Published September 29, 2021 | Published + Supplemental Material
Journal Article Open

A Cooperative DNA Catalyst

An error occurred while generating the citation.

Abstract

DNA catalysts are fundamental building blocks for diverse molecular information-processing circuits. Allosteric control of DNA catalysts has been developed to activate desired catalytic pathways at desired times. Here we introduce a new type of DNA catalyst that we call a cooperative catalyst: a pair of reversible reactions are employed to drive a catalytic cycle in which two signal species, which can be interpreted as an activator and an input, both exhibit catalytic behavior for output production. We demonstrate the role of a dissociation toehold in controlling the kinetics of the reaction pathway and the significance of a wobble base pair in promoting the robustness of the activator. We show near-complete output production with input and activator concentrations that are 0.1 times the gate concentration. The system involves just a double-stranded gate species and a single-stranded fuel species, as simple as the seesaw DNA catalyst, which has no allosteric control. The simplicity and modularity of the design make the cooperative DNA catalyst an exciting addition to strand-displacement motifs for general-purpose computation and dynamics.

Additional Information

© 2021 The Authors. Published by American Chemical Society. ACS AuthorChoice - Attribution-NonCommercial-NoDerivs 2.0 Generic (CC BY-NC-ND 2.0) Received: July 9, 2021; Published: September 15, 2021. D.N.T. and S.R.D. were supported by Caltech internal funds for BE/CS 196, a course on design and construction of programmable molecular systems. D.N.T. was also supported by the Summer Undergraduate Research Fellowships (SURF) Program at Caltech and an NSF award (1908643). S.R.D. was also supported by an NIH/BLP training grant (5 T32 GM 112592-5). L.Q. was supported by an NSF award (1908643). The authors thank E. Winfree for reading and commenting on the manuscript. Author Contributions: D.N.T. and S.R.D. contributed equally. The authors declare no competing financial interest.

Attached Files

Published - jacs.1c07122.pdf

Supplemental Material - ja1c07122_si_001.pdf

Files

ja1c07122_si_001.pdf
Files (3.5 MB)
Name Size Download all
md5:7d57a3fea3024a5b228de11b41165ed3
2.0 MB Preview Download
md5:52bfcf5b7358d0bf989dd5316a5cff20
1.5 MB Preview Download

Additional details

Created:
August 20, 2023
Modified:
December 22, 2023