Nuclease-containing media for resettable operation of DNA logic gates.

We designed and tested a system that allows DNA logic gates to respond multiple times to the addition of oligonucleotide inputs. After producing an output signal, the system spontaneously resets to the background state. This system does not require any operator action to achieve reset of a DNA logic gate, and may become useful for construction of reusable DNA-based computational devices.

[1]  Wei Zhai,et al.  A series of logic gates based on electrochemical reduction of Pb2+ in self-assembled G-quadruplex on the gold electrode. , 2014, Chemical communications.

[2]  F. Simmel.  Towards biomedical applications for nucleic acid nanodevices. , 2007, Nanomedicine.

[3]  Yulia V Gerasimova,et al.  DNA Nanotechnology for Nucleic Acid Analysis: DX Motif‐Based Sensor , 2011, Chembiochem : a European journal of chemical biology.

[4]  Yulia V Gerasimova,et al.  Enzyme-assisted target recycling (EATR) for nucleic acid detection. , 2014, Chemical Society reviews.

[5]  Maxim P Nikitin,et al.  Biocomputing based on particle disassembly. , 2014, Nature nanotechnology.

[6]  I. Willner,et al.  From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. , 2014, Chemical reviews.

[7]  Yulia V Gerasimova,et al.  Connectable DNA logic gates: OR and XOR logics. , 2012, Chemistry, an Asian journal.

[8]  Dmitry M Kolpashchikov,et al.  Molecular logic gates connected through DNA four-way junctions. , 2010, Angewandte Chemie.

[9]  Dmitry M. Kolpashchikov,et al.  Molecular logic gates for DNA analysis: detection of rifampin resistance in M. tuberculosis DNA. , 2012, Angewandte Chemie.

[10]  Cheulhee Jung,et al.  Simple and universal platform for logic gate operations based on molecular beacon probes. , 2012, Small.

[11]  T. Nilsen,et al.  Detection of RNAs by 3'-end labeling and RNase H digestion. , 2014, Cold Spring Harbor protocols.

[12]  Adrian Linacre,et al.  Toehold-mediated nonenzymatic DNA strand displacement as a platform for DNA genotyping. , 2013, Journal of the American Chemical Society.

[13]  Gavin Cloherty,et al.  Thermodynamically modulated partially double-stranded linear DNA probe design for homogeneous real-time PCR , 2007, Nucleic acids research.

[14]  Cuichen Wu,et al.  Nucleic acid based logical systems. , 2014, Chemistry.

[15]  Dmitry M. Kolpashchikov,et al.  An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions , 2012, Scientifica.

[16]  N. Seeman,et al.  DNA double-crossover molecules. , 1993, Biochemistry.

[17]  Yulia V Gerasimova,et al.  Enzyme-assisted binary probe for sensitive detection of RNA and DNA. , 2010, Chemical communications.

[18]  Yulia V. Gerasimova,et al.  Divide and control: split design of multi-input DNA logic gates. , 2015, Chemical communications.

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

[20]  Sanjay Tyagi,et al.  Molecular Beacons: Probes that Fluoresce upon Hybridization , 1996, Nature Biotechnology.

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

[22]  Wei Wang,et al.  Label-free luminescence switch-on detection of T4 polynucleotide kinase activity using a G-quadruplex-selective probe. , 2014, Chemical communications.

[23]  Y. Benenson.  Biomolecular computing systems: principles, progress and potential , 2012, Nature Reviews Genetics.

[24]  Kazuhiro Furukawa,et al.  Allosteric control of a DNA-hydrolyzing deoxyribozyme with short oligonucleotides and its application in DNA logic gates. , 2014, Organic & biomolecular chemistry.

[25]  Dmitry M. Kolpashchikov,et al.  Operating Cooperatively (OC) Sensor for Highly Specific Recognition of Nucleic Acids , 2013, PloS one.

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

[27]  Friedrich C Simmel,et al.  Nucleic acid based molecular devices. , 2011, Angewandte Chemie.

[28]  Saori Nakagawa,et al.  Detection of cytochrome P450 2C19 gene polymorphism from noninvasive samples by cycling probe technology , 2014, Annals of clinical biochemistry.

[29]  Chun-yang Zhang,et al.  Quencher-free fluorescent method for homogeneously sensitive detection of microRNAs in human lung tissues. , 2014, Analytical chemistry.

[30]  Brian M. Frezza,et al.  Modular multi-level circuits from immobilized DNA-based logic gates. , 2007, Journal of the American Chemical Society.

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

[32]  Michael T. Zimmermann,et al.  MACE: model based analysis of ChIP-exo , 2014, Nucleic acids research.

[33]  G. Seelig,et al.  Dynamic DNA nanotechnology using strand-displacement reactions. , 2011, Nature chemistry.

[34]  Itamar Willner,et al.  Biomolecule/nanomaterial hybrid systems for nanobiotechnology. , 2012, Advances in experimental medicine and biology.

[35]  Jing Zhang,et al.  Highly sensitive fluorescence assay of T4 polynucleotide kinase activity and inhibition via enzyme-assisted signal amplification. , 2014, Analytical biochemistry.

[36]  Jing Zhang,et al.  An enzyme-aided amplification strategy for sensitive detection of DNA utilizing graphene oxide (GO) as a fluorescence quencher. , 2014, The Analyst.

[37]  Li Zhang,et al.  Colorimetric Logic Gates Based on Ion-Dependent DNAzymes , 2013 .

[38]  Sheng Lin,et al.  Label-free luminescence switch-on detection of hepatitis C virus NS3 helicase activity using a G-quadruplex-selective probe† †Electronic supplementary information (ESI) available: Compound characterisation and supplementary data. See DOI: 10.1039/c4sc03319a Click here for additional data file. , 2014, Chemical science.

[39]  Teruo Fujii,et al.  Nucleic acids for the rational design of reaction circuits. , 2013, Current opinion in biotechnology.