Betz et al. reported several crystal structures of the large fragment of T. Aquaticus (Taq) DNA polymerase with bound UBP-incorporated DNA duplex. Among these, for the structure in the pre-insertion phase, the UBP are observed to be arranged in a parallel stack (WCF orientation), whereas in the post-insertion structure the DS-DN pair adopts an intercalated structure (nWCF) inside the DNA duplex . Several research groups have used computational tools to investigate structural properties of the UBP-incorporated DNA . Datta et al. investigated the structure of DS-DN incorporated DNA through both QM and MD simulations and showed that the DS-DN distance is found to be consistent with a WCF pairing pattern during MD simulations . Wetmore et al. considered UBP incorporated three nucleotides-long double strands and observed that for DS and DN, QM calculations suggest DS and DN adopt an intercalated nWCF structure, whereas a planar WCF-like configuration has been predicted through MD simulations . Barroso-Flores et al. have reported several conformers of DS and DN inside DNA duplex through their extensive MD simulations . They concluded that an equilibrated structure of DS-DN incorporated DNA duplex may not have been achieved due to sampling time and/or forcefield incompatibility. In summary, unlike natural base pairs, UBPs appear to adopt different conformations in aqueous solution and during different steps of the replication processes as observed from X-Ray crystal structures and computational simulations.