Logic circuit controlled multi-responsive branched DNA scaffolds.

A logic circuit controlled multi-responsive sensing platform built on a three-way DNA junction (TWJ) is reported. It enabled the construction of novel fluorescent sensing platforms responsive to any target out of HIV gene, ATP and pH value, and furthermore were logically regulated by two other targets and then behaved as different logic circuits, which consist of two tandem AND gates or cascaded NAND and INH gates by varying the positions of the fluorescent tags.

[1]  N. Seeman.  Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[2]  X. Qu,et al.  An intelligent 1:2 demultiplexer as an intracellular theranostic device based on DNA/Ag cluster-gated nanovehicles , 2018, Nanotechnology.

[3]  Norio Teramae,et al.  2-Aminopurine-modified abasic-site-containing duplex DNA for highly selective detection of theophylline. , 2009, Journal of the American Chemical Society.

[4]  Ruijie Deng,et al.  Multiresponsive rolling circle amplification for DNA logic gates mediated by endonuclease. , 2014, Analytical chemistry.

[5]  Yi Lu,et al.  A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. , 2003, Journal of the American Chemical Society.

[6]  R. Osman,et al.  Probing structure and dynamics of DNA with 2-aminopurine: effects of local environment on fluorescence. , 2001, Biochemistry.

[7]  I. Willner,et al.  Multiplexed analysis of Hg2+ and Ag+ ions by nucleic acid functionalized CdSe/ZnS quantum dots and their use for logic gate operations. , 2009, Angewandte Chemie.

[8]  Shusheng Zhang,et al.  Diagnosis-Therapy Integrative Systems Based on Magnetic RNA Nanoflowers for Co-drug Delivery and Targeted Therapy. , 2017, Analytical chemistry.

[9]  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.

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

[11]  Ye Teng,et al.  A label-free fluorescent molecular beacon based on DNA-Ag nanoclusters for the construction of versatile Biosensors. , 2015, Biosensors & bioelectronics.

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

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

[14]  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.

[15]  J. Feigon,et al.  Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

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

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

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

[19]  J. Stivers,et al.  2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects. , 1998, Nucleic acids research.

[20]  Jun‐Jie Zhu,et al.  Silver Nanoclusters Beacon as Stimuli-Responsive Versatile Platform for Multiplex DNAs Detection and Aptamer-Substrate Complexes Sensing. , 2017, Analytical chemistry.

[21]  N. Ageyama,et al.  CD4+ T Cells Modified by the Endoribonuclease MazF Are Safe and Can Persist in SHIV-infected Rhesus Macaques , 2014, Molecular therapy. Nucleic acids.

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

[23]  Erik Winfree,et al.  Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. , 2010, Nature nanotechnology.

[24]  Kemin Wang,et al.  Powerful Amplification Cascades of FRET-Based Two-Layer Nonenzymatic Nucleic Acid Circuits. , 2016, Analytical chemistry.

[25]  J. B. Alexander Ross,et al.  Emission kinetics of fluorescent nucleoside analogs , 1998, Photonics West - Biomedical Optics.

[26]  Swapnil Bhatia,et al.  A single-layer platform for Boolean logic and arithmetic through DNA excision in mammalian cells , 2017, Nature Biotechnology.

[27]  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.

[28]  Chunhai Fan,et al.  DNA Nanotechnology-Enabled Drug Delivery Systems. , 2018, Chemical reviews.

[29]  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.

[30]  S. Balasubramanian,et al.  DNA molecular motor driven micromechanical cantilever arrays. , 2005, Journal of the American Chemical Society.

[31]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[32]  Kevin W Plaxco,et al.  A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement. , 2005, Journal of the American Chemical Society.

[33]  W. Gilbert,et al.  Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis , 1988, Nature.

[34]  M Guéron,et al.  Intramolecular folding of a fragment of the cytosine-rich strand of telomeric DNA into an i-motif. , 1994, Nucleic acids research.

[35]  Qian Zhou,et al.  Multidimensional optical sensing platform for detection of heparin and reversible molecular logic gate operation based on the phloxine B/polyethyleneimine system. , 2015, Analytical chemistry.

[36]  I. Willner,et al.  Programmed pH-Driven Reversible Association and Dissociation of Interconnected Circular DNA Dimer Nanostructures. , 2016, Nano letters.

[37]  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 .

[38]  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.

[39]  Zhen Gu,et al.  A Two-Stage Dissociation System for Multilayer Imaging of Cancer Biomarker-Synergic Networks in Single Cells. , 2017, Angewandte Chemie.

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

[41]  B. Nordén,et al.  Electronic Transition Moments of 2-Aminopurine , 1997 .

[42]  I. Willner,et al.  DNA sensors and aptasensors based on the hemin/G-quadruplex-controlled aggregation of Au NPs in the presence of L-cysteine. , 2014, Small.

[43]  Juewen Liu,et al.  2-Aminopurine-modified DNA homopolymers for robust and sensitive detection of mercury and silver. , 2017, Biosensors & bioelectronics.

[44]  Lili Shi,et al.  A DNA nanoswitch-controlled reversible nanosensor , 2016, Nucleic acids research.

[45]  Hanadi F Sleiman,et al.  Development of DNA Nanostructures for High-Affinity Binding to Human Serum Albumin. , 2017, Journal of the American Chemical Society.

[46]  Hongtao Yu,et al.  Distinguishing “Looped-Out” and “Stacked-In” DNA Bulge Conformation Using Fluorescent 2-Aminopurine Replacing a Purine Base , 2002, Journal of biomolecular structure & dynamics.

[47]  Tao Li,et al.  Bifunctional colorimetric oligonucleotide probe based on a G-quadruplex DNAzyme molecular beacon. , 2011, Analytical chemistry.