Base stacking is an important contribution to the structure and stability of DNA and RNA.  To examine the sequence-dependence of three-body interactions in nucleic acids, we extend our previously developed Base Coordinate Reader (BCR) to address three-base configurations.  The BCR recasts the internal coordinates of a base stack into a specific, known set of coordinates, such that individual coordinates can be optimized or frozen.  In this work, we examine all possible canonical three-base stacking configurations in DNA and RNA.  For each base configuration, the BCR is used to recast the internal coordinates, and the intramolecular coordinates are optimized, while the intermolecular coordinates are fixed.  The interaction energy is then computed using spin-component-scaled MP2.  The 3-body interaction energy is computed to examine the coordinated effects of sequence variations.

Three-body effects in base stacking in nucleic acids

248th National Meeting (2014)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.