Oxygen–aromatic contacts in intra-strand base pairs: Analysis of high-resolution DNA crystal structures and quantum chemical calculations

• Published in: Journal of structural biology 2014-07, Vol.187 (1), p.49-57
• Main Authors: Jain, Alok, Krishna Deepak, R.N.V., Sankararamakrishnan, Ramasubbu
• Format: Article
• Language: English
• Subjects: Base Pairing; Base stacking; Computer Simulation; Counterintuitive interactions; Crystallography, X-Ray; Cytosine - chemistry; Dispersion forces; DNA - chemistry; DNA structure stability; Hydrogen Bonding; Lone pair–π interaction; Models, Molecular; Oxygen - chemistry; Quantum Theory; RNA - chemistry; Sequence-dependent structure; Static Electricity; Thermodynamics; Thymine - chemistry
• ISSN: 1047-8477; 1095-8657
• DOI: 10.1016/j.jsb.2014.04.008

Three-dimensional structures of biomolecules are stabilized by a large number of non-covalent interactions and some of them such as van der Waals, electrostatic and hydrogen bond interactions are well characterized. Delocalized π–electron clouds of aromatic residues are known to be involved in cation–π, CH–π, OH–π and π–π interactions. In proteins, many examples have been found in which the backbone carbonyl oxygen of one residue makes close contact with the aromatic center of aromatic residues. Quantum chemical calculations suggest that such contacts may provide stability to the protein secondary structures. In this study, we have systematically analyzed the experimentally determined high-resolution DNA crystal structures and identified 91 examples in which the aromatic center of one base is in close contact (