DNA-Based Dynamic Reaction Networks

Overview

Journal Trends Biochem Sci

Specialty Biochemistry

Date 2018 May 26

PMID 29793809

Citations 25

Authors

Ting Fu

Yifan Lyu

Hui Liu

Ruizi Peng

Xiaobing Zhang

Mao Ye

Weihong Tan

Affiliations

Soon will be listed here.

Abstract

Deriving from logical and mechanical interactions between DNA strands and complexes, DNA-based artificial reaction networks (RNs) are attractive for their high programmability, as well as cascading and fan-out ability, which are similar to the basic principles of electronic logic gates. Arising from the dream of creating novel computing mechanisms, researchers have placed high hopes on the development of DNA-based dynamic RNs and have strived to establish the basic theories and operative strategies of these networks. This review starts by looking back on the evolution of DNA dynamic RNs; in particular' the most significant applications in biochemistry occurring in recent years. Finally, we discuss the perspectives of DNA dynamic RNs and give a possible direction for the development of DNA circuits.

Citing Articles

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Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks.

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References

Sakamoto K, Gouzu H, Komiya K, Kiga D, Yokoyama S, Yokomori T . Molecular computation by DNA hairpin formation. Science. 2000; 288(5469):1223-6. DOI: 10.1126/science.288.5469.1223. View

Ball P . Chemistry meets computing. Nature. 2000; 406(6792):118-20. DOI: 10.1038/35018259. View

Yurke B, Turberfield A, Mills Jr A, Simmel F, Neumann J . A DNA-fuelled molecular machine made of DNA. Nature. 2000; 406(6796):605-8. DOI: 10.1038/35020524. View

Yan H, Zhang X, Shen Z, Seeman N . A robust DNA mechanical device controlled by hybridization topology. Nature. 2002; 415(6867):62-5. DOI: 10.1038/415062a. View

Stojanovic M, Mitchell T, Stefanovic D . Deoxyribozyme-based logic gates. J Am Chem Soc. 2002; 124(14):3555-61. DOI: 10.1021/ja016756v. View

Turberfield A, Mitchell J, Yurke B, Mills Jr A, Blakey M, Simmel F . DNA fuel for free-running nanomachines. Phys Rev Lett. 2003; 90(11):118102. DOI: 10.1103/PhysRevLett.90.118102. View

Stojanovic M, Stefanovic D . A deoxyribozyme-based molecular automaton. Nat Biotechnol. 2003; 21(9):1069-74. DOI: 10.1038/nbt862. View

ALBERTY R, Goldberg R . Standard thermodynamic formation properties for the adenosine 5'-triphosphate series. Biochemistry. 1992; 31(43):10610-5. DOI: 10.1021/bi00158a025. View

Dirks R, Pierce N . Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci U S A. 2004; 101(43):15275-8. PMC: 524468. DOI: 10.1073/pnas.0407024101. View

10.

Kolpashchikov D, Stojanovic M . Boolean control of aptamer binding states. J Am Chem Soc. 2005; 127(32):11348-51. DOI: 10.1021/ja051362f. View

11.

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

12.

Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R, Benenson Y . A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol. 2007; 25(7):795-801. DOI: 10.1038/nbt1307. View

13.

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

14.

Yin P, Choi H, Calvert C, Pierce N . Programming biomolecular self-assembly pathways. Nature. 2008; 451(7176):318-22. DOI: 10.1038/nature06451. View

15.

Benenson Y . Biocomputers: from test tubes to live cells. Mol Biosyst. 2009; 5(7):675-85. PMC: 2714485. DOI: 10.1039/b902484k. View

16.

Zhang D, Winfree E . Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc. 2009; 131(47):17303-14. DOI: 10.1021/ja906987s. View

17.

Soloveichik D, Seelig G, Winfree E . DNA as a universal substrate for chemical kinetics. Proc Natl Acad Sci U S A. 2010; 107(12):5393-8. PMC: 2851759. DOI: 10.1073/pnas.0909380107. View

18.

Elbaz J, Lioubashevski O, Wang F, Remacle F, Levine R, Willner I . DNA computing circuits using libraries of DNAzyme subunits. Nat Nanotechnol. 2010; 5(6):417-22. DOI: 10.1038/nnano.2010.88. View

19.

Medina P, Nolde M, Slack F . OncomiR addiction in an in vivo model of microRNA-21-induced pre-B-cell lymphoma. Nature. 2010; 467(7311):86-90. DOI: 10.1038/nature09284. View

20.

Pei R, Matamoros E, Liu M, Stefanovic D, Stojanovic M . Training a molecular automaton to play a game. Nat Nanotechnol. 2010; 5(11):773-7. DOI: 10.1038/nnano.2010.194. View