Journal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Volume 135, Issue 4, Pages 1306-1316Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ja3063309
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Funding
- National Science Foundation [CHE-1011360, 0851780]
- Vasser Woolley Foundation
- DOE Computational Science Graduate Fellowship [DE-FG02-97ER25308]
- Center for Computational Molecular Science and Technology is funded through a National Science Foundation CRIF Award [CHE-0946869]
- Georgia Tech
- Division Of Chemistry
- Direct For Mathematical & Physical Scien [0851780, 1011360] Funding Source: National Science Foundation
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Symmetry-adapted perturbation theory (SAPT) is applied to pairs of hydrogen-bonded nucleobases to obtain the energetic components of base stacking (electrostatic, exchange-repulsion, induction/polarization, and London dispersion interactions) and how they vary as a function of the helical parameters Rise, Twist, and Slide. Computed average values of Rise and Twist agree well with experimental data for B-form DNA from the Nucleic Acids Database, even though the model computations omitted the backbone atoms (suggesting that the backbone in B-form DNA is compatible with having the bases adopt their ideal stacking geometries). London dispersion forces are the most important attractive component in base stacking, followed by electrostatic interactions. At values of Rise typical of those in DNA (3.36 angstrom), the electrostatic contribution is nearly always attractive, providing further evidence for the importance of charge-penetration effects in pi-pi interactions (a term neglected in classical force fields). Comparison of the computed stacking energies with those from model complexes made of the parent nucleobases purine and 2-pyrimidone indicates that chemical substituents in DNA and RNA account for 20-40% of the base-stacking energy. A lack of correspondence between the SAPT results and experiment for Slide in RNA base-pair steps suggests that the backbone plays a larger role in determining stacking geometries in RNA than in B-form DNA. In comparisons of base-pair steps with thymine versus uracil, the thymine methyl group tends to enhance the strength of the stacking interaction through a combination of dispersion and electrosatic interactions.
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