Selected geometrical parameters associated with the UBP have been monitored including the UBP distance (dDS-DN), which has been calculated by measuring the length between C1' of DS and DN. We have also calculated (UB-NB) (NB=Natural Base), for DS the calculated distances are DC4-DS5 (d4-5) and DG6-DS5 (d6-5) whereas for DN, DC13-DN14 (d13-14) and DG15-DN14 (d15-14) are the calculated distances (Scheme 1). The distance between DC4-DG6(d4-6) is also calculated. The distance between sulphur of DS and oxygen (-OMe) of DN is designated as dO-S. Parameters related to angles have been calculated (<NB-UB-UB) to predict the conformational change of the UBP inside the DNA duplex.