Cascade DNA logic device programmed ratiometric DNA analysis and logic devices based on a fluorescent dual-signal probe of a G-quadruplex DNAzyme.

Herein, two fluorescence sensitive substrates of G-quadruplex/hemin DNAzyme with inverse responses (Scopoletin and Amplex Red) were simultaneously used in one homogeneous system to construct a cascade advanced DNA logic device for the first time (a functional logic device (a three input based DNA calliper) cascade with an advanced non-arithmetic logic gate (1 to 2 decoder)). This cascade logic device was applied to label-free ratiometric target DNA detection and length measurement.

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

[2]  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.

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

[4]  Shaojun Dong,et al.  A new approach to light up DNA/Ag nanocluster-based beacons for bioanalysis , 2013 .

[5]  Erkang Wang,et al.  Measurement of the base number of DNA using a special calliper made of a split G-quadruplex. , 2012, Chemical communications.

[6]  Yiider Tseng,et al.  Effect of length, topology, and concentration on the microviscosity and microheterogeneity of DNA solutions. , 2002, Journal of molecular biology.

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

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

[9]  Wei Wang,et al.  Fluorescence quenching of carbon nitride nanosheet through its interaction with DNA for versatile fluorescence sensing. , 2013, Analytical chemistry.

[10]  B. Révet,et al.  Short unligated sticky ends enable the observation of circularised DNA by atomic force and electron microscopies. , 1998, Nucleic acids research.

[11]  H. Ju,et al.  DNA-regulated silver nanoclusters for label-free ratiometric fluorescence detection of DNA. , 2014, Chemical communications.

[12]  Evgeny Katz,et al.  Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems. , 2015, Angewandte Chemie.

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

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

[15]  A. Skalka,et al.  Characterization of the Self Association of Avian Sarcoma Virus Integrase by Analytical Ultracentrifugation* , 1999, The Journal of Biological Chemistry.

[16]  Fang Zeng,et al.  Carbon-dot-based ratiometric fluorescent sensor for detecting hydrogen sulfide in aqueous media and inside live cells. , 2013, Chemical communications.

[17]  Andreas Offenhäusser,et al.  Multi-level logic gate operation based on amplified aptasensor performance. , 2015, Angewandte Chemie.

[18]  Weihong Tan,et al.  Targeted bioimaging and photodynamic therapy nanoplatform using an aptamer-guided G-quadruplex DNA carrier and near-infrared light. , 2013, Angewandte Chemie.

[19]  Ruijie Deng,et al.  Target-fueled DNA walker for highly selective miRNA detection† †Electronic supplementary information (ESI) available: DNA strand structure and sequences, assembly of DNA strands as noted in the text. See DOI: 10.1039/c5sc02784e Click here for additional data file. , 2015, Chemical science.

[20]  Shaojun Dong,et al.  Four-way junction-driven DNA strand displacement and its application in building majority logic circuit. , 2013, ACS nano.

[21]  Sai Bi,et al.  Target-triggered cascade recycling amplification for label-free detection of microRNA and molecular logic operations. , 2016, Chemical communications.

[22]  A. P. de Silva,et al.  Communicating chemical congregation: a molecular AND logic gate with three chemical inputs as a "lab-on-a-molecule" prototype. , 2006, Journal of the American Chemical Society.

[23]  Evgeny Katz,et al.  Biomolecular information processing : from logic systems to smart sensors and actuators , 2012 .

[24]  Liming Huang,et al.  9-Piperazine substituted perylene-3,4-dicarboximide as a fluorescent probe in ratiometric analysis. , 2011, Chemical communications.

[25]  C. J. Avers,et al.  Nuclear and mitochondrial DNA from wild-type and petite yeast: circularity, length, and buoyant density. , 1969, Proceedings of the National Academy of Sciences of the United States of America.

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

[27]  Huan‐Tsung Chang,et al.  One-pot synthesis of fluorescent oligonucleotide Ag nanoclusters for specific and sensitive detection of DNA. , 2011, Biosensors & bioelectronics.

[28]  Huangxian Ju,et al.  Target-driven DNA association to initiate cyclic assembly of hairpins for biosensing and logic gate operation† †Electronic supplementary information (ESI) available: Supplementary table and figures. See DOI: 10.1039/c5sc01215e Click here for additional data file. , 2015, Chemical science.

[29]  Afshin Beheshti,et al.  DNA electrophoresis in agarose gels: A simple relation describing the length dependence of mobility , 2002, Electrophoresis.

[30]  M. Heagy,et al.  Dual fluorescent N-aryl-2,3- naphthalimides: applications in ratiometric DNA detection and white organic light-emitting devices. , 2010, Organic letters.

[31]  Yunchao Wu,et al.  UV-Light-Induced Improvement of Fluorescence Quantum Yield of DNA-Templated Gold Nanoclusters: Application to Ratiometric Fluorescent Sensing of Nucleic Acids. , 2015, ACS applied materials & interfaces.

[32]  C. McCoy,et al.  A molecular photoionic AND gate based on fluorescent signalling , 1993, Nature.

[33]  Weihong Tan,et al.  Programmable and Multiparameter DNA-Based Logic Platform For Cancer Recognition and Targeted Therapy , 2014, Journal of the American Chemical Society.

[34]  Tao Li,et al.  Enzyme‐Free Unlabeled DNA Logic Circuits Based on Toehold‐Mediated Strand Displacement and Split G‐Quadruplex Enhanced Fluorescence , 2013, Advanced materials.

[35]  R. Miller,et al.  The reaction of coumarins with horseradish peroxidase. , 1975, Plant physiology.

[36]  Yang-Wei Lin,et al.  Fluorescence detection of lead(II) ions through their induced catalytic activity of DNAzymes. , 2011, Analytical chemistry.

[37]  Y. Miura,et al.  Design rationale of thermally responsive microgel particle films that reversibly absorb large amounts of CO2: fine tuning the pKa of ammonium ions in the particles† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5sc01978h , 2015, Chemical science.

[38]  Fang Zeng,et al.  Ratiometric fluorescence assay for γ-glutamyltranspeptidase detection based on a single fluorophore via analyte-induced variation of substitution. , 2014, Chemical communications.

[39]  Stephen J Lippard,et al.  Turn-on and ratiometric mercury sensing in water with a red-emitting probe. , 2007, Journal of the American Chemical Society.

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