(63e) Scaling Laws and Essential Physics of DNA Oligomer Hybridization Rate Constants

DNA hybridization is a fundamental process in biology and, increasingly so, in engineering. Theory and experiment have been developed to predict the scaling of hybridization rates constants for strands of 100 or more base pairs in length; however, the theory for hybridization of short oligomers remains undeveloped. In this work, we couple a recently developed version of the 3-Site-Per-Nucleotide (3SPN) DNA model with Forward Flux Sampling to examine the hybridization of short oligomers. We begin by studying the scaling of the rate constants on length for homogeneous and heterogenous sequences. We then determine the possible sites for nucleation and the mechanisms of hybridization. Lastly, we contrast the mechanisms of hybridization to those observed for DNA melting on the same sequences. These results are discussed in the context of polymer physics theory and previous simulations using simpler models.