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Catalytic Nucleic Acids (DNAzymes) As Functional Units For Logic Gates And Computing Circuits: From Basic Principles To Practical Applications.

R. Orbach, B. Willner, I. Willner
Published 2015 · Computer Science, Medicine

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This feature article addresses the implementation of catalytic nucleic acids as functional units for the construction of logic gates and computing circuits, and discusses the future applications of these systems. The assembly of computational modules composed of DNAzymes has led to the operation of a universal set of logic gates, to field programmable logic gates and computing circuits, to the development of multiplexers/demultiplexers, and to full-adder systems. Also, DNAzyme cascades operating as logic gates and computing circuits were demonstrated. DNAzyme logic systems find important practical applications. These include the use of DNAzyme-based systems for sensing and multiplexed analyses, for the development of controlled release and drug delivery systems, for regulating intracellular biosynthetic pathways, and for the programmed synthesis and operation of cascades.
This paper references
10.1021/JP047706Q
Monomolecular Logic: “Half-Adder” Based on Multistate/Multifunctional Photochromic Spiropyrans
Xuefeng Guo (2004)
10.1021/ja902490x
Universal translators for nucleic acid diagnosis.
John M. Picuri (2009)
10.1093/NAR/22.9.1600
Intramolecular folding of a fragment of the cytosine-rich strand of telomeric DNA into an i-motif.
J. L. Leroy (1994)
10.1039/b924832c
A graphene-based fluorescent nanoprobe for silver(I) ions detection by using graphene oxide and a silver-specific oligonucleotide.
Yanqin Wen (2010)
Chem
Z. Zhang (2013)
10.1016/J.CCR.2010.01.001
Signal processing with multicomponent systems based on metal complexes
M. Amelia (2010)
10.1073/pnas.0800723105
A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures
Y. Weizmann (2008)
10.1126/science.1227268
Three-Dimensional Structures Self-Assembled from DNA Bricks
Yonggang Ke (2012)
10.1016/1074-5521(94)90014-0
A DNA enzyme that cleaves RNA.
R. Breaker (1994)
10.1021/nn300997f
Graphene-based aptamer logic gates and their application to multiplex detection.
L. Wang (2012)
10.1126/SCIENCE.2200121
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
C. Tuerk (1990)
10.1002/chem.201201995
Nucleic acid driven DNA machineries synthesizing Mg2+-dependent DNAzymes: an interplay between DNA sensing and logic-gate operations.
R. Orbach (2012)
10.1002/anie.200802018
A simple unimolecular multiplexer/demultiplexer.
M. Amelia (2008)
10.1039/C1JM12343B
Sequential logic and random access memory (RAM): a molecular approach
G. D. Ruiter (2011)
Y
L. Zhang (2013)
10.1021/JA047486U
Pseudohexagonal 2D DNA crystals from double crossover cohesion.
Baoquan Ding (2004)
10.1039/b926003j
Ion-induced DNAzyme switches.
Simcha Shimron (2010)
10.1126/science.1154533
Assembling Materials with DNA as the Guide
Faisal A. Aldaye (2008)
Chem
F. Wang (2012)
10.1002/cbic.201300471
Deoxyribozyme Cascade for Visual Detection of Bacterial RNA
Y. V. Gerasimova (2013)
10.1038/nature04586
Folding DNA to create nanoscale shapes and patterns
P. Rothemund (2006)
10.1038/90256
In vitro selection of nucleoprotein enzymes
M. P. Robertson (2001)
10.1038/28998
Design and self-assembly of two-dimensional DNA crystals
E. Winfree (1998)
DNA structure: Revisiting the Watson-Crick double helix
M. Bansal (2003)
10.1002/CPHC.200600260
DNA tile based self-assembly: building complex nanoarchitectures.
Chenxiang Lin (2006)
10.1126/science.1200520
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
Lulu Qian (2011)
Chem
J. Andreasson (2007)
10.1038/364042A0
A molecular photoionic AND gate based on fluorescent signalling
P. Silva (1993)
10.1039/b719856f
Detection of mercury(II) based on Hg2+ -DNA complexes inducing the aggregation of gold nanoparticles.
Chi-Wei Liu (2008)
10.1021/ja500619w
Programmable pH-triggered DNA nanoswitches.
Andrea Idili (2014)
10.1038/nature10262
Neural network computation with DNA strand displacement cascades
Lulu Qian (2011)
10.1002/ANIE.200604524
Electronic aptamer-based sensors.
I. Willner (2007)
10.1021/cr900323b
Binary probes for nucleic acid analysis.
D. Kolpashchikov (2010)
10.1038/nature07971
Self-assembly of a nanoscale DNA box with a controllable lid
E. Andersen (2009)
10.1039/B604119C
Molecular recognition via base-pairing.
J. Sessler (2007)
10.1002/anie.201405692
Switchable bifunctional stimuli-triggered poly-N-isopropylacrylamide/DNA hydrogels.
W. Guo (2014)
Sci
M. Kahan-Hanum (1535)
10.1515/9783486731620-002
I
John B. Shoven (1824)
10.1016/j.copbio.2010.06.001
Functional nucleic acid nanostructures and DNA machines.
Carsten Teller (2010)
10.1021/JA036909+
Molecular logic: a half-subtractor based on tetraphenylporphyrin.
S. Langford (2003)
10.1021/ac9010809
Highly sensitive electrochemical sensor for mercury(II) ions by using a mercury-specific oligonucleotide probe and gold nanoparticle-based amplification.
Zhiqiang Zhu (2009)
10.1039/c1cc12795k
pH-programmable DNAzyme nanostructures.
Simcha Shimron (2011)
10.1016/J.TIBS.2005.01.007
From genes to machines: DNA nanomechanical devices.
N. Seeman (2005)
10.1039/B615450F
Diagnosing viruses by the rolling circle amplified synthesis of DNAzymes.
Zoya Cheglakov (2007)
10.1021/BI00494A001
Single-strand DNA triple-helix formation.
R. Haener (1990)
10.1021/CR960009C
Nucleic Acid Selection and the Challenge of Combinatorial Chemistry.
S. Osborne (1997)
10.1038/nature02551
An autonomous molecular computer for logical control of gene expression
Y. Benenson (2004)
10.1021/nl303894h
Switching photonic and electrochemical functions of a DNAzyme by DNA machines.
X. Liu (2013)
10.1038/nbt862
A deoxyribozyme-based molecular automaton
M. Stojanovic (2003)
Angew
C. W. Brown (2014)
10.1038/345836A0
Formation of a stable triplex from a single DNA strand.
V. Sklenár̆ (1990)
10.1038/nnano.2008.164
Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding.
Sherri Rinker (2008)
10.1039/c4cs00342j
Molecules with a sense of logic: a progress report.
J. Andréasson (2015)
10.1002/ANIE.200603856
Molecular 2:1 digital multiplexer.
J. Andréasson (2007)
10.1177/001452469000101110
"J."
G.G. Stokes (1890)
10.1039/b718428j
DNAzymes for sensing, nanobiotechnology and logic gate applications.
I. Willner (2008)
10.1136/BMJ.323.7325.1375/A
I and i
K. Barraclough (2001)
10.1073/pnas.1633515100
Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA
Chunhai Fan (2003)
10.1021/JA973346R
Stability of Chimeric DNA/RNA Cytosine Tetrads: Implications for i-Motif Formation by RNA
D. Collin (1998)
10.1016/j.copbio.2012.11.011
Nucleic acids for the rational design of reaction circuits.
Adrien Padirac (2013)
Nat
R. R. Breaker (1997)
10.1016/j.chembiol.2010.02.003
Nucleic acid detection using MNAzymes.
Y. V. Gerasimova (2010)
10.1006/JMBI.1993.1241
Energetics of a stable intramolecular DNA triple helix formation.
J. Völker (1993)
10.1038/nnano.2008.3
Reconfigurable, braced, three-dimensional DNA nanostructures.
R. P. Goodman (2008)
10.1006/JMBI.1996.0472
Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.
S. Nonin (1996)
Nat
J. Elbaz (2010)
10.1126/science.1148532
Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA
D. Y. Zhang (2007)
10.1038/nnano.2009.50
Enzyme cascades activated on topologically programmed DNA scaffolds.
Ofer I. Wilner (2009)
10.1021/ja311385y
Smart mesoporous SiO2 nanoparticles for the DNAzyme-induced multiplexed release of substrates.
Zhanxia Zhang (2013)
10.1021/nl300051g
pH-programmable DNA logic arrays powered by modular DNAzyme libraries.
Johann Elbaz (2012)
10.1021/JP4027892
Colorimetric Logic Gates Based on Ion-Dependent DNAzymes
L. Zhang (2013)
10.1002/ANIE.200503208
DNA-templated self-assembly of two-dimensional and periodical gold nanoparticle arrays.
J. Sharma (2006)
10.1002/chem.201201479
Detection of metal ions (Cu2+, Hg2+) and cocaine by using ligation DNAzyme machinery.
Fuan Wang (2012)
Chem
R. Orbach (2014)
10.1021/JA016756V
Deoxyribozyme-based logic gates.
M. Stojanovic (2002)
10.1021/JP074429P
A molecule-based 1: 2 Digital demultiplexer
J. Andréasson (2007)
10.1002/ANIE.200701369
Forty years of in vitro evolution.
G. F. Joyce (2007)
10.1002/anie.200902538
A pH-triggered, fast-responding DNA hydrogel.
E. Cheng (2009)
Chem
S. Shimron (2010)
Chem
S. J. Langford (2003)
10.1039/c1cc12290h
DNAzyme crosslinked hydrogel: a new platform for visual detection of metal ions.
Haoxue Lin (2011)
10.1073/pnas.0909380107
DNA as a universal substrate for chemical kinetics
David Soloveichik (2010)
10.1039/b808686a
Specific interactions between silver(I) ions and cytosine-cytosine pairs in DNA duplexes.
A. Ono (2008)
10.1002/ANIE.200700047
Design of molecular logic devices based on a programmable DNA-regulated semisynthetic enzyme.
N. Gianneschi (2007)
10.1021/JA058564W
A molecular full-adder and full-subtractor, an additional step toward a moleculator.
D. Margulies (2006)
10.1039/B600282J
Supramolecular architectures generated by self-assembly of guanosine derivatives.
J. Davis (2007)
10.1039/C4SC00914B
A full-adder based on reconfigurable DNA-hairpin inputs and DNAzyme computing modules
R. Orbach (2014)
10.1021/am303189h
Nucleic acid/quantum dots (QDs) hybrid systems for optical and photoelectrochemical sensing.
R. Freeman (2013)
10.1038/346818A0
In vitro selection of RNA molecules that bind specific ligands
A. Ellington (1990)
10.1039/b919417g
pH-triggered switchable Mg2+-dependent DNAzymes.
Johann Elbaz (2010)
10.1039/c1cs15054e
DNA-guided display of proteins and protein ligands for the interrogation of biology.
F. Diezmann (2011)
10.1039/C3SC52752B
DNAzyme-based 2:1 and 4:1 multiplexers and 1:2 demultiplexer
R. Orbach (2014)
10.1002/1439-7633(20020301)3:2/3<242::AID-CBIC242>3.0.CO;2-F
DNA‐Directed Assembly of Bienzymic Complexes from In Vivo Biotinylated NAD(P)H:FMN Oxidoreductase and Luciferase
C. Niemeyer (2002)
Chem
D. Margulies (2006)
10.1039/c3nr02653a
Switchable mechanical DNA "arms" operating on nucleic acid scaffolds associated with electrodes or semiconductor quantum dots.
Gilad Pelossof (2013)
10.1039/c3cc49140d
Reversible Ag(+)-crosslinked DNA hydrogels.
W. Guo (2014)
10.1021/ac901773b
Aptamer-DNAzyme hairpins for amplified biosensing.
Carsten Teller (2009)
10.1002/anie.201402691
Signal propagation in multi-layer DNAzyme cascades using structured chimeric substrates.
Carl W. Brown (2014)
10.1021/BI051871U
Deoxyribozyme-based three-input logic gates and construction of a molecular full adder.
H. Lederman (2006)
10.1002/ANIE.200700269
Colorimetric detection of mercuric ion (Hg2+) in aqueous media using DNA-functionalized gold nanoparticles.
J. Lee (2007)
10.1073/PNAS.0400731101
Stochastic computing with biomolecular automata
R. Adar (2004)
10.1002/anie.201004406
"Illusionary" polymerase activity triggered by metal ions: use for molecular logic-gate operations.
K. Park (2010)
10.1007/128_2013_515
DNA-based machines.
Fuan Wang (2014)
Chem
R. Orbach (2014)
10.1038/nnano.2010.88
DNA computing circuits using libraries of DNAzyme subunits.
Johann Elbaz (2010)
10.1021/CR0306743
Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy.
M. Famulok (2007)
10.1002/chem.200802004
Cooperative multicomponent self-assembly of nucleic acid structures for the activation of DNAzyme cascades: a paradigm for DNA sensors and aptasensors.
Johann Elbaz (2009)
10.1021/ar300011g
"Fitting" makes "sensing" simple: label-free detection strategies based on nucleic acid aptamers.
Y. Du (2013)
10.1021/nn800727x
Fluorescent DNA nanotags based on a self-assembled DNA tetrahedron.
Hayriye Ozhalici-Unal (2009)
10.1073/pnas.1219672110
Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates
R. Orbach (2012)
10.1126/science.1132493
Enzyme-Free Nucleic Acid Logic Circuits
Georg Seelig (2006)
10.1021/nl400078g
Switchable catalytic acrylamide hydrogels cross-linked by hemin/G-quadruplexes.
Chun-hua Lu (2013)
10.1021/JA9900398
Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy
C. Mao (1999)
10.1021/nn404613v
DNA nanotechnology: from sensing and DNA machines to drug-delivery systems.
Chun-hua Lu (2013)
10.1038/srep01535
A library of programmable DNAzymes that operate in a cellular environment
M. Kahan-Hanum (2013)
10.1016/j.bios.2008.10.019
Au nanoparticles grafted sandwich platform used amplified small molecule electrochemical aptasensor.
Y. Du (2009)
Chem
J. Elbaz (2009)
10.1021/ac3002269
Amplified surface plasmon resonance and electrochemical detection of Pb2+ ions using the Pb2+-dependent DNAzyme and hemin/G-quadruplex as a label.
Gilad Pelossof (2012)
10.1021/nl803887y
Sensing of UO22+ and design of logic gates by the application of supramolecular constructs of ion-dependent DNAzymes.
Michal Moshe (2009)
10.1021/cr200104q
Functionalized DNA nanostructures.
Ofer I. Wilner (2012)
10.1126/science.1206938
Organization of Intracellular Reactions with Rationally Designed RNA Assemblies
C. Delebecque (2011)
10.1021/nl901165f
Scaffolded DNA origami of a DNA tetrahedron molecular container.
Yonggang Ke (2009)



This paper is referenced by
10.1039/c7sc00361g
Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00361g Click here for additional data file.
Ru-Ru Gao (2017)
10.1021/acsami.5b02156
Programmed DNAzyme-Triggered Dissolution of DNA-Based Hydrogels: Means for Controlled Release of Biocatalysts and for the Activation of Enzyme Cascades.
S. Lilienthal (2015)
10.1007/s00604-017-2565-9
Enzyme-free amplified detection of circulating microRNA by making use of DNA circuits, a DNAzyme, and a catalytic hairpin assembly
J. Luo (2017)
10.1002/cphc.201700046
Unconventional Nonlinear Input-Output Response in a Luminescent Molecular Switch by Inner Filtering Effects.
M. Baroncini (2017)
10.1016/J.SNB.2018.11.002
Proximity binding-induced DNA assembly as signal translator and enzyme-catalyzed cleavage recycle as signal amplifier for highly sensitive electrochemical assay of target DNA
Xiaoyu Hua (2019)
10.1039/c5cc06105a
Photocatalytic oxidation of TMB with the double stranded DNA-SYBR Green I complex for label-free and universal colorimetric bioassay.
X. Zhang (2015)
10.1021/acs.nanolett.6b00789
DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles.
N. Wu (2016)
10.1007/s00604-015-1565-x
G-quadruplex based impedimetric 2-hydroxyfluorene biosensor using hemin as a peroxidase enzyme mimic
G. Liang (2015)
10.1007/s00604-019-3615-2
Fluorometric detection of silver(I) using cytosine-Ag(I)-cytosine pair formation, DNA assembly and the AND logic operation of a multiple-component DNAzyme
Y. Xu (2019)
10.1002/chem.201704824
A Novel Reconfigurable Logic Unit Based on the DNA-Templated Potassium-Concentration-Dependent Supramolecular Assembly.
Chunrong Yang (2018)
10.1039/c7sc01765k
Stimuli-responsive nucleic acid-functionalized metal–organic framework nanoparticles using pH- and metal-ion-dependent DNAzymes as locks† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc01765k Click here for additional data file.
W. Chen (2017)
10.1002/chem.201606043
Why DNA Is a More Effective Scaffold than RNA in Nucleic Acid-Based Asymmetric Catalysis-Supramolecular Control of Cooperative Effects.
Jasmin J Marek (2017)
10.1039/c5cc04412j
Biomacromolecular logic gate, encoder/decoder and keypad lock based on DNA damage with electrochemiluminescence and electrochemical signals as outputs.
S. Liu (2015)
10.1021/acssensors.6b00601
Multi-Amplified Sensing of MicroRNA by a Small DNA Fragment-Driven Enzymatic Cascade Reaction.
Eunjung Kim (2017)
10.1021/acs.langmuir.8b00478
DNA-Responsive SiO2 Nanoparticles, Metal-Organic Frameworks, and Microcapsules for Controlled Drug Release.
M. Vázquez-González (2018)
10.1016/J.SNB.2018.06.027
Graphene oxide/silver nanoclusters based logic devices and their application to multiplexed analysis of miRNA
Siqi Zhang (2018)
10.1002/cphc.201700109
Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles.
E. A. Campbell (2017)
10.1016/j.compbiolchem.2020.107374
Enzyme-free and DNA-based universal platform for the construction of various logic devices based on graphene oxide and G-quadruplex
Yue Wang (2020)
10.12688/f1000research.8601.1
Thirty-five years of research into ribozymes and nucleic acid catalysis: where do we stand today?
S. Müller (2016)
10.1039/c7cc04083k
Instrument-free visual detection of tetracycline on an autocatalytic DNA machine using a caged G-quadruplex as the signal reporter.
J. Chen (2017)
10.1039/c5sc04832j
Rational design of supramolecular hemin/G-quadruplex–dopamine aptamer nucleoapzyme systems with superior catalytic performance† †Electronic supplementary information (ESI) available: Oxidation of ABTS2–, additional figures of computational simulations, kinetic curves, and parameters of the switchabl
H. B. Albada (2016)
10.1039/c9me00090a
Half adder and half subtractor logic gates based on nicking enzymes
Y. Zhao (2019)
10.1002/anie.202009579
Sharp Switching of DNAzyme Activity through the Formation of a Cu(II)-mediated Carboxyimidazole Base Pair.
M. Shionoya (2020)
10.1002/anie.201603265
Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits.
Y. V. Gerasimova (2016)
10.1016/j.tibs.2018.11.001
Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications.
S. Kumar (2019)
10.1039/c8cc09345h
A stimuli-responsive DNAzyme displaying Boolean logic-gate responses.
Ayaka Banno (2019)
10.1039/d0me00082e
Supra-molecular agents running tasks intelligently (SMARTI): recent developments in molecular logic-based computation
Chaoyi Yao (2020)
10.1039/c6nr04069a
A label-free and enzyme-free system for operating various logic devices using poly(thymine)-templated CuNPs and SYBR Green I as signal transducers.
Changtong Wu (2016)
10.1002/anie.201503054
Stimuli-responsive DNA-functionalized nano-/microcontainers for switchable and controlled release.
Chun-hua Lu (2015)
10.1007/s11426-019-9657-0
A pH-regulated stimuli-responsive strategy for RNA-cleaving DNAzyme
Shasha Lu (2019)
10.1039/c9sc00205g
Switching transcription with bacterial RNA polymerase through photocaging, photorelease and phosphorylation reactions in the major groove of DNA† †Electronic supplementary information (ESI) available: Contains detailed experimental procedures, characterization data and additional figures and gels. S
Zuzana Vaníková (2019)
10.1002/adma.201804540
The Pathway to Intelligence: Using Stimuli-Responsive Materials as Building Blocks for Constructing Smart and Functional Systems.
Xuan Zhang (2019)
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