Gas-phase DNA oligonucleotide structures. A QM/MM and atoms in molecules study.
QM/MM calculations have been employed to investigate the role of hydrogen bonding and pi-stacking in single- and double-stranded DNA oligonucleotides. DFT calculations and Atoms in Molecules analysis on QM/MM-optimized structures allow characterization and estimation of the energies of pi-stacking and hydrogen-bond interactions. This shows that pi-stacking interactions depend on the number and the nature of the DNA bases for single-stranded nucleotides; for instance, guanines are found to be involved in strong hydrogen bonds, whereas adenines interact mainly via stacking interactions. The role of interbase hydrogen bonding was explored: the -NH2 groups of guanine, adenine, and cytosine participate in N-H...O and N-H...N interactions. These are much stronger in single-strand oligonucleotides, where the -NH2 groups are highly nonplanar. In double-stranded DNA, the strong base-pairing hydrogen bonds of complementary bases lead to more planar -NH2 groups, which tend to be involved in pi-stacking interactions rather than H-bonds. The use of AIM also allows us to evaluate the interplay of pi-stacking and H-bonding, suggesting that cooperativity does occur, but is generally limited to about 1-2 kcal/mol.
Robertazzi
Arturo
A
School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK.
Platts
James A
JA
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D005740:Gases / Q000737:chemistry; D006860:Hydrogen Bonding; D008956:Models, Chemical; D009841:Oligonucleotides / Q000737:chemistry*; D011789:Quantum Theory
D005740:Gases; D009841:Oligonucleotides; D004247:DNA