  To gain a deeper insight into cellular processes such as transcription and
translation, one needs to uncover the mechanisms controlling the
configurational changes of nucleic acids. As a step toward this aim, we present
here a novel mesoscopic-level computational model that provides a new window
into nucleic acid dynamics. We model a single-stranded nucleic as a polymer
chain whose monomers are the nucleosides. Each monomer comprises a bead
representing the sugar molecule and a pin representing the base. The bead-pin
complex can rotate about the backbone of the chain. We consider pairwise
stacking and hydrogen-bonding interactions. We use a modified Monte Carlo
dynamics that splits the dynamics into translational bead motion and rotational
pin motion. By performing a number of tests we first show that our model is
physically sound. We then focus on the study of a the kinetics of a DNA
hairpin--a single-stranded molecule comprising two complementary segments
joined by a non-complementary loop--studied experimentally. We find that
results from our simulations agree with experimental observations,
demonstrating that our model is a suitable tool for the investigation of the
hybridization of single strands.
