A label-free and enzyme-free system for operating various logic devices using poly(thymine)-templated CuNPs and SYBR Green I as signal transducers.

For the first time by integrating fluorescent polyT-templated CuNPs and SYBR Green I, a basic INHIBIT gate and four advanced logic circuits (2-to-1 encoder, 4-to-2 encoder, 1-to-2 decoder and 1-to-2 demultiplexer) have been conceptually realized under label-free and enzyme-free conditions. Taking advantage of the selective formation of CuNPs on ss-DNA, the implementation of these advanced logic devices were achieved without any usage of dye quenching groups or other nanomaterials like graphene oxide or AuNPs since polyA strands not only worked as an input but also acted as effective inhibitors towards polyT templates, meeting the aim of developing bio-computing with cost-effective and operationally simple methods. In short, polyT-templated CuNPs, as promising fluorescent signal reporters, are successfully applied to fabricate advanced logic devices, which may present a potential path for future development of molecular computations.

[1]  Evgeny Katz,et al.  Majority and minority gates realized in enzyme-biocatalyzed systems integrated with logic networks and interfaced with bioelectronic systems. , 2014, The journal of physical chemistry. B.

[2]  Andreas Offenhäusser,et al.  An electrochemically transduced XOR logic gate at the molecular level. , 2010, Angewandte Chemie.

[3]  Igor L. Medintz,et al.  Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology. , 2016, Nanoscale.

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

[5]  L. Prodi,et al.  Luminescence applied in sensor science , 2011 .

[6]  S. Dong,et al.  DNA-templated Ag nanoclusters as signal transducers for a label-free and resettable keypad lock. , 2013, Chemical communications.

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

[8]  Friedrich C Simmel,et al.  Nucleic acid based molecular devices. , 2011, Angewandte Chemie.

[9]  Yaqing Liu,et al.  Integration of graphene oxide and DNA as a universal platform for multiple arithmetic logic units. , 2014, Chemical communications.

[10]  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.

[11]  Shaojun Dong,et al.  A visible multi-digit DNA keypad lock based on split G-quadruplex DNAzyme and silver microspheres. , 2013, Chemical communications.

[12]  E. Katz Biocomputing - tools, aims, perspectives. , 2015, Current opinion in biotechnology.

[13]  Yaqing Liu,et al.  Enzyme-free and DNA-based multiplexer and demultiplexer. , 2015, Chemical communications.

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

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

[16]  Kemin Wang,et al.  Poly(thymine)-templated fluorescent copper nanoparticles for ultrasensitive label-free nuclease assay and its inhibitors screening. , 2013, Analytical chemistry.

[17]  Wei Hong,et al.  A resettable and reprogrammable DNA-based security system to identify multiple users with hierarchy. , 2014, ACS nano.

[18]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

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

[20]  Takafumi Miyamoto,et al.  Synthesizing biomolecule-based Boolean logic gates. , 2013, ACS synthetic biology.

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

[22]  Uwe Pischel,et al.  Smart molecules at work--mimicking advanced logic operations. , 2010, Chemical Society reviews.

[23]  Changtong Wu,et al.  An enzyme-free and DNA-based Feynman gate for logically reversible operation. , 2015, Chemical communications.

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

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

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

[27]  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.

[28]  Erkang Wang,et al.  Metal nanoclusters: New fluorescent probes for sensors and bioimaging , 2014 .

[29]  Kemin Wang,et al.  Poly(thymine)-templated selective formation of fluorescent copper nanoparticles. , 2013, Angewandte Chemie.

[30]  Z. Li,et al.  A label-free method for detecting biothiols based on poly(thymine)-templated copper nanoparticles. , 2015, Biosensors & bioelectronics.

[31]  Xiao-yan Li,et al.  A sensitive assay for trypsin using poly(thymine)-templated copper nanoparticles as fluorescent probes. , 2015, The Analyst.

[32]  E. Wang,et al.  Transistor functions based on electrochemical rectification. , 2013, Angewandte Chemie.

[33]  R. Breaker,et al.  Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes , 2005, Nature Biotechnology.

[34]  Chen Su,et al.  Enzymatic polymerization of poly(thymine) for the synthesis of copper nanoparticles with tunable size and their application in enzyme sensing. , 2015, Chemical communications.

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

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