Abstract
Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon 305-806, KoreaReceived July 15, 2012, Accepted August 7, 2012Thrombin binding aptamter (TBA-15) is a 15-mer guanine-rich oligonucleotide. This DNA apamer specificallybinds to the thrombin protein involved in blood coagulation. Using extensive umbrella sampling moleculardynamics simulation method at all atom level, we investigated the potential of mean force (PMF) upon pullingthe DNA aptamer from the binding mode of aptamer/thrombin complex. From this calculation, the free energycost for a full dissociation of this aptamer/protein complex is 17 kcal/mol, indicating a substantial bindingaffinity of TBA-15. Interestingly, this PMF reveals noticeable plateau regions along the pulling coordinate.Possible structural changes of this complex in the plateau were investigated in details.Key Words : TBA-15, Thrombin binding aptamer, Umbralla sampling, Potential of mean forceIntroductionA single stranded guanine (G)-rich oligonucleotide is offundamental importance, since this G-rich strand constitutesan overhang of telomeres by adopting G-quadruplexes vianon-canonical base pair interactions.
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