Where Quantum Biochemistry Meets Structural Bioinformatics: Excited Conformationally-Tautomeric States of the Classical A·T DNA Base Pair

Abstract

This Chapter summarizes recent quantum-chemical (QM) investigations of the novel conformational and tautomeric states on the potential energy hypersurface of the classical A·T/A·U nucleobase pairs. For the first time, it was observed 28 local minima for each base pair excluding enantiomers - planar, non-planar base pairs and structures with wobble geometry. Considered excited conformationally-tautomeric states of the classical A·T DNA base pair have been revealed in the Nucleic Acid Database by structural bioinformatics. These data shed light on the biological significance of the unusual A·T/A·U nucleobase pairs for the functioning of the nucleic acids at the quantum level.

Novel mechanisms of the conformational transformations of the biologically important G·C nucleobase pairs in Watson–Crick, Hoogsteen and wobble configurationsviathe mutual rotations of the bases around the intermolecular H-bonds: a QM/QTAIM study

“…In the classical conformational analysis of the nucleic acids, DNA and RNA, rotations of their structural fragments around the ordinary chemical bonds and bending of their rings, especially sugar residues, are considered as the source of their structural variability. 1 However, the pairs of the nucleotide bases, stabilized by the participation of the intermolecular Hbonds, are usually considered as conformationally conservative, despite their so structures. 2,3 Their structural variability is usually associated with their insignicant deviations from planarity, which do not change the conguration of the base pairs.…”

“…2,3 Their structural variability is usually associated with their insignicant deviations from planarity, which do not change the conguration of the base pairs. 1 This structural variability can be induced by different external factorsstacking of neighboring pairs of bases, interaction with proteins, ligands of various nature and structure etc.…”