Intramolecular CH…O Hydrogen Bonds in the AI and BI DNA-like Conformers of Canonical Nucleosides and their Watson-Crick Pairs. Quantum Chemical and AIM Analysis

Abstract

The aim of this work is to cast some light on the H-bonds in double-stranded DNA in its AI and BI forms. For this purpose, we have performed the MP2 and DFT quantum chemical calculations of the canonical nucleoside conformers, relative to the AI and BI DNA forms, and their Watson-crick pairs, which were regarded as the simplest models of the double- stranded DNA. Based on the atoms-in-molecules analysis (AIM), five types of the CH…O hydrogen bonds, involving bases and sugar, were detected numerically from 1 to 3 per a conformer: C2′H…O5′, C1′H…O2, C6H…O5′, C8H…O5′, and C6H…O4′. The energy values of H-bonds occupy the range of 2.3–5.6 kcal/mol, surely exceeding the kT value (0.62 kcal/mol). The nucleoside CH…O hydrogen bonds appeared to “survive” turns of bases against the sugar, sometimes in rather large ranges of the angle χ values, pertinent to certain conformations, which points out to the source of the DNA lability, necessary for the conformational adaptation in processes of its functioning. The calculation of the interactions in the dA·T nucleoside pair gives evidence, that additionally to the N6H…O4 and N1…N3H canonical H-bonds, between the bases adenine and thymine the third one (C2H…O2) is formed, which, though being rather weak (about 1 kcal/mol), satisfies the AIM criteria of H-bonding and may be classified as a true H-bond. The total energy of all the CH…O nontraditional intramolecular H-bonds in DNA nucleoside pairs appeared to be commensurable with the energy of H-bonds between the bases in Watson-Crick pairs, which implies their possible important role in the DNA shaping.

Key words:

• The AI and BI DNA forms
• Watson-Crick 2′-deoxyribonucleosides pairs as the simplest DNA models
• The CH…O hydrogen bond energy
• Quantum chemical
• AIM analysis.