Skip to main content

Autonomous Biomolecular Computer Modeled after Retroviral Replication

  • Conference paper
Book cover DNA Computing (DNA 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2943))

Included in the following conference series:

Abstract

We designed a retroviral computer, of which hardware is composed of DNA/RNA dependent DNA polymerase, transcriptase, RNaseH, and DNA and RNA strands. Sequences of DNA strands define functions and RNA single strands work as arguments and return values for each function. In this paper, we show that computational jobs, such as encoding of input data and AND/OR operation, can work on this computer. By combining multiple functions, more complex molecular programs for gene analysis can be constructed. Experimental study showed that some functions were actually executed in vitro autonomously. Since this computer has originally derived from the retrovirus mechanism, we expect an in vivo computer will be realized from this technology, which detects the cell state through gene expression patterns, and controls the cell conditions with output RNA. It may provide a powerful tool for both research and clinical application.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994)

    Article  Google Scholar 

  2. Lipton, R.J.: DNA solution of hard computational problems. Science 268, 542–545 (1995)

    Article  Google Scholar 

  3. Braich, R.S., Chelyapov, N., Johnson, C., Rothemund, P.W., Adleman, L.: Solution ofa 20-variable 3-SAT problem on a DNA computer. Science 296, 499–502 (2002)

    Article  Google Scholar 

  4. Nakajima, T., Sakai, Y., Suyama, A.: Solving a 10-variable 43-clause instance of 3-SAT problems on DNA computer automatically executing a basic instruction set. In: Preliminary Proc. of The Eighth International Meeting on DNA Based Computers, p. 332 (2002)

    Google Scholar 

  5. Suyama, A., Nishida, N., Kurata, K., Omagari, K.: Gene expression analysis by DNA computing. In: Miyano, S., Shamir, R., Takagi, T. (eds.) Currents in Computational Molecular Biology, pp. 12–13. Universal Academy Press, Inc., Tokyo (2000)

    Google Scholar 

  6. Nishida, N., Wakui, M., Tokunaga, K., Suyama, A.: Highly specific and quantitative gene expression profiling based on DNA computing. Genome Informatics 12, 259–260 (2001)

    Google Scholar 

  7. Mills Jr., A.P.: Gene expression profiling diagnosis through DNA molecularcomputation. Trends Biotechnol. 20, 137–140 (2002)

    Article  Google Scholar 

  8. Morimoto, N., Kiyohara, H., Sugimura, N., Karaki, S., Nakajima, T., Makino, T., Nishida, N., Suyama, A.: Automated processing system for gene expression profiling based on DNA computing technologies. In: Preliminary Proc. of The Eighth International Meeting on DNA Based Computers, p. 331 (2002)

    Google Scholar 

  9. Normile, D.: DNA-based computer takes aim at genes. Science 295, 951 (2002)

    Article  Google Scholar 

  10. Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., Shapiro, E.: Programmable and autonomous computing machine made of biomolecules. Nature 414, 430–434 (2001)

    Article  Google Scholar 

  11. Guatelli, J.C., Whitfield, K.M., Kwoh, D.Y., Barringer, K.J., Richman, D.D., Gingeras, T.R.: Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc. Natl. Acad. Sci. USA. 87, 1874–1878 (1990)

    Article  Google Scholar 

  12. Ehricht, R., Kirner, T., Ellinger, T., Foerster, P., McCaskill, J.S.: Monitoring the amplification of CATCH, a 3SR based cooperatively coupled isothermal amplification system, by fluorimetric methods. Nucleic Acids Res. 25, 4697–4699 (1997)

    Article  Google Scholar 

  13. Yoshida, H., Suyama, A.: Solution to 3-SAT by breadth first search. DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society 54, 9–22 (2000)

    MathSciNet  Google Scholar 

  14. Wakui, M., Yamaguchi, A., Sakurai, D., Ogasawara, K., Yokochi, T., Tsuchiya, N., Ikeda, Y., Tokunaga, K.: Genes highly expressed in the early phase of murine graft-versus-host reaction. Biochem. Biophys. Res. Commun. 282, 200–206 (2001)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Nitta, N., Suyama, A. (2004). Autonomous Biomolecular Computer Modeled after Retroviral Replication. In: Chen, J., Reif, J. (eds) DNA Computing. DNA 2003. Lecture Notes in Computer Science, vol 2943. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24628-2_20

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-24628-2_20

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20930-0

  • Online ISBN: 978-3-540-24628-2

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics