Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits.

DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.

[1]  J. Piccirilli,et al.  Spinach RNA aptamer detects lead(II) with high selectivity. , 2015, Chemical communications.

[2]  D. Kolpashchikov,et al.  A universal split spinach aptamer (USSA) for nucleic acid analysis and DNA computation. , 2017, Chemical communications.

[3]  Jing Li,et al.  Stem-directed growth of highly fluorescent silver nanoclusters for versatile logic devices. , 2013, Nanoscale.

[4]  Khalid K. Alam,et al.  A Fluorescent Split Aptamer for Visualizing RNA–RNA Assembly In Vivo , 2017, bioRxiv.

[5]  Yalin Tang,et al.  Construction of DNA logic gates utilizing a H+/Ag+ induced i-motif structure. , 2014, Chemical communications.

[6]  Wei-Hua Huang,et al.  Programmable DNA-responsive microchip for the capture and release of circulating tumor cells by nucleic acid hybridization , 2018, Nano Research.

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

[8]  Timothy K Lu,et al.  Synthetic circuits integrating logic and memory in living cells , 2013, Nature Biotechnology.

[9]  Changtong Wu,et al.  Effective construction of a AuNPs–DNA system for the implementation of various advanced logic gates , 2016 .

[10]  D. Endy,et al.  Rewritable digital data storage in live cells via engineered control of recombination directionality , 2012, Proceedings of the National Academy of Sciences.

[11]  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.

[12]  Yalin Tang,et al.  Real-time monitoring of DNA G-quadruplexes in living cells with a small-molecule fluorescent probe , 2018, Nucleic acids research.

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

[14]  N. Sugimoto,et al.  DNA logic gates based on structural polymorphism of telomere DNA molecules responding to chemical input signals. , 2006, Angewandte Chemie.

[15]  Dmitry M. Kolpashchikov,et al.  Nuclease-containing media for resettable operation of DNA logic gates. , 2015, Chemical communications.

[16]  E. Novellino,et al.  Common G-Quadruplex Binding Agents Found to Interact With i-Motif-Forming DNA: Unexpected Multi-Target-Directed Compounds , 2018, Front. Chem..

[17]  Nicolas H Voelcker,et al.  Sequence-addressable DNA logic. , 2008, Small.

[18]  Guonan Chen,et al.  Design of a DNA electronic logic gate (INHIBIT gate) with an assaying application for Ag+ and cysteine. , 2011, Chemical communications.

[19]  Raphael D. Levine,et al.  A full-adder based on reconfigurable DNA-hairpin inputs and DNAzyme computing modules , 2014 .

[20]  Lili Shi,et al.  Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds , 2017, Nucleic acids research.

[21]  Sai Bi,et al.  Triggered and catalyzed self-assembly of hyperbranched DNA structures for logic operations and homogeneous CRET biosensing of microRNA. , 2016, Chemical communications.

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

[23]  Sarah W. Burge,et al.  Quadruplex DNA: sequence, topology and structure , 2006, Nucleic acids research.

[24]  Shaojun Dong,et al.  Cascade DNA logic device programmed ratiometric DNA analysis and logic devices based on a fluorescent dual-signal probe of a G-quadruplex DNAzyme. , 2016, Chemical communications.

[25]  Katrin Paeschke,et al.  DNA secondary structures: stability and function of G-quadruplex structures , 2012, Nature Reviews Genetics.

[26]  Yalin Tang,et al.  Thrombin Ultrasensitive Detection Based on Chiral Supramolecular Assembly Signal-Amplified Strategy Induced by Thrombin-Binding Aptamer. , 2017, Analytical chemistry.

[27]  Tao Li,et al.  Potassium-lead-switched G-quadruplexes: a new class of DNA logic gates. , 2009, Journal of the American Chemical Society.

[28]  Alexander Deiters,et al.  Small Molecule Release and Activation through DNA Computing. , 2017, Journal of the American Chemical Society.

[29]  Longhua Tang,et al.  Toehold-initiated rolling circle amplification for visualizing individual microRNAs in situ in single cells. , 2014, Angewandte Chemie.

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

[31]  Yibing Yin,et al.  Catalytic Hairpin Assembly Actuated DNA Nanotweezer for Logic Gate Building and Sensitive Enzyme-Free Biosensing of MicroRNAs. , 2016, Analytical chemistry.

[32]  Samie R Jaffrey,et al.  In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies. , 2015, Chemistry & biology.

[33]  Dongsheng Liu,et al.  A pH-triggered, fast-responding DNA hydrogel. , 2009, Angewandte Chemie.

[34]  Vijay Gokhale,et al.  Design and synthesis of an expanded porphyrin that has selectivity for the c-MYC G-quadruplex structure. , 2005, Journal of the American Chemical Society.

[35]  Shaojun Dong,et al.  Exploiting Polydopamine Nanospheres to DNA Computing: A Simple, Enzyme-Free and G-Quadruplex-Free DNA Parity Generator/Checker for Error Detection during Data Transmission. , 2017, ACS applied materials & interfaces.

[36]  Xiaogang Qu,et al.  Combination of Graphene Oxide and Thiol‐Activated DNA Metallization for Sensitive Fluorescence Turn‐On Detection of Cysteine and Their Use for Logic Gate Operations , 2011 .

[37]  Jing Zheng,et al.  Rationally designed molecular beacons for bioanalytical and biomedical applications. , 2015, Chemical Society reviews.

[38]  Hung-Yin Lin,et al.  A simple three-input DNA-based system works as a full-subtractor , 2015, Scientific reports.

[39]  Dinshaw J. Patel,et al.  Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics , 2007, Nucleic acids research.

[40]  Junhua Chen,et al.  A label-free and enzyme-free platform with a visible output for constructing versatile logic gates using caged G-quadruplex as the signal transducer† †Electronic supplementary information (ESI) available: Experimental details and supplementary figures. See DOI: 10.1039/c7sc04007e , 2017, Chemical science.

[41]  Yalin Tang,et al.  Formation of Human Telomeric G-quadruplex Structures Induced by the Quaternary Benzophenanthridine Alkaloids: Sanguinarine, Nitidine, and Chelerythrine , 2010 .

[42]  Grigory S. Filonov,et al.  Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution , 2014, Journal of the American Chemical Society.

[43]  Juan Zhao,et al.  Molecular "light switch" for G-quadruplexes and i-motif of human telomeric DNA: [Ru(phen)2(dppz)]2+. , 2010, Dalton transactions.

[44]  A. Phan,et al.  Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter , 2005, Nature chemical biology.

[45]  G. Walker,et al.  Strand displacement amplification--an isothermal, in vitro DNA amplification technique. , 1992, Nucleic acids research.

[46]  Yuanyuan Du,et al.  Intelligent Sensors of Lead Based on a Reconfigurable DNA-Supramolecule Logic Platform. , 2018, Analytical chemistry.

[47]  Xiaoqing Zhu,et al.  Tyramine Hydrochloride Based Label-Free System for Operating Various DNA Logic Gates and a DNA Caliper for Base Number Measurements. , 2017, Chemphyschem : a European journal of chemical physics and physical chemistry.

[48]  S. Yao,et al.  Enzyme-Activated G-Quadruplex Synthesis for in Situ Label-Free Detection and Bioimaging of Cell Apoptosis. , 2017, Analytical chemistry.

[49]  Hyun-Jin Kang,et al.  The Transcriptional Complex Between the BCL2 i-Motif and hnRNP LL Is a Molecular Switch for Control of Gene Expression That Can Be Modulated by Small Molecules , 2014, Journal of the American Chemical Society.

[50]  Yalin Tang,et al.  A dual-site simultaneous binding mode in the interaction between parallel-stranded G-quadruplex [d(TGGGGT)]4 and cyanine dye 2,2′-diethyl-9-methyl-selenacarbocyanine bromide , 2012, Nucleic acids research.

[51]  S. Jaffrey,et al.  Structure and Mechanism of RNA Mimics of Green Fluorescent Protein. , 2015, Annual review of biophysics.

[52]  Shaojun Dong,et al.  A DNA-based parity generator/checker for error detection through data transmission with visual readout and an output-correction function† †Electronic supplementary information (ESI) available: Scheme S1, Tables S1–S3 and Fig. S1–S11. See DOI: 10.1039/c6sc04056j Click here for additional data file. , 2016, Chemical science.

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

[54]  Jean-Louis Mergny,et al.  Combination of i-motif and G-quadruplex structures within the same strand: formation and application. , 2013, Angewandte Chemie.

[55]  S. Balasubramanian,et al.  Quantitative visualization of DNA G-quadruplex structures in human cells. , 2013, Nature chemistry.

[56]  Jiming Hu,et al.  Multiple types of logic gates based on a single G-quadruplex DNA strand , 2014, Scientific Reports.

[57]  Itamar Willner,et al.  Catalytic nucleic acids (DNAzymes) as functional units for logic gates and computing circuits: from basic principles to practical applications. , 2015, Chemical communications.

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

[59]  Yalin Tang,et al.  Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism , 2009, Nucleic acids research.

[60]  Hailong Li,et al.  Implementation of Arithmetic Functions on a Simple and Universal Molecular Beacon Platform , 2015, Advanced science.

[61]  Fang Pu,et al.  DNA-based logic gates operating as a biomolecular security device. , 2011, Chemical communications.

[62]  J. Szostak,et al.  A DNA aptamer that binds adenosine and ATP. , 1995, Biochemistry.

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

[64]  Andrew D. Ellington,et al.  Diagnostic Applications of Nucleic Acid Circuits , 2014, Accounts of chemical research.

[65]  C. C. Hardin,et al.  Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids , 2000, Biopolymers.

[66]  Itamar Willner,et al.  DNAzymes for sensing, nanobiotechnology and logic gate applications. , 2008, Chemical Society reviews.

[67]  Shouzhuo Yao,et al.  G-quadruplex-based fluorometric biosensor for label-free and homogenous detection of protein acetylation-related enzymes activities. , 2017, Biosensors & bioelectronics.

[68]  Ryan J. White,et al.  DNA biomolecular-electronic encoder and decoder devices constructed by multiplex biosensors , 2012 .

[69]  I. Willner,et al.  Multiplexed aptasensors and amplified DNA sensors using functionalized graphene oxide: application for logic gate operations. , 2012, ACS nano.

[70]  Yong Xia,et al.  DNA-based visual majority logic gate with one-vote veto function , 2015, Chemical science.

[71]  Shaojun Dong,et al.  DNA-based advanced logic circuits for nonarithmetic information processing , 2015 .

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

[73]  Junlin Wen,et al.  Concatenated logic circuits based on a three-way DNA junction: a keypad-lock security system with visible readout and an automatic reset function. , 2014, Angewandte Chemie.

[74]  Bingling Li,et al.  Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly. , 2013, Journal of the American Chemical Society.

[75]  Weian Zhao,et al.  Colorimetric and ultrasensitive bioassay based on a dual-amplification system using aptamer and DNAzyme. , 2012, Analytical chemistry.

[76]  R. D. Levine,et al.  Continuous variables logic via coupled automata using a DNAzyme cascade with feedback† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc03892a Click here for additional data file. , 2016, Chemical science.

[77]  Xiaogang Qu,et al.  A label-free, quadruplex-based functional molecular beacon (LFG4-MB) for fluorescence turn-on detection of DNA and nuclease. , 2011, Chemistry.

[78]  Tao Li,et al.  Ion-tuned DNA/Ag fluorescent nanoclusters as versatile logic device. , 2011, ACS nano.

[79]  Shankar Balasubramanian,et al.  A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes. , 2008, Biochemistry.

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

[81]  Raphael D. Levine,et al.  DNAzyme-based 2:1 and 4:1 multiplexers and 1:2 demultiplexer , 2014 .

[82]  Jian Sun,et al.  Photo-Induced Electron Transfer-Based Versatile Platform with G-Quadruplex/Hemin Complex as Quencher for Construction of DNA Logic Circuits. , 2018, Analytical chemistry.

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

[84]  Michael Famulok,et al.  Input-Dependent Induction of Oligonucleotide Structural Motifs for Performing Molecular Logic , 2012, Journal of the American Chemical Society.

[85]  Wei Zhou,et al.  Na+-Induced Conformational Change of Pb2+-Stabilized G-Quadruplex and Its Influence on Pb2+ Detection. , 2016, Analytical chemistry.

[86]  B. Yan,et al.  Intelligent Molecular Searcher from Logic Computing Network Based on Eu(III) Functionalized UMOFs for Environmental Monitoring , 2017 .

[87]  D. Chan,et al.  G-quadruplexes for luminescent sensing and logic gates , 2013, Nucleic acids research.

[88]  Yuanyuan Du,et al.  A Novel Reconfigurable Logic Unit Based on the DNA-Templated Potassium-Concentration-Dependent Supramolecular Assembly. , 2018, Chemistry.

[89]  N. Khashab,et al.  Probing structural changes of self assembled i-motif DNA. , 2015, Chemical communications.

[90]  C. Yang,et al.  Molekulartechnische DNA‐Modifizierung: Molecular Beacons , 2009 .

[91]  The formation pathway of i-motif tetramers , 2009, Nucleic acids research.

[92]  E. Yeow,et al.  A single thiazole orange molecule forms an exciplex in a DNA i-motif. , 2014, Chemical communications.

[93]  Ronghua Yang,et al.  Fabricating a reversible and regenerable Raman-active substrate with a biomolecule-controlled DNA nanomachine. , 2012, Journal of the American Chemical Society.

[94]  Ka-Ho Leung,et al.  Label-free luminescent oligonucleotide-based probes. , 2013, Chemical Society reviews.

[95]  Vladimir Privman,et al.  Enzyme-based logic systems for information processing. , 2009, Chemical Society reviews.

[96]  M. Dinger,et al.  I-motif DNA structures are formed in the nuclei of human cells , 2018, Nature Chemistry.

[97]  Dmitry M Kolpashchikov,et al.  Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles. , 2017, Chemphyschem : a European journal of chemical physics and physical chemistry.

[98]  Chun-Yu Hsu,et al.  Molecular beacon-based half-adder and half-subtractor. , 2012, Chemical communications.

[99]  S. Jaffrey,et al.  RNA Mimics of Green Fluorescent Protein , 2011, Science.

[100]  Jiye Shi,et al.  Hybridization chain reaction amplification of microRNA detection with a tetrahedral DNA nanostructure-based electrochemical biosensor. , 2014, Analytical chemistry.

[101]  Jean-Louis Mergny,et al.  How long is too long? Effects of loop size on G-quadruplex stability , 2010, Nucleic acids research.

[102]  Scott G Harroun,et al.  Programmable DNA switches and their applications. , 2018, Nanoscale.

[103]  Zhengping Li,et al.  One-step ultrasensitive detection of microRNAs with loop-mediated isothermal amplification (LAMP). , 2011, Chemical communications.

[104]  Fei Zhang,et al.  DNA based arithmetic function: a half adder based on DNA strand displacement. , 2016, Nanoscale.

[105]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[106]  D. Chan,et al.  Crystal violet as a fluorescent switch-on probe for i-motif: label-free DNA-based logic gate. , 2011, The Analyst.

[107]  Yalin Tang,et al.  Distinct G-quadruplex structures of human telomeric DNA formed by the induction of sanguinarine and nitidine under salt-deficient condition. , 2010, Fitoterapia.

[108]  Shaojun Dong,et al.  A label-free and enzyme-free system for operating various logic devices using poly(thymine)-templated CuNPs and SYBR Green I as signal transducers. , 2016, Nanoscale.

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

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

[111]  Hua Cui,et al.  Molecular encoder-decoder based on an assembly of graphene oxide with dye-labelled DNA. , 2014, Chemical communications.

[112]  Qiuping Guo,et al.  A new class of homogeneous nucleic acid probes based on specific displacement hybridization. , 2002, Nucleic acids research.

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

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

[115]  Yalin Tang,et al.  Verification of intramolecular hybrid/parallel g-quadruplex structure under physiological conditions using novel cyanine dye H-aggregates: both in solution and on Au film. , 2010, Analytical chemistry.

[116]  Tao Li,et al.  Lead(II)-induced allosteric G-quadruplex DNAzyme as a colorimetric and chemiluminescence sensor for highly sensitive and selective Pb2+ detection. , 2010, Analytical chemistry.

[117]  Shaojun Dong,et al.  Label-free and enzyme-free platform for the construction of advanced DNA logic devices based on the assembly of graphene oxide and DNA-templated AgNCs. , 2016, Nanoscale.

[118]  Xiang Zhou,et al.  Novel amplex red oxidases based on noncanonical DNA structures: property studies and applications in microRNA detection. , 2014, Analytical chemistry.

[119]  Scott L Cockroft,et al.  Simultaneous G-Quadruplex DNA Logic. , 2018, Chemistry.

[120]  Ming Zhou,et al.  G-Quadruplex-based DNAzyme for colorimetric detection of cocaine: using magnetic nanoparticles as the separation and amplification element. , 2011, The Analyst.

[121]  Ryan R. Richardson,et al.  Two- and three-input TALE-based AND logic computation in embryonic stem cells , 2013, Nucleic acids research.

[122]  Matthew R. Lakin,et al.  Catalytic Molecular Logic Devices by DNAzyme Displacement , 2014, Chembiochem : a European journal of chemical biology.

[123]  Na Li,et al.  Thiazole orange as a fluorescent probe: Label-free and selective detection of silver ions based on the structural change of i-motif DNA at neutral pH. , 2016, Talanta.

[124]  E. Wang,et al.  Implementation of half adder and half subtractor with a simple and universal DNA-based platform , 2013 .

[125]  Xiaogang Qu,et al.  Versatile logic devices based on programmable DNA-regulated silver-nanocluster signal transducers. , 2012, Chemistry.

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

[127]  Rahul Sarpeshkar,et al.  Synthetic analog computation in living cells , 2013, Nature.

[128]  G. Parkinson,et al.  Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures , 2006, Nucleic acids research.

[129]  Tao Li,et al.  G-quadruplex-based DNAzyme for sensitive mercury detection with the naked eye. , 2009, Chemical communications.

[130]  Jiming Hu,et al.  Logic gates based on G-quadruplexes: principles and sensor applications , 2015, Microchimica Acta.

[131]  Yulia V Gerasimova,et al.  Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits. , 2016, Angewandte Chemie.

[132]  Shaojun Dong,et al.  An intelligent universal system yields double results with half the effort for engineering a DNA “Contrary Logic Pairs” library and various DNA combinatorial logic circuits , 2017 .

[133]  Yuanyuan Du,et al.  A versatile DNA-supramolecule logic platform for multifunctional information processing , 2018, NPG Asia Materials.

[134]  A. Ono,et al.  Hg(II) ion specifically binds with T:T mismatched base pair in duplex DNA. , 2010, Chemistry.

[135]  Shaojun Dong,et al.  Introducing Ratiometric Fluorescence to MnO2 Nanosheet-Based Biosensing: A Simple, Label-Free Ratiometric Fluorescent Sensor Programmed by Cascade Logic Circuit for Ultrasensitive GSH Detection. , 2017, ACS applied materials & interfaces.

[136]  Bin Zhao,et al.  Genetically Encoded Catalytic Hairpin Assembly for Sensitive RNA Imaging in Live Cells. , 2018, Journal of the American Chemical Society.

[137]  Yang Cai,et al.  Fluorogenic substrate screening for G-quadruplex DNAzyme-based sensors. , 2013, Biosensors & bioelectronics.

[138]  D. Stefanovic,et al.  Exercises in Molecular Computing , 2014, Accounts of chemical research.

[139]  L F Landweber,et al.  Molecular computation: RNA solutions to chess problems , 2000, Proc. Natl. Acad. Sci. USA.

[140]  Colin D. Medley,et al.  Molecular engineering of DNA: molecular beacons. , 2009, Angewandte Chemie.

[141]  Chunhai Fan,et al.  Target-responsive structural switching for nucleic acid-based sensors. , 2010, Accounts of chemical research.

[142]  Yi Xiao,et al.  Label-free, dual-analyte electrochemical biosensors: a new class of molecular-electronic logic gates. , 2010, Journal of the American Chemical Society.

[143]  Shaojun Dong,et al.  A simple, label-free, electrochemical DNA parity generator/checker for error detection during data transmission based on “aptamer-nanoclaw”-modulated protein steric hindrance† †Electronic supplementary information (ESI) available: Table S1 and Fig. S1–S7. See DOI: 10.1039/c8sc02482k , 2018, Chemical science.

[144]  D. Hourcade,et al.  The amplification of ribosomal RNA genes involves a rolling circle intermediate. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[145]  Chih-Ching Huang,et al.  Highly selective DNA-based sensor for lead(II) and mercury(II) ions. , 2009, Analytical chemistry.

[146]  E. Westhof,et al.  iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications , 2016, Nucleic acids research.

[147]  E. Wang,et al.  Label-free G-quadruplex-specific fluorescent probe for sensitive detection of copper(II) ion. , 2013, Biosensors & bioelectronics.

[148]  Yalin Tang,et al.  Quantification of the Na+/K+ ratio based on the different response of a newly identified G-quadruplex to Na+ and K+. , 2013, Chemical communications.

[149]  Tao Li,et al.  Parallel G-quadruplex-specific fluorescent probe for monitoring DNA structural changes and label-free detection of potassium ion. , 2010, Analytical chemistry.

[150]  D. Patel,et al.  Solution structure of a parallel-stranded G-quadruplex DNA. , 1993, Journal of molecular biology.

[151]  David R Walt,et al.  Intelligent medical diagnostics via molecular logic. , 2009, Journal of the American Chemical Society.

[152]  J. Collins,et al.  Complex cellular logic computation using ribocomputing devices , 2017, Nature.

[153]  Dongsheng Liu,et al.  DNA nanotechnology based on i-motif structures. , 2014, Accounts of chemical research.

[154]  Yalin Tang,et al.  Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: I. recognizing mixed G-quadruplex in human telomeres. , 2009, Chemical communications.

[155]  R. Pei,et al.  Berberine as a novel light-up i-motif fluorescence ligand and its application in designing molecular logic systems. , 2016, Chemical communications.

[156]  Itamar Willner,et al.  Graphene oxide/nucleic-acid-stabilized silver nanoclusters: functional hybrid materials for optical aptamer sensing and multiplexed analysis of pathogenic DNAs. , 2013, Journal of the American Chemical Society.

[157]  I. Willner,et al.  Coherent activation of DNA tweezers: a "SET-RESET" logic system. , 2009, Angewandte Chemie.

[158]  Yalin Tang,et al.  i-Motif-modulated fluorescence detection of silver(I) with an ultrahigh specificity. , 2015, Analytica chimica acta.

[159]  A. Suksamrarn,et al.  A mass spectrometric investigation of novel quadruplex DNA-selective berberine derivatives. , 2010, Chemical communications.

[160]  I. Willner,et al.  Functionalized DNA nanostructures. , 2012, Chemical reviews.

[161]  Ru-Ru Gao,et al.  Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing , 2017, Chemical science.

[162]  E. Wang,et al.  Label-free colorimetric detection of aqueous mercury ion (Hg2+) using Hg2+-modulated G-quadruplex-based DNAzymes. , 2009, Analytical chemistry.

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

[164]  Pai Peng,et al.  Logic circuit controlled multi-responsive branched DNA scaffolds. , 2018, Chemical communications.

[165]  S. Maiti,et al.  i-Motif formation with locked nucleic acid (LNA). , 2007, Angewandte Chemie.

[166]  Y. Chai,et al.  A reagentless and disposable electronic genosensor: from multiplexed analysis to molecular logic gates. , 2011, Chemical communications.

[167]  Ying Zhu,et al.  A RET-supported logic gate combinatorial library to enable modeling and implementation of intelligent logic functions , 2015, Chemical science.