Catalytic DNA Polymerization Can Be Expedited by Active Product Release

27 January 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


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, because a small deviation from the optimal conditions slows down the process dramatically. Here we show how an ATP-dependent helicase, Rep-X, can drive certain dehybridization reactions in designed DNA reaction networks at rates independent of sequence length, thereby decoupling the rates of hybridization and dehybridization. To illustrate this principle, 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: in the strong substrate-hairpin binding regime, Rep-X expedites the reaction almost one hundred-fold. Our results provide an example of how ATP consumption can drive specific dehybridization reactions in designed DNA reaction networks and how this consumption can be harnessed to expedite reactions beyond their equilibrium rates.


DNA nanotechnology

Supplementary materials

Supplementary Information
Contains Supplementary Methods, Table of DNA sequences, and Extended data figures


Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.