The nWCFP1 structures, characterized by intercalation, exhibit the smallest DS-DN distances (dDS-DN) (figure ). By contrast, the WCF structure, akin to the natural BP orientations, displays an evident increase in distance. Notably, the nWCFP2 and nWCFPO structures reveal fluctuating dDS-DN values, suggesting the formation of distorted intercalated arrangements. Overall, AMBER based simulations are in agreement with the AMOEBA based simulation which suggest that flexibility and conformational change of the DS-DN are not an artifact of the force fields or sampling time; rather it is a feature of the UBP-incorporated DNA. The analysis of three replicates further emphasizes randomness in conformational change of the UBP with a biased towards generating nWCF structures as more prevalent conformers.