Binding of cationic conjugated polymers to DNA: Atomistic simulations of adducts involving the Dickerson's dodecamer

We here describe the investigation at the atomistic level of the structure, stability, and dynamics of several complexes resulting from the interaction of oxidized poly(3,4-ethylenedioxythiophene) with the well-known Dickerson's dodecamer sequence. Four specific arrangements have been selected as referential structures for molecular dynamics simulations, and the resulting independent trajectories tend to converge in two distinguishable models with the strongest interactions. The first one presents a coiled DNA strand enveloping the oligomer chain, whereas in the second model, the conducting polymer chain and the disorganized DNA strand are facing side-by-side. Analysis of the intermolecular interactions indicates that the electrostatic interactions involving the negatively charged DNA phosphates and the positively charged units of the oligomer are much more frequent in the first model. In addition, aside from these electrostatic interactions, specific O•••H and S•••H hydrogen bonds, stacking, and N-H••• interactions have been detected. Among all of these four specific interactions, we show that the stacking is the most abundant and shows the best stability, whereas O•••H hydrogen bonds are also frequent with long lifetimes. At the end, we have to underline that these specific interactions are predominant for the thymine and the guanine, which is in perfect agreement with previous experimental observations.