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Aqueous Computing with DNA Hairpin-Based RAM

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DNA Computing (DNA 2004)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3384))

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Abstract

DNA RAM can eliminate the computational overhead of sequence design because the same RAM can be used for various computations once it is made. In this paper, we report a new method to construct RAM by using the hairpin structure of DNA, and the 4-bit RAM that we actually constructed with this method. We conducted an experiment to distinguish all 16 states of the 4-bit RAM, and another to verify our achievement of a successive writing operation. Finally, we performed aqueous computing with this 4-bit RAM.

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References

  1. Baum, E.B.: Building an Associative Memory Vastly Larger Than the Brain. Science 268, 583–585 (1995)

    Article  Google Scholar 

  2. Reif, J.H., LaBean, T.H., Pirrung, M., Rana, V.S., Guo, B., Kingsford, C., Wickham, G.S.: Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability. In: Jonoska, N., Seeman, N.C. (eds.) DNA 2001. LNCS, vol. 2340, pp. 231–247. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  3. Kashiwamura, S., Yamamoto, M., Kameda, A., Shiba, T., Ohuchi, A.: Hierarchical DNA Memory Based on Nested PCR. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 112–123. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  4. Chen, J., Deaton, R., Wang, Y.: A DNA-based Memory with In Vitro Learning and Associative Recall. In: Chen, J., Reif, J.H. (eds.) DNA 2003. LNCS, vol. 2943, pp. 127–136. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  5. Head, T., Yamamura, M., Gal, S.: Aqueous Computing: Writing on Molecules. In: Proceedings of the Congress on Evolutionary Computation, pp. 1006–1010 (1999)

    Google Scholar 

  6. Head, T., Rozenberg, G., Bladergroen, R.S., Breek, C.K.D., Lommerse, P.H.M., Spaink, H.P.: Computing with DNA by operating on plasmids. BioSystems 57, 87–93 (2000)

    Article  Google Scholar 

  7. Yamamura, M., Hiroto, Y., Matoba, T.: Another Realization of Aqueous Computing with Peptide Nucleic Acid. In: Jonoska, N., Seeman, N.C. (eds.) DNA 2001. LNCS, vol. 2340, pp. 213–222. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  8. Head, T.: Circular Suggestions for DNA Computing. World Scientific, Singapore (1999) (submitted)

    Google Scholar 

  9. Uejima, H., Hagiya, M.: Secondary Structure Design of Multi-state DNA Machine Based on Sequential Structure Transitions. In: Chen, J., Reif, J.H. (eds.) DNA 2003. LNCS, vol. 2943, pp. 80–91. Springer, Heidelberg (2004)

    Google Scholar 

  10. Kameda, A., Yamamoto, M., Uejima, H., Hagiya, M., Sakamoto, K., Ohuchi, A.: Conformational addressing using the hairpin structure of single-strand DNA. In: Chen, J., Reif, J.H. (eds.) DNA 2003. LNCS, vol. 2943, pp. 197–201. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  11. Takahashi, N., Kameda, A., Yamamoto, M., Ohuchi, A.: Construction and verification of DNA hairpin-based RAM. In: Proceedings of The Ninth International Symposium on Artificial Life and Robotics (AROB 9th 2004), vol. 2, pp. 388–391 (2004)

    Google Scholar 

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© 2005 Springer-Verlag Berlin Heidelberg

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Takahashi, N., Kameda, A., Yamamoto, M., Ohuchi, A. (2005). Aqueous Computing with DNA Hairpin-Based RAM. In: Ferretti, C., Mauri, G., Zandron, C. (eds) DNA Computing. DNA 2004. Lecture Notes in Computer Science, vol 3384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11493785_31

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  • DOI: https://doi.org/10.1007/11493785_31

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-26174-2

  • Online ISBN: 978-3-540-31844-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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