Connectable DNA logic gates: OR and XOR logics.

Modern computer processors are based on semiconductor logic gates connected to each other in complex circuits. This study contributes to the development of a new class of connectable logic gates made of DNA in which the transfer of oligonucleotide fragments as input/output signals occurs upon hybridization of DNA sequences. The DNA strands responsible for a logic function form associates containing immobile DNA four-way junction structures when the signal is high and dissociate into separate strands when the signal is low. A basic set of logic gates (NOT, AND, and OR) was designed. Two NOT gates, two AND gates, and an OR gate were connected in a network that corresponds to an XOR logic function. The design of the logic gates presented here may contribute to the development of the first biocompatible molecular computer.

[1]  Colin D. Medley,et al.  Molecular engineering of DNA: molecular beacons. , 2009, Angewandte Chemie.

[2]  Nicolas H Voelcker,et al.  Sequence-addressable DNA logic. , 2008, Small.

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

[4]  A. Prasanna de Silva,et al.  Chemical approaches to nanometre-scale logic gates , 2006 .

[5]  Yaakov Benenson,et al.  Biocomputers: from test tubes to live cells. , 2009, Molecular bioSystems.

[6]  Fan Yang,et al.  Colorimetric logic gates for small molecules using split/integrated aptamers and unmodified gold nanoparticles. , 2011, Chemical communications.

[7]  Sanjay Tyagi,et al.  Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. , 2006, Clinica chimica acta; international journal of clinical chemistry.

[8]  Daoben Zhu,et al.  Fluorescence logic-signal-based multiplex detection of nucleases with the assembly of a cationic conjugated polymer and branched DNA. , 2009, Angewandte Chemie.

[9]  Uwe Pischel,et al.  Chemische Strategien für den Aufbau molekularer Logikelemente zur Addition und Subtraktion , 2007 .

[10]  Xuemei Li,et al.  Multiplexed sensing of mercury(II) and silver(I) ions: a new class of DNA electrochemiluminescent-molecular logic gates. , 2011, Biosensors & bioelectronics.

[11]  Nadrian C. Seeman,et al.  An Overview of Structural DNA Nanotechnology , 2007, Molecular biotechnology.

[12]  De-Ming Kong,et al.  Design of a fluorescent DNA IMPLICATION logic gate and detection of Ag+ and cysteine with triphenylmethane dye/G-quadruplex complexes. , 2010, Biosensors & bioelectronics.

[13]  D. Kolpashchikov,et al.  Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids. , 2011, Chemistry.

[14]  Philip Ball,et al.  Chemistry meets computing , 2000, Nature.

[15]  W. Bloch,et al.  Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres , 2005, Nucleic acids research.

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

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

[19]  D. Lilley,et al.  Structures of helical junctions in nucleic acids , 2000, Quarterly Reviews of Biophysics.

[20]  Dmitry M Kolpashchikov,et al.  Molecular logic gates connected through DNA four-way junctions. , 2010, Angewandte Chemie.

[21]  Chunhai Fan,et al.  Construction of molecular logic gates with a DNA-cleaving deoxyribozyme. , 2006, Angewandte Chemie.

[22]  Gang Bao,et al.  Hybridization kinetics and thermodynamics of molecular beacons. , 2003, Nucleic acids research.

[23]  Milan N Stojanovic,et al.  Networking particles over distance using oligonucleotide-based devices. , 2007, Journal of the American Chemical Society.

[24]  P. Rothemund Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[25]  D. Ye,et al.  Molecular beacons: an optimal multifunctional biological probe. , 2008, Biochemical and biophysical research communications.

[26]  Milan N Stojanovic,et al.  Molecular computing with deoxyribozymes. , 2008, Progress in nucleic acid research and molecular biology.

[27]  Sai Bi,et al.  Colorimetric logic gates based on supramolecular DNAzyme structures. , 2010, Angewandte Chemie.

[28]  A. P. de Silva,et al.  Molecular logic gates and luminescent sensors based on photoinduced electron transfer. , 2011, Topics in current chemistry.

[29]  Darko Stefanovic,et al.  Deoxyribozyme-based logic gates. , 2002, Journal of the American Chemical Society.

[30]  Hao Yan,et al.  DNA origami: a history and current perspective. , 2010, Current opinion in chemical biology.

[31]  Sanjay Tyagi,et al.  Molecular Beacons: Probes that Fluoresce upon Hybridization , 1996, Nature Biotechnology.

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

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

[34]  C. Yang,et al.  Molekulartechnische DNA‐Modifizierung: Molecular Beacons , 2009 .

[35]  E. Wang,et al.  G-quadruplex DNAzyme based molecular catalytic beacon for label-free colorimetric logic gates. , 2011, Biomaterials.

[36]  Friedrich C. Simmel,et al.  Nukleinsäure‐basierte molekulare Werkzeuge , 2011 .

[37]  N. Seeman,et al.  Symmetric immobile DNA branched junctions. , 1993, Biochemistry.

[38]  R. Brow,et al.  Structure of GeO2–P2O5 glasses studied by x-ray and neutron diffraction , 2006, Journal of physics. Condensed matter : an Institute of Physics journal.

[39]  A. P. de Silva,et al.  Molecular-scale logic gates. , 2004, Chemistry.

[40]  D. Kolpashchikov,et al.  A Single Molecular Beacon Probe Is Sufficient for the Analysis of Multiple Nucleic Acid Sequences , 2010, Chembiochem : a European journal of chemical biology.

[41]  N. Seeman,et al.  Holliday junction crossover topology. , 1994, Journal of molecular biology.

[42]  Uwe Pischel,et al.  Chemical approaches to molecular logic elements for addition and subtraction. , 2007, Angewandte Chemie.

[43]  D. Chan,et al.  Crystal violet as a fluorescent switch-on probe for i-motif: label-free DNA-based logic gate. , 2011, The Analyst.

[44]  Dmitry M Kolpashchikov,et al.  A binary DNA probe for highly specific nucleic Acid recognition. , 2006, Journal of the American Chemical Society.

[45]  Albert Paul Malvino,et al.  Digital computer electronics , 1977 .

[46]  Jing Yang,et al.  Circular DNA logic gates with strand displacement. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[47]  N. Seeman Nanomaterials based on DNA. , 2010, Annual review of biochemistry.

[48]  Wataru Yoshida,et al.  Photonic Boolean logic gates based on DNA aptamers. , 2007, Chemical communications.

[49]  Erik Winfree,et al.  Thermodynamic Analysis of Interacting Nucleic Acid Strands , 2007, SIAM Rev..

[50]  Andrew D. Hamilton,et al.  Digital analysis of protein properties by an ensemble of DNA quadruplexes. , 2009, Journal of the American Chemical Society.

[51]  J. Macdonald,et al.  Deoxyribozyme-based ligase logic gates and their initial circuits. , 2005, Journal of the American Chemical Society.

[52]  Brian M. Frezza,et al.  Modular multi-level circuits from immobilized DNA-based logic gates. , 2007, Journal of the American Chemical Society.

[53]  Young Jun Seo,et al.  Quencher-free molecular beacons: a new strategy in fluorescence based nucleic acid analysis. , 2008, Chemical Society reviews.

[54]  J. Cha,et al.  Recent advances in DNA-based directed assembly on surfaces. , 2010, Nanoscale.

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

[56]  Y. Chai,et al.  A reagentless and disposable electronic genosensor: from multiplexed analysis to molecular logic gates. , 2011, Chemical communications.

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

[58]  N. Sugimoto,et al.  DNA logic gates based on structural polymorphism of telomere DNA molecules responding to chemical input signals. , 2006, Angewandte Chemie.