Collect. Czech. Chem. Commun. 2003, 68, 2231-2282

Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies

Jiří Šponera,b,* and Pavel Hobzab,*

a Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
b J. Heyrovský Institute of Physical Chemistry and Centre for Complex Molecular Systems and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic


Ab initio quantum-chemical calculations with inclusion of electron correlation significantly contributed to our understanding of molecular interactions of DNA and RNA bases. Some of the most important findings are introduced in the present overview: structures and energies of hydrogen bonded base pairs, nature of base stacking, interactions between metal cations and nucleobases, nonplanarity of isolated nucleobases and other monomer properties, tautomeric equilibria of nucleobases, out-of-plane hydrogen bonds and amino acceptor interactions. The role of selected molecular interactions in nucleic acids is discussed and representative examples where these interactions occur are given. Also, accuracy of density functional theory, semiempirical methods, distributed multipole analysis and empirical potentials is commented on. Special attention is given to our very recent reference calculations on base stacking and H-bonding. Finally, we briefly comment on the relationship between advanced ab initio quantum-chemical methods and large-scale explicit solvent molecular dynamics simulations of nucleic acids.

Keywords: Molecular interactions; Nucleobases; Purines; Pyrimidines; Base pairs; DNA; RNA; Nucleic acids; Ab initio calculations; Quantum chemistry; Electron correlation.

References: 152 live references.