Persistence Length of Single Stranded DNA: Effect of Length, Sequence and Surface

Abstract

The knowledge of the DNA persistence length indicates the chain's flexibility which is related to the possible final folded state of DNA and provides the means for understanding DNA's structure in solution and on surfaces. The persistence length of ssDNA depends on the rigidity of the backbone and an intra-chain repulsion due to negatively charged backbone. In order to determine the contributions of rigidity and electrostatics on persistence length of ssDNA we conducted series of molecular dynamics simulations with regular and neutralized DNA of various length and sequences. We found that persistence length is largely determined by the flexibility of the backbone. However the electrostatic contribution to the persistence length is sequence dependent due to differences in base stacking and hydrogen bonding network.To investigate the effect of surface on the structure and dynamics of single stranded DNA (ssDNA) we performed molecular dynamics simulations of surface constrained ssDNA. We observed that surface grafting of ssDNA significantly changes its folding pathway, pi-pi stacking interaction, persistence length, and end to end distance when compared to free ssDNA. Moreover, we found that the number of bases and sequence play an important role in structure and dynamics of ssDNA constrained on the surface. Our research provided atomistic understanding of dynamics and conformational changes of single stranded DNA under various conditions; the length and sequence dependence as well as the effect of surface immobilization.