Catalytic DNA Polymerization Can Be Expedited by Active Product Release

The sequence-specific hybridization of DNA facilitates its use as a building block for designer nanoscale structures and reaction networks that perform computations. However, the strong binding energy of Watson-Crick base pairing that underlies this specificity also causes the DNA dehybridization rate to depend sensitively on sequence length and temperature. This strong dependency imposes stringent constraints on the design of multi-step DNA reactions. Here we show how an ATP-dependent helicase, Rep-X, can drive specific dehybridization reactions at rates independent of sequence length, removing the constraints of equilibrium on DNA hybridization and dehybridization. To illustrate how this new capacity can speed up designed DNA reaction networks, we show that Rep-X extends the range of conditions where the primer exchange reaction, which catalytically adds a domain provided by a hairpin template to a DNA substrate, proceeds rapidly.

Automated summary

The specific hybridization of DNA can be used as a building block for nanoscale structures and reaction networks. However, the strong binding energy of Watson-Crick base pairing causes the dehybridization rate of DNA to depend on sequence length and temperature. In this study, the ATP-dependent helicase Rep-X is shown to drive specific dehybridization reactions at rates independent of sequence length, removing the constraints of equilibrium on DNA hybridization and dehybridization. Additionally, Rep-X is demonstrated to accelerate the primer exchange reaction in designed DNA reaction networks.