title: Oxygen-aromatic contacts in intra-strand base pairs: analysis of high-resolution DNA crystal structures and quantum chemical calculations.
abstract: 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 (<3.5Ǻ) with the oxygen atom of preceding (Group-I) or succeeding base (Group-II). Examples from Group-I are overwhelmingly observed and cytosine or thymine is the preferred base contributing oxygen atom in Group-I base pairs. A similar analysis of high-resolution RNA structures surprisingly did not yield many examples of oxygen-aromatic contact of similar type between bases. Ab initio quantum chemical calculations on compounds based on DNA crystal structures and model compounds show that interactions between the bases in base pairs with oxygen-aromatic contacts are energetically favorable. Decomposition of interaction energies indicates that dispersion forces are the major cause for energetically stable interaction in these base pairs. We speculate that oxygen-aromatic contacts in intra-strand base pairs in a DNA structure may have biological significance.
authors.affiliation: Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.
authors.forename: Alok
authors.initials: A
authors.lastname: Jain
authors.affiliation: Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.
authors.forename: R N V
authors.initials: RNV
authors.lastname: Krishna Deepak
authors.affiliation: Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India. Electronic address: rsankar@iitk.ac.in.
authors.forename: Ramasubbu
authors.initials: R
authors.lastname: Sankararamakrishnan
mesh_terms: D020029:Base Pairing; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010100:Oxygen / Q000737:chemistry*; D011789:Quantum Theory; D012313:RNA / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry
chemical_list: D012313:RNA; D003596:Cytosine; D004247:DNA; D013941:Thymine; D010100:Oxygen
keywords: Base stacking; Counterintuitive interactions; DNA structure stability; Dispersion forces; Lone pair–π interaction; Sequence-dependent structure