DNA Triplexes-Guided Assembly of G-Quadruplexes for Constructing Label-free Fluorescent Logic Gates.

Assembly of G-quadruplexes guided by DNA triplexes in a controlled manner is achieved for the first time. The folding of triplex sequences in acidic conditions brings two separated guanine-rich sequences together and subsequently a G-quadruplex structure is formed in the presence of K(+) . Based on this novel platform, label-free fluorescent logic gates, such as AND, INHIBIT, and NOR, are constructed with ions as input and the fluorescence of a G-quadruplex-specific fluorescent probe NMM as output.

[1]  N. Sugimoto,et al.  Development of new functional nanostructures consisting of both DNA duplex and quadruplex. , 2010, Chemical communications.

[2]  Xiaogang Qu,et al.  Nucleic Acids and Smart Materials: Advanced Building Blocks for Logic Systems , 2014, Advanced materials.

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

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

[5]  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.

[6]  N. Luedtke,et al.  Fluorescent Probes for G‐Quadruplex Structures , 2013, Chembiochem : a European journal of chemical biology.

[7]  J. Mergny,et al.  Tri-G-quadruplex: controlled assembly of a G-quadruplex structure from three G-rich strands. , 2012, Angewandte Chemie.

[8]  N. Araki,et al.  Silver ion unusually stabilizes the structure of a parallel-motif DNA triplex. , 2009, Journal of the American Chemical Society.

[9]  Itamar Willner,et al.  Chemiluminescent and chemiluminescence resonance energy transfer (CRET) detection of DNA, metal ions, and aptamer-substrate complexes using hemin/G-quadruplexes and CdSe/ZnS quantum dots. , 2011, Journal of the American Chemical Society.

[10]  Dipankar Sen,et al.  A sodium-potassium switch in the formation of four-stranded G4-DNA , 1990, Nature.

[11]  Itamar Willner,et al.  pH-programmable DNA logic arrays powered by modular DNAzyme libraries. , 2012, Nano letters.

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

[13]  D. Arya.  New approaches toward recognition of nucleic acid triple helices. , 2011, Accounts of chemical research.

[14]  B. Saccà,et al.  DNA nanomachines and nanostructures involving quadruplexes. , 2006, Organic & biomolecular chemistry.

[15]  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.

[16]  Jean-Louis Mergny,et al.  "Nano-oddities": unusual nucleic acid assemblies for DNA-based nanostructures and nanodevices. , 2014, Accounts of chemical research.

[17]  Yahui Guo,et al.  A H+/Ag+ dual-target responsive label-free light-up probe based on a DNA triplex. , 2015, Chemistry, an Asian journal.

[18]  Itamar Willner,et al.  Catalytic beacons for the detection of DNA and telomerase activity. , 2004, Journal of the American Chemical Society.

[19]  W. Gao,et al.  Luminescence switch-on detection of protein tyrosine kinase-7 using a G-quadruplex-selective probe , 2015, Chemical science.

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

[21]  Weihong Tan,et al.  A Single DNA Molecule Nanomotor , 2002 .

[22]  Baoquan Ding,et al.  Smart nanomachines based on DNA self-assembly. , 2013, Small.

[23]  Modi Wang,et al.  Conjugating a groove-binding motif to an Ir(iii) complex for the enhancement of G-quadruplex probe behavior† †Electronic supplementary information (ESI) available: Compound characterisation and supplementary data. See DOI: 10.1039/c6sc00001k , 2016, Chemical science.

[24]  Jean-Louis Mergny,et al.  A metal-mediated conformational switch controls G-quadruplex binding affinity. , 2008, Angewandte Chemie.

[25]  Yingfu Li,et al.  DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex. , 1998, Chemistry & biology.

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

[27]  Tao Li,et al.  Enhanced catalytic DNAzyme for label-free colorimetric detection of DNA. , 2007, Chemical communications.

[28]  Itamar Willner,et al.  DNA switches: from principles to applications. , 2015, Angewandte Chemie.

[29]  Victoria Savikhin,et al.  N‐methylmesoporphyrin IX fluorescence as a reporter of strand orientation in guanine quadruplexes , 2014, The FEBS journal.

[30]  Itamar Willner,et al.  DNA-Schalter: Grundlagen und Anwendungen , 2015 .

[31]  R. Pei,et al.  G-Quadruplex DNAzyme Biosensor for Quantitative Detection of T4 Polynucleotide Kinase Activity by Using Split-to-intact G-Quadruplex DNAzyme Conversion , 2016 .

[32]  Lihua Lu,et al.  Detection of nicking endonuclease activity using a G-quadruplex-selective luminescent switch-on probe , 2014 .

[33]  Tao Li,et al.  A lead(II)-driven DNA molecular device for turn-on fluorescence detection of lead(II) ion with high selectivity and sensitivity. , 2010, Journal of the American Chemical Society.

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

[35]  Dik-Lung Ma,et al.  Simple DNA-based logic gates responding to biomolecules and metal ions , 2013 .

[36]  Yinan Qin,et al.  G-quadruplex-based ultrasensitive and selective detection of histidine and cysteine. , 2013, Biosensors & bioelectronics.

[37]  Yahui Guo,et al.  Label-free logic modules and two-layer cascade based on stem-loop probes containing a G-quadruplex domain. , 2014, Chemistry, an Asian journal.

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

[39]  Deming Kong,et al.  Ag+ and cysteine quantitation based on G-quadruplex-hemin DNAzymes disruption by Ag+. , 2010, Analytical chemistry.

[40]  J. Chaires,et al.  Sequence and structural selectivity of nucleic acid binding ligands. , 1999, Biochemistry.

[41]  Francesco Ricci,et al.  Programmable pH-triggered DNA nanoswitches. , 2014, Journal of the American Chemical Society.

[42]  T. Majima,et al.  Conformational changes of non-B DNA. , 2011, Chemical Society reviews.

[43]  I. Willner,et al.  Logic gates and antisense DNA devices operating on a translator nucleic Acid scaffold. , 2009, ACS nano.

[44]  Heather Duschl,et al.  DNA-enabled integrated molecular systems for computation and sensing. , 2014, Accounts of chemical research.

[45]  B. Gatto,et al.  Nucleic acid aptamers based on the G-quadruplex structure: therapeutic and diagnostic potential. , 2009, Current medicinal chemistry.