Molecular logic computing model based on self-assembly of DNA nanoparticles

In this paper, a logic computing model was constructed using a DNA nanoparticle, combined with color change technology of DNA/Au nanoparticle conjugates, and DNA computing. Several important technologies are utilized in this molecular computing model: DNA self-assembly, DNA/Au nanoparticle conjugation, and the color change resulting from Au nanoparticle aggregation. The simple logic computing model was realized by a color change, resulting from changing of DNA self-assembly. Based on this computing model, a set of operations computing model was also established, by which a simple logic problem was solved. To enlarge the applications of this logic nanocomputing system, a molecular detection method was developed for H1N1 virus gene detection.

[1]  Jie Chao,et al.  Dynamic Patterning Programmed by DNA Tiles Captured on a DNA Origami Substrate , 2009, Nature nanotechnology.

[2]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[3]  Evgeny Katz,et al.  Switchable electrode controlled by enzyme logic network system: approaching physiologically regulated bioelectronics. , 2009, Journal of the American Chemical Society.

[4]  Younan Xia,et al.  Cover Picture: Shape‐Controlled Synthesis of Metal Nanocrystals: Simple Chemistry Meets Complex Physics? (Angew. Chem. Int. Ed. 1/2009) , 2009 .

[5]  Lloyd M. Smith,et al.  DNA Computing on Surfaces : the Chemical Implementation , 2000 .

[6]  Ankur Jain,et al.  Heat conduction through a DNA-gold composite. , 2009, Nano letters.

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

[8]  Darko Stefanovic,et al.  A deoxyribozyme-based molecular automaton , 2003, Nature Biotechnology.

[9]  J. Storhoff,et al.  A DNA-based method for rationally assembling nanoparticles into macroscopic materials , 1996, Nature.

[10]  Hao Yan,et al.  Control of Self-Assembly of DNA Tubules Through Integration of Gold Nanoparticles , 2009, Science.

[11]  Erik Winfree,et al.  Catalyzed relaxation of a metastable DNA fuel. , 2006, Journal of the American Chemical Society.

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

[13]  A. Turberfield,et al.  DNA fuel for free-running nanomachines. , 2003, Physical review letters.

[14]  J. Reif,et al.  Logical computation using algorithmic self-assembly of DNA triple-crossover molecules , 2000, Nature.

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

[16]  Faisal A. Aldaye,et al.  Dynamic DNA templates for discrete gold nanoparticle assemblies: control of geometry, modularity, write/erase and structural switching. , 2007, Journal of the American Chemical Society.

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

[18]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[19]  Shi V. Liu Debating controversies can enhance creativity , 2000, Nature.

[20]  Viswanadham Garimella,et al.  Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes , 2004, Nature Biotechnology.

[21]  Faisal A. Aldaye,et al.  Sequential self-assembly of a DNA hexagon as a template for the organization of gold nanoparticles. , 2006, Angewandte Chemie.

[22]  Wensheng Shi,et al.  Fluorescent logic gates chemically attached to silicon nanowires. , 2009, Angewandte Chemie.

[23]  Wojciech Macyk,et al.  Light-driven OR and XOR programmable chemical logic gates. , 2006, Journal of the American Chemical Society.

[24]  A. Paul Alivisatos,et al.  Pyramidal and chiral groupings of gold nanocrystals assembled using DNA scaffolds. , 2009, Journal of the American Chemical Society.

[25]  Itamar Willner,et al.  Concatenated logic gates using four coupled biocatalysts operating in series , 2006, Proceedings of the National Academy of Sciences.

[26]  Russell P. Goodman,et al.  Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication , 2005, Science.

[27]  N. Pierce,et al.  Rewritable Memory by Controllable Nanopatterning of DNA , 2004 .

[28]  P D Kaplan,et al.  DNA solution of the maximal clique problem. , 1997, Science.

[29]  Majid Darehmiraki A New Solution for Maximal Clique Problem based Sticker Model , 2009, Biosyst..

[30]  Evgeny Katz,et al.  Biofuel cell controlled by enzyme logic systems. , 2009, Journal of the American Chemical Society.