Under these circumstances we have divided our work into two parts. In the first part we investigate the UBPincorporated DNA duplex in aqueous solution, aiming to investigate the inherent structural attributes of DS-DN within DNA duplex strands through classical MD simulations. Recognizing the significance of non-covalent interactions in UBP stabilization, we have carried out simulations with the multipolar/polarizable AMOEBA forcefield, alongside the fixed-charge non-polarizable AMBER force field. The organization of the paper is as follows: In the next section, we describe the development of forcefield parameters for UBP and simulations details. Next, we discuss the results for the investigation of dynamical structural properties of UBP-incorporated DNA by placing DS-DN in the middle of a dsDNA strand with different orientations with both short and long fragments of DNA. Subsequently, we describe the investigation of the same with UBP placed in terminal position within the DNA, followed by concluding remarks.