A molecular device: A DNA molecular lock driven by the nicking enzymes

Graphical abstract (A) Schematic of YES gate cascade circuit. The logic circuit is composed of substrates YS and Y2 and reporter YR. The 3- and 5-ends of YR were modified with quencher BHQ1 and fluorophore 6-FAM, respectively. The nicking enzyme Nt. AlwI, denoted as E1 in the figure, is used as the input signal of the cascade circuit. (B) YES gate cascade circuit logic symbol and its truth table. (C) Native PAGE analysis of YES gate cascade circuit. The DNA strands involved are labeled above the PAGE. Lane 1–Lane 4 are the substrates of the cascade circuit. In Lane 5, in the presence of an input signal E1, the output products W4 and R are generated. In Lane 6, when the input signal E1 is absent, no output product is generated. In Lane 7, the output product is R. ([S]: [Y1]: [Y2]: [YR] = 4:3:2:1.) (D) Fluorescence kinetics analysis of YES gate cascade circuit. The fluorescent signal is measured once a minute as the substrates are mixed. The input of each curve is marked on the right, where E1 refers to the nicking enzyme Nt. AlwI. In the presence of E1, a significant increase in the fluorescent signal can be observed, as shown in curve 1. However, in the absence of E1, no significant increase in the fluorescent signal is observed, as shown in curve 2. ([S]: [Y1]: [Y2]: [YR] = 4:2:1:1.)

[1]  Kun Wang,et al.  A label-free and universal platform for the construction of an odd/even detector for decimal numbers based on graphene oxide and DNA-stabilized silver nanoclusters. , 2017, Nanoscale.

[2]  Itamar Willner,et al.  Catalytic Nucleic Acids (DNAzymes) as Functional Units for Logic Gates and Computing Circuits: From Basic Principles to Practical Applications , 2015 .

[3]  C. O’Sullivan,et al.  DNA biosensors based on gold nanoparticles-modified graphene oxide for the detection of breast cancer biomarkers for early diagnosis. , 2017, Bioelectrochemistry.

[4]  Xiaogang Qu,et al.  Nucleic acid-mesoporous silica nanoparticle conjugates for keypad lock security operation. , 2013, Chemical communications.

[5]  Zhenyu Lin,et al.  Electrochemiluminescence biosensor for miRNA-21 based on toehold-mediated strand displacement amplification with Ru(phen)32+ loaded DNA nanoclews as signal tags. , 2020, Biosensors & bioelectronics.

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

[7]  Francesco Ricci,et al.  Programmable Bivalent Peptide–DNA Locks for pH-Based Control of Antibody Activity , 2019, ACS central science.

[8]  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.

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

[10]  Igor L. Medintz,et al.  A DNAzyme-mediated logic gate for programming molecular capture and release on DNA origami. , 2016, Chemical communications.

[11]  De-Ming Kong,et al.  Terminal deoxynucleotidyl transferase-activated nicking enzyme amplification reaction for specific and sensitive detection of DNA methyltransferase and polynucleotide kinase. , 2019, Biosensors & bioelectronics.

[12]  Itamar Willner,et al.  Autonomous replication of nucleic acids by polymerization/nicking enzyme/DNAzyme cascades for the amplified detection of DNA and the aptamer-cocaine complex. , 2013, Analytical chemistry.

[13]  Guodong Liu,et al.  Smart engineering of a dual-DNA machine with a high signal-to-noise ratio for one-pot robust and sensitive miRNA signaling. , 2019, Chemical communications.

[14]  F. Simmel,et al.  Principles and Applications of Nucleic Acid Strand Displacement Reactions. , 2019, Chemical reviews.

[15]  Andrew J. Lee,et al.  DNA nanostructures: A versatile lab-bench for interrogating biological reactions , 2019, Computational and structural biotechnology journal.

[16]  Qiang Zhang,et al.  Half adder and half subtractor logic gates based on nicking enzymes , 2019 .

[17]  Fei Ma,et al.  Catalytic Self-Assembly of Quantum Dot-Based MicroRNA Nanosensor Directed by Toehold-Mediated Strand Displacement Cascade. , 2019, Nano letters.

[18]  Penghua Zhang,et al.  Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI , 2007, Nucleic acids research.

[19]  Ralf Seidel,et al.  Efficient preparation of internally modified single-molecule constructs using nicking enzymes , 2010, Nucleic acids research.

[20]  王全立,et al.  DNA nanotechnology , 2003 .

[21]  R. Levine,et al.  DNA computing circuits using libraries of DNAzyme subunits. , 2010, Nature nanotechnology.

[22]  Omer Lustgarten,et al.  A Molecular Secret Sharing Scheme. , 2018, Angewandte Chemie.

[23]  C. Mao,et al.  DNA nanotechnology. , 2004, BioTechniques.

[24]  Yan Du,et al.  Smart Sensing Based on DNA-Metal Interaction Enables a Label-Free and Resettable Security Model of Electrochemical Molecular Keypad Lock. , 2017, ACS sensors.

[25]  Jing Li,et al.  An aptamer-based keypad lock system. , 2012, Chemical communications.

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

[27]  Dhananjay Bhattacharyya,et al.  Unzipping and binding of small interfering RNA with single walled carbon nanotube: a platform for small interfering RNA delivery. , 2012, The Journal of chemical physics.

[28]  Yan Du,et al.  A DNA-based and electrochemically transduced keypad lock system with reset function. , 2012, Chemistry.

[29]  Soumadwip Ghosh,et al.  Spontaneous Unzipping of Xylonucleic Acid Assisted by a Single-Walled Carbon Nanotube: A Computational Study. , 2016, The journal of physical chemistry. B.

[30]  Shalin Shah,et al.  Renewable Time-Responsive DNA Circuits. , 2018, Small.

[31]  C. Mastrangelo,et al.  Self‐Destructing Secured Microchips by On‐Chip Triggered Energetic and Corrosive Attacks for Transient Electronics , 2018, Advanced Materials Technologies.

[32]  Soumadwip Ghosh,et al.  Unzipping of Double-Stranded Ribonucleic Acids by Graphene and Single-Walled Carbon Nanotube: Helix Geometry versus Surface Curvature , 2016 .

[33]  Xiaojun Qu,et al.  A quantum dot-labelled aptamer/graphene oxide system for the construction of a half-adder and half-subtractor with high resettability. , 2017, Chemical communications.

[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]  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.

[36]  Kun Wang,et al.  Reconfigurable and resettable arithmetic logic units based on magnetic beads and DNA. , 2015, Nanoscale.

[37]  Bingzhi Li,et al.  Signal amplification by strand displacement in a carbon dot based fluorometric assay for ATP , 2018, Microchimica Acta.

[38]  Feng Li,et al.  Fluorescence biosensing strategy based on mercury ion-mediated DNA conformational switch and nicking enzyme-assisted cycling amplification for highly sensitive detection of carbamate pesticide. , 2016, Biosensors & bioelectronics.

[39]  Leila Motiei,et al.  Authorizing multiple chemical passwords by a combinatorial molecular keypad lock. , 2013, Journal of the American Chemical Society.

[40]  Peng Zhang,et al.  Nicking enzyme-assisted signal-amplifiable Hg2+ detection using upconversion nanoparticles. , 2019, Analytica chimica acta.

[41]  Yun Xiang,et al.  Target-catalyzed assembly formation of metal-ion dependent DNAzymes for non-enzymatic and label-free amplified ATP detection , 2018, Sensors and Actuators B: Chemical.

[42]  Claude E. Shannon,et al.  Communication theory of secrecy systems , 1949, Bell Syst. Tech. J..

[43]  Igor L Medintz,et al.  Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR. , 2017, ACS sensors.

[44]  Qin Liu,et al.  A Secure Self-Destructing Scheme for Electronic Data , 2010, 2010 IEEE/IFIP International Conference on Embedded and Ubiquitous Computing.

[45]  Mengmeng Yan,et al.  Design of nuclease-based target recycling signal amplification in aptasensors. , 2016, Biosensors & bioelectronics.

[46]  Zai-Sheng Wu,et al.  Sensitive detection of cancer gene based on a nicking-mediated RCA of circular DNA nanomachine , 2017 .

[47]  Jie Chao,et al.  DNA origami cryptography for secure communication , 2019, Nature Communications.

[48]  Carl Prévost-Tremblay,et al.  Antibody-powered nucleic acid release using a DNA-based nanomachine , 2017, Nature Communications.

[49]  Kun Wang,et al.  Autonomous DNA nanomachine based on cascade amplification of strand displacement and DNA walker for detection of multiple DNAs. , 2018, Biosensors & bioelectronics.

[50]  Ovidiu Banias,et al.  Combined Malicious Node Discovery and Self-Destruction Technique for Wireless Sensor Networks , 2009, 2009 Third International Conference on Sensor Technologies and Applications.

[51]  Satoshi Murata,et al.  Unzipping and shearing DNA with electrophoresed nanoparticles in hydrogels. , 2017, Physical chemistry chemical physics : PCCP.

[52]  Bin Wang,et al.  Tabu Variable Neighborhood Search for Designing DNA Barcodes , 2020, IEEE Transactions on NanoBioscience.

[53]  Nicholas J Porubsky,et al.  Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering. , 2017, Journal of the American Chemical Society.

[54]  Baoquan Ding,et al.  A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo , 2018, Nature Biotechnology.

[55]  Kurt V Gothelf,et al.  Chemistries for DNA Nanotechnology. , 2019, Chemical reviews.