DNA As a Universal Substrate for Chemical Kinetics

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2010 Mar 6

PMID 20203007

Citations 118

Authors

David Soloveichik

Georg Seelig

Erik Winfree

Affiliations

Soon will be listed here.

Abstract

Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions. By using strand displacement reactions as a primitive, we construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously, reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into real chemical systems. We illustrate our method on the Lotka-Volterra oscillator, a limit-cycle oscillator, a chaotic system, and systems implementing feedback digital logic and algorithmic behavior.

Citing Articles

Quantitative Analysis of the Effect of Fluorescent Labels on DNA Strand Displacement Reaction.

Toyonari M, Aso K, Nakakuki T Micromachines (Basel). 2025; 15(12.

PMID: 39770220 PMC: 11676983. DOI: 10.3390/mi15121466.

Kombucha-Proteinoid Crystal Bioelectric Circuits.

Mougkogiannis P, Nikolaidou A, Adamatzky A ACS Omega. 2024; 9(45):45386-45401.

PMID: 39554456 PMC: 11561624. DOI: 10.1021/acsomega.4c07319.

Abstraction-based segmental simulation of reaction networks using adaptive memoization.

Helfrich M, Andriushchenko R, ceska M, Kretinsky J, Marticek S, Safranek D BMC Bioinformatics. 2024; 25(1):350.

PMID: 39516723 PMC: 11549863. DOI: 10.1186/s12859-024-05966-5.

NucleoCraft: The Art of Stimuli-Responsive Precision in DNA and RNA Bioengineering.

Yu L, Chen L, Satyabola D, Prasad A, Yan H BME Front. 2024; 5:0050.

PMID: 39290204 PMC: 11407293. DOI: 10.34133/bmef.0050.

A biomimetic branching signal-passing tile assembly model with dynamic growth and disassembly.

Fu D, Reif J J R Soc Interface. 2024; 21(217):20230755.

PMID: 39163031 PMC: 11335017. DOI: 10.1098/rsif.2023.0755.

References

Zhang D, Turberfield A, Yurke B, Winfree E . Engineering entropy-driven reactions and networks catalyzed by DNA. Science. 2007; 318(5853):1121-5. DOI: 10.1126/science.1148532. View

Ran T, Kaplan S, Shapiro E . Molecular implementation of simple logic programs. Nat Nanotechnol. 2009; 4(10):642-8. DOI: 10.1038/nnano.2009.203. View

Keasling J . Synthetic biology for synthetic chemistry. ACS Chem Biol. 2008; 3(1):64-76. DOI: 10.1021/cb7002434. View

Panyutin I, Hsieh P . Formation of a single base mismatch impedes spontaneous DNA branch migration. J Mol Biol. 1993; 230(2):413-24. DOI: 10.1006/jmbi.1993.1159. View

Hjelmfelt A, Weinberger E, Ross J . Chemical implementation of neural networks and Turing machines. Proc Natl Acad Sci U S A. 1991; 88(24):10983-7. PMC: 53057. DOI: 10.1073/pnas.88.24.10983. View

Gartner Z, Tse B, Grubina R, Doyon J, Snyder T, Liu D . DNA-templated organic synthesis and selection of a library of macrocycles. Science. 2004; 305(5690):1601-5. PMC: 2814051. DOI: 10.1126/science.1102629. View

Panyutin I, Hsieh P . The kinetics of spontaneous DNA branch migration. Proc Natl Acad Sci U S A. 1994; 91(6):2021-5. PMC: 43301. DOI: 10.1073/pnas.91.6.2021. View

Buchler N, Gerland U, Hwa T . On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A. 2003; 100(9):5136-41. PMC: 404558. DOI: 10.1073/pnas.0930314100. View

Reynaldo L, Vologodskii A, Neri B, Lyamichev V . The kinetics of oligonucleotide replacements. J Mol Biol. 2000; 297(2):511-20. DOI: 10.1006/jmbi.2000.3573. View

10.

Ashkenasy G, Ghadiri M . Boolean logic functions of a synthetic peptide network. J Am Chem Soc. 2004; 126(36):11140-1. PMC: 1829323. DOI: 10.1021/ja046745c. View

11.

Benner S, Sismour A . Synthetic biology. Nat Rev Genet. 2005; 6(7):533-43. PMC: 7097405. DOI: 10.1038/nrg1637. View

12.

Andrianantoandro E, Basu S, Karig D, Weiss R . Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol. 2006; 2:2006.0028. PMC: 1681505. DOI: 10.1038/msb4100073. View

13.

Win M, Liang J, Smolke C . Frameworks for programming biological function through RNA parts and devices. Chem Biol. 2009; 16(3):298-310. PMC: 2713350. DOI: 10.1016/j.chembiol.2009.02.011. View

14.

Levskaya A, Chevalier A, Tabor J, Simpson Z, Lavery L, Levy M . Synthetic biology: engineering Escherichia coli to see light. Nature. 2005; 438(7067):441-2. DOI: 10.1038/nature04405. View

15.

Green C, Tibbetts C . Reassociation rate limited displacement of DNA strands by branch migration. Nucleic Acids Res. 1981; 9(8):1905-18. PMC: 326811. DOI: 10.1093/nar/9.8.1905. View

16.

Weinstock P, Wetmur J . Branch capture reactions: effect of recipient structure. Nucleic Acids Res. 1990; 18(14):4207-13. PMC: 331180. DOI: 10.1093/nar/18.14.4207. View

17.

Seelig G, Soloveichik D, Zhang D, Winfree E . Enzyme-free nucleic acid logic circuits. Science. 2006; 314(5805):1585-8. DOI: 10.1126/science.1132493. View

18.

Qian L, Winfree E . A simple DNA gate motif for synthesizing large-scale circuits. J R Soc Interface. 2011; 8(62):1281-97. PMC: 3140723. DOI: 10.1098/rsif.2010.0729. View

19.

Okamoto M, Sakai T, Hayashi K . Switching mechanism of a cyclic enzyme system: role as a "chemical diode". Biosystems. 1987; 21(1):1-11. DOI: 10.1016/0303-2647(87)90002-5. View

20.

Klonowski W . Simplifying principles for chemical and enzyme reaction kinetics. Biophys Chem. 1983; 18(2):73-87. DOI: 10.1016/0301-4622(83)85001-7. View