A Cooperative DNA Catalyst
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
Name | Size | Download all |
---|---|---|
md5:7d57a3fea3024a5b228de11b41165ed3
|
2.0 MB | Preview Download |
md5:52bfcf5b7358d0bf989dd5316a5cff20
|
1.5 MB | Preview Download |
Additional details
- PMCID
- PMC8609974
- Eprint ID
- 110958
- DOI
- 10.1021/jacs.1c07122
- Resolver ID
- CaltechAUTHORS:20210917-235251911
- Caltech
- BE/CS 196
- Caltech Summer Undergraduate Research Fellowship (SURF)
- NSF
- CCF-1908643
- NIH Predoctoral Fellowship
- 5 T32 GM 112592-5
- Created
-
2021-09-20Created from EPrint's datestamp field
- Updated
-
2023-07-10Created from EPrint's last_modified field
- Caltech groups
- Division of Biology and Biological Engineering