In this work, we use symmetry-adapted perturbation theory (SAPT) to characterize non-covalent interactions between small molecule ligands and DNA/RNA aptamers.  Fragments of the ligand and aptamer are isolated from the crystal structure using a custom-developed analysis program.  The aptamer is protonated to neutralize charge, and the interaction energy of the ligand/aptamer complex is computed using SAPT in the PSI4 program package. Ligand aptamer interaction energies are critical to understanding aptamer binding events and developing ways to leverage these binding events in therapeutic compounds.

Computational characterization of ligand/aptamer interactions in DNA and RNA

248th National Meeting (2014)

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