Structure and dynamics of Okazaki fragment models

Three-dimensional structures of anticancer drugs bound to, and incorporated within, nucleic acids have proved beneficial in rationalizing how these drugs provide their anti-neoplastic functionality. We describe the NMR solution structure of an Okazaki fragment model containing the nucleoside analogs gemcitabine. The analog structures are compared with the reference structure to analyze the structural effect of nucleoside analog incorporation on the Okazaki fragment, and rationalize why these analogs lead to premature chain termination. Recent developments in molecular dynamics force field technology have enabled increasingly realistic simulations of biomolecular structure and dynamics. Increasing computer speeds, coupled with decreasing costs, enables larger systems to be studied in greater detail, with longer sampling intervals, and greater diversity of starting structures. The Okazaki fragment model as well as an analog-containing Okazaki fragment model were submitted to unrestrained molecular dynamics using the Cornell et al. force field, demonstrating the unsuitability of this force field in accurately simulating RNA-containing nucleic acid duplexes. Four simulations for ten nanoseconds each were performed on an all-RNA Okazaki fragment model, using the Cornell et al. and the Wang et al. force fields to determine the cause of the force field's shortcomings.