Our DFT results are consistent with the UBP orientation observed in the post-insertion structure in Taq, 32, 38 which show DS and DN form an intercalated structure inside the DNA duplex with the sulfur and methoxy group on the same side. SAPT analysis suggests that the dispersion component is the major contributing factor in total energy to stabilize the UBP as an intercalated structure (Table ). The NCI index analysis also shows significant non-covalent interaction between DS and DN in the intercalated structures (Figure ). For nWCF orientations, a larger d4-6 represents in-phase placement of UBP whereas a decreased d4-6 denotes outerphase orientations of UBP inside the DNA duplex. Two distinct structural transformational processes have been observed during the simulations that lead to the generation of several conformers (Figure ) i) intra-strand flipping which transforms the geometry of the UBP from SYN to ANTI and vice versa, ii) inter-strand flipping leading to reorient the DS and DN upside down (Figure ).