Abstract
Molecular computing executed via local interactions of spatially contiguous sets of molecules has potential advantages of (i) speed due to increased local concentration of reacting species, (ii) generally sharper switching behavior and higher precision due to single molecule interactions, (iii) parallelism since each circuit operates independently of the others and (iv) modularity and scalability due to the ability to reuse DNA sequences in spatially separated regions. We propose detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates. The circuits act via enzyme-free DNA hybridization reaction cascades. Our designs include composable OR, AND and propagation Boolean gates, and techniques to achieve higher degree fan-in and fan-out. A biophysical model of localized hybridization reactions is used to estimate the effect of locality on reaction rates. We also use the Visual DSD simulation software in conjunction with localized reaction rates to simulate a localized circuit for computing the square root of a four bit number.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Adleman, L.: Molecular Computation of Solutions to Combinatorial Problems. Science 266(5178), 1021–1024 (1994)
Sherman, W., Seeman, N.: A Precisely Controlled DNA Biped Walking Device. Nano Letters 4, 1203–1207 (2004)
Zhang, D., Turberfield, A., Yurke, B., Winfree, E.: Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA. Science 318, 1121–1125 (2007)
Yin, P., Choi, H., Calvert, C., Pierce, N.: Programming Biomolecular Self-assembly Pathways. Nature 451(7176), 318–322 (2008)
Dirks, R., Pierce, N.: Triggered Amplification by Hybridization Chain Reaction. Proceedings of the National Academy of Sciences of the United States of America 101(43), 15275–15278 (2004)
Sakamoto, K., Kiga, D., Momiya, K., Gouzu, H., Yokoyama, S., Ikeda, S., Sugiyama, H., Hagiya, M.: State Transitions by Molecules. Biosystems, 81–91 (1999)
Qian, L., Winfree, E.: Scaling up Digital Circuit Computation with DNA Strand Displacement Cascades. Science 332(6034), 1196–1201 (2011)
Rothemund, P., Winfree, E.: The Program-Size Complexity of Self-Assembled Squares. In: Symposium on Theory of Computing, pp. 459–468 (2000)
Turberfield, A., Mitchell, J., Yurke, B., Mills, A., Blakey, M., Simmel, F.: DNA Fuel for Free-Running Nanomachines. Physical Review Letters 90(11) (2003)
Seelig, G., Yurke, B., Winfree, E.: Catalyzed Relaxation of a Metastable DNA Fuel. Journal of the American Chemical Society 128(37), 12211–12220 (2006)
He, Y., Liu, D.: Autonomous Multistep Organic Synthesis in a Single Isothermal Solution Mediated by a DNA Walker. Nature Nanotechnology 5(11), 778–782 (2010)
Gu, H., Chao, J., Xiao, S.-J., Seeman, N.: A Proximity-based Programmable DNA Nanoscale Assembly Line. Nature 465(7295), 202–205 (2010)
Yan, H., Park, S.H., Finkelstein, G., Reif, J., LaBean, T.: DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires. Science 301(5641), 1882–1884 (2003)
Rothemund, P.: Folding DNA to Create Nanoscale Shapes and Patterns. Nature 440, 297–302 (2006)
Qian, L., Winfree, E.: A Simple DNA Gate Motif for Synthesizing Large-scale Circuits. DNA Computing, 70–89 (2009)
Cardelli, L.: Two-Domain DNA Strand Displacement. DCM, 47–61 (2010)
Park, S.-H., Yin, P., Liu, Y., Reif, J., LaBean, T., Yan, H.: Programmable DNA Self-assemblies for Nanoscale Organization of Ligands and Proteins. Nano Letters 5, 729–733 (2005)
Pistol, C., Dwyer, C.: Scalable, Low-cost, Hierarchical Assembly of Programmable DNA Nanostructures. Nanotechnology 18, 125305–125309 (2007)
Lin, C., Liu, Y., Yan, H.: Self-Assembled Combinatorial Encoding Nanoarrays for Multiplexed Biosensing. Nano Letters 7(2), 507–512 (2007)
Douglas, S., Dietz, H., Liedl, T., Hogberg, B., Graf, F., Shih, W.: Self-assembly of DNA into Nanoscale Three-dimensional Shapes. Nature 459(7245), 414–418 (2009)
Dietz, H., Douglas, S., Shih, W.: Folding DNA into Twisted and Curved Nanoscale Shapes. Science 325(5941), 725–730 (2009)
Zhang, D.: Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions. DNA 16, 162–175 (2010)
Dirks, R., Bois, J., Schaeffer, J., Winfree, E., Pierce, N.: Thermodynamic Analysis of Interacting Nucleic Acid Strands. SIAM Review 49, 65–88 (2007)
Park, S.H., Pistol, C., Ahn, S.J., Reif, J., Lebeck, A., LaBean, C.D.T.: Finite-Size, Fully Addressable DNA Tile Lattices Formed by Hierarchical Assembly Procedures. Angewandte Chemie International Edition 45(5), 735–739 (2006)
Genot, A., Zhang, D., Bath, J., Turberfield, A.: Remote Toehold: A Mechanism for Flexible Control of DNA Hybridization Kinetics. Journal of American Chemical Society 133(7), 2177–2182 (2011)
Phillips, A., Cardelli, L.: A Programming Language for Composable DNA Circuits. Journal of The Royal Society Interface 6(11), 419–436 (2009)
Zhang, D.Y., Winfree, E.: Control of DNA Strand Displacement Kinetics Using Toehold Exchange. Journal of the American Chemical Society 131(48), 17303–17314 (2009)
Lakin, M., Youssef, S., Cardelli, L., Phillips, A.: Abstractions for DNA Circuit Design. Journal of The Royal Society Interface (in press, 2011)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Chandran, H., Gopalkrishnan, N., Phillips, A., Reif, J. (2011). Localized Hybridization Circuits. In: Cardelli, L., Shih, W. (eds) DNA Computing and Molecular Programming. DNA 2011. Lecture Notes in Computer Science, vol 6937. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23638-9_8
Download citation
DOI: https://doi.org/10.1007/978-3-642-23638-9_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-23637-2
Online ISBN: 978-3-642-23638-9
eBook Packages: Computer ScienceComputer Science (R0)