DNA and RNA aptamers are a structurally diverse class of small nucleic acids known to interact with a wide range of molecular targets.  These targets include environmental and biological sensors, which could have therapeutic applications as nucleic acid targeting drugs or in drug delivery systems.  In this work, we examine the binding energetics of two DNA aptamers with argininamide derivatives.   The interaction energy between the ligand and aptamer will be computed using correlated electronic structure methods, energy decomposition schemes, and density functional techniques designed to capture medium range electron correlation.  Additionally, molecular dynamics simulations will be utilized to sample the conformational space of the ligand/aptamer system to determine how conformational changes affect the interaction energy.   Conformational sampling is critical to developing an complete picture of the binding energetics of these systems.

Analysis of small molecule ligands with DNA aptamers:  Conformational sampling and interaction energy determinations

251st National Meeting (2016)

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