(418cn) Understanding Structure and Dynamics of Single Stranded DNA: Effect of Charges, Backbone, Length and Bases

Single stranded DNA (ssDNA) has been known as an important intermediate material in many key biochemical process, as well as novel materials in nano-biotechnology, such as biosensors and drug delivery vectors. It has been reported that structural flexibility of ssDNA plays an important role in understanding biochemical process in the cell and their applications. To elucidate the role of the ssDNA constituents including backbone, charges, length and bases on the structure and dynamics of ssDNA, we performed molecular dynamics (MD) simulation  on regular ssDNA, neutralized ssDNA where all negative charges were removed, and backbone where all bases were truncated. In this study, we demonstrated different folding pathways of each case showing that regular ssDNA can form loop-like structures via internal non-bonded interactions, but neutralized ssDNA and backbone fold into entangled structure. By comparing folding pathway with persistence length and radius of gyration of each case, we found the importance of negative charges on stiffness of ssDNA. Moreover, it is shown that internal base pairing and pi-pi stacking between bases play a pivotal role in stiffness of ssDNA, which can’t be fully explained by conventional polyelectrolyte theories. Overall, our study suggests the pivotal factors which can affect the structure and dynamics of ssDNA and explains the discrepancies between estimations by MD simulations and theories, which can give an insight on understanding of self-assembly of nucleic acid based materials and designing its applications.