Nucleic acid based logical systems.

Researchers increasingly visualize a significant role for artificial biochemical logical systems in biological engineering, much like digital logic circuits in electrical engineering. Those logical systems could be utilized as a type of servomechanism to control nanodevices in vitro, monitor chemical reactions in situ, or regulate gene expression in vivo. Nucleic acids (NA), as carriers of genetic information with well-regulated and predictable structures, are promising materials for the design and engineering of biochemical circuits. A number of logical devices based on nucleic acids (NA) have been designed to handle various processes for technological or biotechnological purposes. This article focuses on the most recent and important developments in NA-based logical devices and their evolution from in vitro, through cellular, even towards in vivo biological applications.

[1]  Dmitry M Kolpashchikov,et al.  Boolean control of aptamer binding states. , 2005, Journal of the American Chemical Society.

[2]  M. Win,et al.  Higher-Order Cellular Information Processing with Synthetic RNA Devices , 2008, Science.

[3]  Le A. Trinh,et al.  Programmable in situ amplification for multiplexed imaging of mRNA expression , 2010, Nature Biotechnology.

[4]  Darko Stefanovic,et al.  Deoxyribozyme-based logic gates. , 2002, Journal of the American Chemical Society.

[5]  E. Shapiro,et al.  An autonomous molecular computer for logical control of gene expression , 2004, Nature.

[6]  Y. Benenson.  RNA-based computation in live cells. , 2009, Current opinion in biotechnology.

[7]  E. Winfree,et al.  Construction of an in vitro bistable circuit from synthetic transcriptional switches , 2006, Molecular systems biology.

[8]  E. Shapiro,et al.  Detection of multiple disease indicators by an autonomous biomolecular computer. , 2011, Nano letters.

[9]  R. Weiss,et al.  A universal RNAi-based logic evaluator that operates in mammalian cells , 2007, Nature Biotechnology.

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

[11]  Xi Chen,et al.  Shaping up nucleic acid computation. , 2010, Current opinion in biotechnology.

[12]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

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

[14]  Luca Cardelli,et al.  Programmable chemical controllers made from DNA. , 2013, Nature nanotechnology.

[15]  Cuichen Wu,et al.  A logical molecular circuit for programmable and autonomous regulation of protein activity using DNA aptamer-protein interactions. , 2012, Journal of the American Chemical Society.

[16]  Weihong Tan,et al.  DNA branch migration reactions through photocontrollable toehold formation. , 2013, Journal of the American Chemical Society.

[17]  Jehoshua Bruck,et al.  Neural network computation with DNA strand displacement cascades , 2011, Nature.

[18]  G. Church,et al.  Next-Generation Digital Information Storage in DNA , 2012, Science.

[19]  Milan N. Stojanovic,et al.  Autonomous Molecular Cascades for Evaluation of Cell Surfaces , 2013, Nature nanotechnology.

[20]  Alexander Deiters,et al.  DNA computation in mammalian cells: microRNA logic operations. , 2013, Journal of the American Chemical Society.

[21]  Shawn M. Douglas,et al.  A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads , 2012, Science.

[22]  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.

[23]  R. Murray,et al.  Timing molecular motion and production with a synthetic transcriptional clock , 2011, Proceedings of the National Academy of Sciences.

[24]  D. Stefanovic,et al.  Training a molecular automaton to play a game. , 2010, Nature nanotechnology.

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

[26]  Weihong Tan,et al.  Locked nucleic acid molecular beacons. , 2005, Journal of the American Chemical Society.

[27]  Peng Yin,et al.  Optimizing the specificity of nucleic acid hybridization. , 2012, Nature chemistry.

[28]  Cuichen Wu,et al.  Engineering a cell-surface aptamer circuit for targeted and amplified photodynamic cancer therapy. , 2013, ACS nano.

[29]  Philip Ball,et al.  Chemistry meets computing , 2000, Nature.

[30]  Jonathan Bath,et al.  Reversible logic circuits made of DNA. , 2011, Journal of the American Chemical Society.

[31]  Erik Winfree,et al.  Robustness and modularity properties of a non-covalent DNA catalytic reaction , 2010, Nucleic acids research.

[32]  J. Macdonald,et al.  Deoxyribozyme-based ligase logic gates and their initial circuits. , 2005, Journal of the American Chemical Society.

[33]  R. Levine,et al.  DNA computing circuits using libraries of DNAzyme subunits. , 2010, Nature nanotechnology.

[34]  Yaakov Benenson,et al.  Biocomputers: from test tubes to live cells. , 2009, Molecular bioSystems.

[35]  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 .

[36]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[37]  Yan Liu,et al.  Three-input majority logic gate and multiple input logic circuit based on DNA strand displacement. , 2013, Nano letters.

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

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

[40]  Y. Sakai,et al.  Programming an in vitro DNA oscillator using a molecular networking strategy , 2011, Molecular systems biology.

[41]  Yan Du,et al.  Aptamer-controlled biofuel cells in logic systems and used as self-powered and intelligent logic aptasensors. , 2010, Journal of the American Chemical Society.

[42]  Weihong Tan,et al.  DNA aptamer–micelle as an efficient detection/delivery vehicle toward cancer cells , 2009, Proceedings of the National Academy of Sciences.

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

[44]  Georg Seelig,et al.  Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA. , 2013, Nature chemistry.

[45]  A. Deiters,et al.  DNA computation: a photochemically controlled AND gate. , 2012, Journal of the American Chemical Society.

[46]  Ewan Birney,et al.  Towards practical, high-capacity, low-maintenance information storage in synthesized DNA , 2013, Nature.

[47]  Hong Qian,et al.  Oscillations and multiscale dynamics in a closed chemical reaction system: second law of thermodynamics and temporal complexity. , 2008, The Journal of chemical physics.