Coarse-grained modeling of DNA oligomer hybridization: length, sequence, and salt effects

A recently published coarse-grained DNA model [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization mechanism of DNA oligomers. Forward flux sampling is used to construct ensembles of reactive trajectories from which the effects of sequence, length, and ionic strength are revealed. Heterogeneous sequences are observed to hybridize via the canonical zippering mechanism. In contrast, homogeneous sequences hybridize through a slithering mechanism, while more complex base pair displacement processes are observed for repetitive sequences. In all cases, the formation of non-native base pairs leads to an increase in the observed hybridization rate constants beyond those observed in sequences where only native base pairs are permitted. The scaling of rate constants with length is captured by extending existing hybridization theories to account for the formation of non-native base pairs. Furthermore, that scaling is found to be similar for oligomeric and polymeric systems, suggesting that similar physics is involved.