PROBING THE STACKING INTERACTION IN NUCLEIC ACIDS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Whereas the ab-initio electronic structure methods are successful in calculations involving hydrogen bonding between nucleic acids bases, they fail when applied to stacking interaction. That failure has been attributed to the inadequate ellectronic correlations and it is implied that expansion of the basis set may improve the results. I would like to explore a conceptually different approach to stacking and perform calculations for complexes involving hydrogenated and/or dehydrogenated radicals of nucleic acid bases and base pairs. The exploratory calculations will be performed at the B3LYP/aug-cc-pVDZ level. Inspite of using a rather modest basis set for this problem, the calculations will require significant computational resources due to the large number of atoms in the considered clusters. If successful, the exploratory calculations will be extended to include the phosphate-sugar links between the bases and to calculate structures of small oligonucleotides.