Inter-strand flipping can be recognized by the pattern shift of UB-NB distance, transitioning between high and low values (Figure ). Flexibility of the UBP is also synchronized with the RMSD values; distorted UBP-incorporated DNA shows higher RMSD whereas sudden change of RMSD values implies structural transformation. Three sets of replicates have yielded varying conformer distributions, suggesting a stochastic arrangement of the conformers. Overall, AMOEBA force field simulations suggest a dynamical nature of the UBP intercalated ds-DNA, with multiple conformational orientations inside the DNA duplex, where nWCF-DNA structures exhibit the largest occurrence.