The polymorphic nature of double helical DNA, as expounded by Stanley Bram in the 1970s
(1), is now well established (2-4). The interconversions between alternative conformations …

Systematic study of nuclear Overhauser effects vis-a-vis local helical parameters, sugar puckers, and glycosidic torsions in B DNA; insensitivity of NOE to local …

NB Ul'yanov, AA Gorin, VB Zhurkin, BC Chen… - Biochemistry, 1992 - ACS Publications
Revised Manuscript Received February 20, 1992 abstract: A method has been developedto
solve structures of DNA oligomers in solution from the experimental NOE data. The method …

Hydrogen bonding, stacking and cation binding of DNA bases

J Šponer, J Leszczynski, P Hobza - Journal of Molecular Structure …, 2001 - Elsevier
Ab initio quantum chemical calculations with inclusion of electron correlation effects
significantly contributed to our understanding of molecular interactions of DNA bases. Some …