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Autonomous programmable DNA nanorobotic devices using DNAzymes

Publication ,  Journal Article
Reif, JH; Sahu, S
Published in: Theoretical Computer Science
April 1, 2009

A major challenge in nanoscience is the design of synthetic molecular devices that run autonomously (that is, without externally mediated changes per work-cycle) and are programmable (that is, their behavior can be modified without complete redesign of the device). DNA-based synthetic molecular devices have the advantage of being relatively simple to design and engineer, due to the predictable secondary structure of DNA nanostructures and the well-established biochemistry used to manipulate DNA nanostructures. However, ideally we would like to minimize the use of protein enzymes in the design of a DNA-based synthetic molecular device. We present the design of a class of DNA-based molecular devices using DNAzyme. These DNAzyme-based devices are autonomous, programmable, and further require no protein enzymes. The basic principle involved is inspired by a simple but ingenious molecular device due to Tian et al. [Y. Tian, Y. He, Y. Chen, P. Yin, C. Mao, A DNAzyme that walks processively and autonomously along a one-dimensional track, Angew. Chem. Intl. Ed. 44 (2005) 4355-4358] that used DNAzyme to traverse on a DNA nanostructure, but was not programmable in the sense defined above (it did not execute computations). Our DNAzyme-based designs include (1) a finite state automaton, DNAzyme FSA that executes finite state transitions using DNAzymes, (2) extensions to it including probabilistic automaton and non-deterministic automaton, and (3) its application as a DNAzyme router for programmable routing of nanostructures on a 2D DNA addressable lattice. Furthermore, we give a medical-related application, DNAzyme doctor that provides transduction of nucleic acid expression: it can be programmed to respond to the underexpression or overexpression of various strands of RNA, with a response by the release of an RNA. (The behavior of our nucleic acid transduction devices is similar to those of the prior paper of Benenson [Y. Benenson, B. Gil, U. Ben-Dor, R. Adar, E. Shapiro, An autonomous molecular computer for logical control of gene expression, Nature 429 (2004) 423-429], but ours have the advantage that they operate without the use of any protein enzymes.). © 2008 Elsevier B.V. All rights reserved.

Duke Scholars

Published In

Theoretical Computer Science

DOI

ISSN

0304-3975

Publication Date

April 1, 2009

Volume

410

Issue

15

Start / End Page

1428 / 1439

Related Subject Headings

  • Computation Theory & Mathematics
  • 49 Mathematical sciences
  • 46 Information and computing sciences
  • 08 Information and Computing Sciences
  • 01 Mathematical Sciences
 

Citation

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Reif, J. H., & Sahu, S. (2009). Autonomous programmable DNA nanorobotic devices using DNAzymes. Theoretical Computer Science, 410(15), 1428–1439. https://doi.org/10.1016/j.tcs.2008.12.003
Reif, J. H., and S. Sahu. “Autonomous programmable DNA nanorobotic devices using DNAzymes.” Theoretical Computer Science 410, no. 15 (April 1, 2009): 1428–39. https://doi.org/10.1016/j.tcs.2008.12.003.
Reif JH, Sahu S. Autonomous programmable DNA nanorobotic devices using DNAzymes. Theoretical Computer Science. 2009 Apr 1;410(15):1428–39.
Reif, J. H., and S. Sahu. “Autonomous programmable DNA nanorobotic devices using DNAzymes.” Theoretical Computer Science, vol. 410, no. 15, Apr. 2009, pp. 1428–39. Scopus, doi:10.1016/j.tcs.2008.12.003.
Reif JH, Sahu S. Autonomous programmable DNA nanorobotic devices using DNAzymes. Theoretical Computer Science. 2009 Apr 1;410(15):1428–1439.
Journal cover image

Published In

Theoretical Computer Science

DOI

ISSN

0304-3975

Publication Date

April 1, 2009

Volume

410

Issue

15

Start / End Page

1428 / 1439

Related Subject Headings

  • Computation Theory & Mathematics
  • 49 Mathematical sciences
  • 46 Information and computing sciences
  • 08 Information and Computing Sciences
  • 01 Mathematical Sciences