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Catalyzed relaxation of a metastable DNA fuel

Seelig, Georg and Yurke, Bernard and Winfree, Erik (2006) Catalyzed relaxation of a metastable DNA fuel. Journal of the American Chemical Society, 128 (37). pp. 12211-12220. ISSN 0002-7863. https://resolver.caltech.edu/CaltechAUTHORS:20110309-104200898

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Abstract

Practically all of life's molecular processes, from chemical synthesis to replication, involve enzymes that carry out their functions through the catalytic transformation of metastable fuels into waste products. Catalytic control of reaction rates will prove to be as useful and ubiquitous in nucleic-acid-based engineering as it is in biology. Here we report a metastable DNA "fuel" and a corresponding DNA "catalyst" that improve upon the original hybridization-based catalyst system (Turberfield et al. Phys. Rev. Lett. 90, 118102-1118102-4) by more than 2 orders of magnitude. This is achieved by identifying and purifying a fuel with a kinetically trapped metastable configuration consisting of a "kissing loop" stabilized by flanking helical domains; the catalyst strand acts by opening a helical domain and allowing the complex to relax to its ground state by a multistep pathway. The improved fuel/catalyst system shows a roughly 5000-fold acceleration of the uncatalyzed reaction, with each catalyst molecule capable of turning over in excess of 40 substrates. With k_(cat)/K_M ≈ 10^7/M/min, comparable to many protein enzymes and ribozymes, this fuel system becomes a viable component enabling future DNA-based synthetic molecular machines and logic circuits. As an example, we designed and characterized a signal amplifier based on the fuel-catalyst system. The amplifier uses a single strand of DNA as input and releases a second strand with unrelated sequence as output. A single input strand can catalytically trigger the release of more than 10 output strands.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/ja0635635 DOIArticle
ORCID:
AuthorORCID
Yurke, Bernard0000-0003-3913-2855
Winfree, Erik0000-0002-5899-7523
Additional Information:© 2006 American Chemical Society. Received May 22, 2006. Publication Date (Web): August 26, 2006. We thank Richard W. Roberts for use of his Elutrap. G.S. was supported by the Swiss National Science Foundation and the Center for Biological Circuit design at Caltech. E.W. acknowledges NSF Awards #0093846, #0533064, and #0506468. B.Y. thanks the Moore Foundation for a Moore Distinguished Scholar Fellowship. Preliminary results for this work were previously reported.[37]
Funders:
Funding AgencyGrant Number
Swiss National Science Foundation (SNSF)UNSPECIFIED
Caltech Center for Biological Circuit DesignUNSPECIFIED
NSF0093846
NSFCHE-0533064
NSFDMS-0506468
Gordon and Betty Moore FoundationUNSPECIFIED
Issue or Number:37
Record Number:CaltechAUTHORS:20110309-104200898
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20110309-104200898
Official Citation:Catalyzed Relaxation of a Metastable DNA Fuel Georg Seelig,Bernard Yurke, and, and Erik Winfree,, Journal of the American Chemical Society 2006 128 (37), 12211-12220
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:22755
Collection:CaltechAUTHORS
Deposited By: Lucinda Acosta
Deposited On:20 Oct 2011 22:50
Last Modified:25 Feb 2020 02:58

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