The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.

ABSTRACT: The kinetics of DNA hybridization are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridize at different rates are not well understood. Secondary structure is one predictable factor that influences hybridization rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. In this context, we measured hybridization rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify our observations. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment w

SUBMITTER: Hertel S 

PROVIDER: S-EPMC9371923 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature