Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study

Biophys J. 1997 Jul;73(1):76-87. doi: 10.1016/S0006-3495(97)78049-4.

Abstract

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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Composition
  • Base Sequence
  • Calorimetry
  • DNA / chemistry*
  • Deoxyribose
  • Models, Chemical
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Oligodeoxyribonucleotides / chemistry*
  • Potentiometry
  • Quantum Theory
  • Thermodynamics

Substances

  • Oligodeoxyribonucleotides
  • Deoxyribose
  • DNA