To examine the dynamics of polyarginine-DNA interactions, we determined when each of the polyarginine chains was in contact with DNA during the last 50 ns of each simulation (Figure ). In all three simulations, there are peptide chains that form a long-lasting interaction with the DNA duplex as well as chains that do not interact with the DNA. In the case of R20 (Figure ), four of the six R20 chains are always in contact with the DNA during this time period, while the other two chains remain free in solution. In the case of the R6 and, especially, the R3 simulations, interactions between the DNA and the peptide chains are more dynamic, and DNApeptide interactions continue to break and/or form. Such changes in DNA-polyarginine interactions were rare in the R6 simulation, as a single R6 chain that had a long-lasting interaction with DNA broke away approximately 90 ns into the simulation. An additional R6 chain made contact with DNA during only a single snapshot relatively late in the simulation. Dynamic interactions between DNA and R3 chains (Figure ) were more common, with seven peptide chains breaking away from the DNA after being in contact for more than ~5 ns. The relationship between interaction stability and polyarginine chain length can be explained by considering the number of residues of each peptide that interact with DNA. Of the R3 chains bound to DNA, only ~2 residues were in contact with the DNA at any given time. In contrast, ~5 arginine residues of each R6 chain and ~10 residues of each R20 chain were in contact with the DNA. Therefore, the release of an R6 or R20 chain that was bound to DNA would typically require the disruption of more DNAarginine residue interactions than the release of an R3 chain.