Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study.
Base-stacking interactions in canonical and crystal B-DNA and in Z-DNA steps are studied using the ab initio quantum-chemical method with inclusion of electron correlation. The stacking energies in canonical B-DNA base-pair steps vary from -9.5 kcal/mol (GG) to -13.2 kcal/mol (GC). The many-body nonadditivity term, although rather small in absolute value, influences the sequence dependence of stacking energy. The base-stacking energies calculated for CGC and a hypothetical TAT sequence in Z-configuration are similar to those in B-DNA. Comparison with older quantum-chemical studies shows that they do not provide even a qualitatively correct description of base stacking. We also evaluate the base-(deoxy)ribose stacking geometry that occurs in Z-DNA and in nucleotides linked by 2',5'-phosphodiester bonds. Although the molecular orbital analysis does not rule out the charge-transfer n-pi* interaction of the sugar 04' with the aromatic base, the base-sugar contact is stabilized by dispersion energy similar to that of stacked bases. The stabilization amounts to almost 4 kcal/mol and is thus comparable to that afforded by normal base-base stacking. This enhancement of the total stacking interaction could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation.
Sponer
J
J
J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic. sponer@indy.jh-inst.cas.cz
Gabb
H A
HA
Leszczynski
J
J
Hobza
P
P
D001482:Base Composition; D001483:Base Sequence; D002151:Calorimetry; D004247:DNA / Q000737:chemistry*; D003855:Deoxyribose; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011199:Potentiometry; D011789:Quantum Theory; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides; D003855:Deoxyribose; D004247:DNA