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I will present my investigation of the structural and dynamical aspects of UBP-incorporated DNA using AMBER
and polarizable AMOEBA force field in MD simulations, both in solution and in Taq DNA polymerase (Taq) system.
We have considered D5SICS (DS)-dNaM (DN) as UBP, one of the most efficiently replicated UBPs, which interacts
with one another through hydrophobic interactions and forms an unconventional intercalated base pair. Both the
UBs have been parameterized for AMBER and AMOEBA force fields. In aqueous solution, UBP-incorporated DNA
exhibits flexible DNA structure forming both Watson-Crick (WC) and non-Watson Crick (nWC) Geometry. However,
the flexibility of the UBP has been arrested when the DNA is bound with Taq, forming only nWC geometry.
Molecular level inspection depicts that specific residues around the UBP stabilize the UBP to stay as nWC
structures through coulombic and vdW interactions. Conformational analysis suggests Taq allows and further
stabilizes some specific conformers whereas significant distortion has been observed for other conformers.
Overall, our detailed analysis predicts the structural understanding of UBP-incorporated DNA and the role of taq
in stabilization through systematic classical molecular dynamics. |