We investigated structural aspects, conformational changes, and stability of DS-DN incorporated DNA duplex by considering both short and long forms of DNA duplex simulated with both polarizable AMOEBA and AMBER force fields. It was found from both force fields that unlike natural base pairs, UBP can persist as both WCF and nWCF conformers inside DNA duplex with flexible orientations and random conformational change, which agrees with the previous simulated results with AMBER and CHARMM forcefields. This could suggest that the flexibility of UBP inside DNA is not an artifact of the forcefields, but rather it is an intrinsic property of this DS-DN incorporated DNA. It is evident from our analysis that conformational orientation perturbs the stability of the neighboring cBP mostly for shorter fragments of DNA, which reflects on the populations of the conformers. In shorter DNA strands, nWCF conformers are predominant whereas equal distributions are noticed for long-DNA. Our simulated results also suggest the fluctuating nature of DS and DN in the terminal position.