A DNA Network as an Information Processing System

Biomolecular systems that can process information are sought for computational applications, because of their potential for parallelism and miniaturization and because their biocompatibility also makes them suitable for future biomedical applications. DNA has been used to design machines, motors, finite automata, logic gates, reaction networks and logic programs, amongst many other structures and dynamic behaviours. Here we design and program a synthetic DNA network to implement computational paradigms abstracted from cellular regulatory networks. These show information processing properties that are desirable in artificial, engineered molecular systems, including robustness of the output in relation to different sources of variation. We show the results of numerical simulations of the dynamic behaviour of the network and preliminary experimental analysis of its main components.

[1]  A. Arkin,et al.  Motifs, modules and games in bacteria. , 2003, Current opinion in microbiology.

[2]  A. Turberfield,et al.  DNA fuel for free-running nanomachines. , 2003, Physical review letters.

[3]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .

[4]  W. Han,et al.  アルミニウム単結晶中の変形が誘起したマイクロツインと積層欠陥 | 文献情報 | J-GLOBAL 科学技術総合リンクセンター , 2008 .

[5]  Russell P. Goodman,et al.  Reconfigurable, braced, three-dimensional DNA nanostructures. , 2008, Nature nanotechnology.

[6]  Uri Alon,et al.  An Introduction to Systems Biology , 2006 .

[7]  A. Turberfield,et al.  Mechanism for a directional, processive, and reversible DNA motor. , 2009, Small.

[8]  Darko Stefanovic,et al.  A deoxyribozyme-based molecular automaton , 2003, Nature Biotechnology.

[9]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

[10]  Peter J. Denning,et al.  Computing is a natural science , 2007, CACM.

[11]  Alexander van Oudenaarden,et al.  Material for A General Mechanism for Network-Dosage Compensation in Gene Circuits , 1656 .

[12]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[13]  Robert M. Dirks,et al.  Triggered amplification by hybridization chain reaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[14]  G. Seelig,et al.  DNA as a universal substrate for chemical kinetics , 2010, Proceedings of the National Academy of Sciences.

[15]  U. Alon,et al.  The incoherent feedforward loop can provide fold-change detection in gene regulation. , 2009, Molecular cell.

[16]  S. Basu,et al.  Spatiotemporal control of gene expression with pulse-generating networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Andrew J Turberfield,et al.  DNA hairpins: fuel for autonomous DNA devices. , 2006, Biophysical journal.

[18]  Ehud Shapiro,et al.  Molecular implementation of simple logic programs. , 2009, Nature nanotechnology.

[19]  W. Lim,et al.  Defining Network Topologies that Can Achieve Biochemical Adaptation , 2009, Cell.

[20]  E. Shapiro,et al.  Programmable and autonomous computing machine made of biomolecules , 2001, Nature.

[21]  A. Turberfield,et al.  DNA nanomachines. , 2007, Nature nanotechnology.

[22]  Bernard Yurke,et al.  Using DNA to Power Nanostructures , 2003, Genetic Programming and Evolvable Machines.

[23]  Zhen Xie,et al.  Molecular Systems Biology Peer Review Process File Synthetic Incoherent Feed-forward Circuits Show Adaptation to the Amount of Their Genetic Template. Transaction Report , 2022 .

[24]  D. Y. Zhang,et al.  Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.

[25]  N. Pierce,et al.  A synthetic DNA walker for molecular transport. , 2004, Journal of the American Chemical Society.

[26]  U. Alon.  Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.

[27]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[28]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[29]  N. Seeman,et al.  A precisely controlled DNA biped walking device , 2004 .

[30]  Ruojie Sha,et al.  A Bipedal DNA Brownian Motor with Coordinated Legs , 2009, Science.

[31]  F. Simmel,et al.  DNA nanodevices. , 2005, Small.

[32]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[33]  A. Turberfield,et al.  Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. , 2008, Physical review letters.

[34]  Grzegorz Rozenberg,et al.  The many facets of natural computing , 2008, Commun. ACM.

[35]  O. Urakawa,et al.  Small - , 2007 .

[36]  N. Seeman.  DNA in a material world , 2003, Nature.

[37]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[38]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[39]  J. Macdonald,et al.  Medium scale integration of molecular logic gates in an automaton. , 2006, Nano letters.

[40]  Richard A. Muscat,et al.  A programmable molecular robot. , 2011, Nano letters.

[41]  Uri Alon,et al.  The incoherent feed-forward loop can generate non-monotonic input functions for genes , 2008, Molecular systems biology.

[42]  A. Turberfield,et al.  Direct observation of stepwise movement of a synthetic molecular transporter. , 2011, Nature nanotechnology.