Skip to main content

DNA-based Cryptography

  • Chapter
Aspects of Molecular Computing

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2950))

Abstract

Recent research has considered DNA as a medium for ultra-scale computation and for ultra-compact information storage. One potential key application is DNA-based, molecular cryptography systems. We present some procedures for DNA-based cryptography based on one-time-pads that are in principle unbreakable. Practical applications of cryptographic systems based on one-time-pads are limited in conventional electronic media by the size of the one-time-pad; however DNA provides a much more compact storage medium, and an extremely small amount of DNA suffices even for huge one-time-pads. We detail procedures for two DNA one-time-pad encryption schemes: (i) a substitution method using libraries of distinct pads, each of which defines a specific, randomly generated, pair-wise mapping; and (ii) an XOR scheme utilizing molecular computation and indexed, random key strings. These methods can be applied either for the encryption of natural DNA or for artificial DNA encoding binary data. In the latter case, we also present a novel use of chip-based DNA micro-array technology for 2D data input and output. Finally, we examine a class of DNA steganography systems, which secretly tag the input DNA and then hide it within collections of other DNA. We consider potential limitations of these steganographic techniques, proving that in theory the message hidden with such a method can be recovered by an adversary. We also discuss various modified DNA steganography methods which appear to have improved security.

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. Barnes, W.M.: PCR amplification of up to 35-kb DNA with high fidelity and high yield from bacteriophage templates. Proc. Natl. Acad. Sci. 91, 2216–2220 (1994)

    Article  Google Scholar 

  3. Baum, E.B.: Building an associative memory vastly larger than the brain. Science 268, 583–585 (1995)

    Article  Google Scholar 

  4. Bell, T., Witten, I.H., Cleary, J.G.: Modeling for Text Compression. ACM Computing Surveys 21(4), 557–592 (1989)

    Article  Google Scholar 

  5. Boneh, D., Dunworth, C., Lipton, R.J.: Breaking DES Using a Molecular Computer. In: Baum, E.B., Lipton, R.J. (eds.) DNA Based Computers. DIMACS: Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, Providence (1996)

    Google Scholar 

  6. Blanchard, A.P., Kaiser, R.J.: High-density oligonucleotide arrays. Biosens. Bioelec. 11, 687–690 (1996)

    Article  Google Scholar 

  7. Boneh, D., Dunworth, C., Lipton, R.J., Sgall, J.: Making DNA computers error resistant. In: Landwaber, L., Baum, E. (eds.) DNA based computer II. DIMACS series in Discrete Math. and Theoretical Comp. Sci, vol. 44 (1999)

    Google Scholar 

  8. Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern, D., Winkler, J., Lockhart, D.J., Morris, M.S., Fodor, S.P.A.: Accessing genetic information with high-density DNA arrays. Science 274, 610–614 (1996)

    Article  Google Scholar 

  9. Cover, T.M., Thomas, J.A.: Elements of Information Theory. John Wiley & Sons, New York (1991)

    Book  MATH  Google Scholar 

  10. Deaton, R., Murphy, R.C., Garzon, M., Franceschetti, D.R., Stevens Jr., S.E.: Good Encodings for DNA-based Solutions to Combinatorial Problems. In: Landwaber, L., Baum, E. (eds.) DNA based computer II. DIMACS series in Discrete Math. and Theoretical Comp. Sci, vol. 44 (1999); Proceedings of the Second Annual Meeting on DNA Based Computers. DIMACS: Series in Discrete Mathematics and Theoretical Computer Science, pp. 1052–1798. American Mathematical Society, Providence (1996)

    Google Scholar 

  11. Deaton, R., Murphy, R.C., Garzon, M., Franceschetti, D.R., Stevens Jr., S.E.: Reliability and efficiency of a DNA-based computation. Phys. Rev. Lett. 80, 417–420 (1998)

    Article  Google Scholar 

  12. Fodor, S., Read, J.L., Pirrung, M.C., Stryer, L., Tsai Lu, A., Solas, D.: Lightdirected spatially addressable parallel chemical synthesis. Science 251, 767–773 (1991)

    Article  Google Scholar 

  13. Frutos, A.G., Thiel, A.J., Condon, A.E., Smith, L.M., Corn, R.M.: DNA Computing at Surfaces: 4 Base Mismatch Word Design. In: Rubin, H., Wood, D. (eds.) DNA based computer III. DIMACS series in Discrete Math. and Theoretical Comp. Sci, vol. 48, p. 238 (1999)

    Google Scholar 

  14. Gray, J.M., Frutos, T.G., Michael Berman, A., Condon, A.E., Lagally, M.G., Smith, L.M., Corn, R.M.: Reducing Errors in DNA Computing by Appropriate Word Design (November 1996)

    Google Scholar 

  15. Grumbach, S., Tahi, F.: A new challenge for compression algorithms: genetic sequences. Inf. Proc. and Management 30(6), 875–886 (1994)

    Article  MATH  Google Scholar 

  16. Guarnieri, F., Fliss, M., Bancroft, C.: Making DNA Add. Science 273, 220–223 (1996)

    Article  Google Scholar 

  17. Gupta, V., Parthasarathy, S., Zaki, M.J.: Arithmetic and Logic Operations with DNA. In: Rubin, H., Wood, D. (eds.) DNA based computer III. DIMACS series in Discrete Math. and Theoretical Comp. Sci, vol. 48, pp. 212–220 (1999)

    Google Scholar 

  18. Hagiya, M., Arita, M., Kiga, D., Sakamoto, K., Yokoyama, S.: Towards Parallel Evaluation and Learning of Boolean μ-Formulas with Molecules. In: Rubin, H., Wood, D. (eds.) DNA based computer III. DIMACS series in Discrete Math. and Theoretical Comp. Sci., vol. 48, pp. 105–114 (1999)

    Google Scholar 

  19. Head, T.: Splicing schemes and DNA. In: Rozenberg, G., Salomaa, A. (eds.) Lindenmayer Systems; Impact on Theoretical computer science and developmental biology, pp. 371–383. Springer, Berlin (1992)

    Google Scholar 

  20. Henikoff, S., Henikoff, J.G.: Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89, 10915–10919 (1992)

    Article  Google Scholar 

  21. Kahn, D.: The Codebreakers. Macmillan, New York (1967)

    Google Scholar 

  22. Klein, J.P., Leete, T.H., Rubin, H.: A biomolecular implementation of logical reversible computation with minimal energy dissipation. In: Kari, L., Rubin, H., Wood, D.H. (eds.) Proceedings 4th DIMACS Workshop on DNA Based Computers, pp. 15–23. University of Pennysylvania, Philadelphia (1998)

    Google Scholar 

  23. Kotera, M., Bourdat, A.G., Defrancq, E., Lhomme, J.: A highly efficient synthesis of oligodeoxyribonucleotides containing the 2’-deoxyribonolactone lesion. J. Am. Chem. Soc. 120, 11810–11811 (1998)

    Article  Google Scholar 

  24. LaBean, T.H., Butt, T.R.: Methods and materials for producing gene libraries, U.S. Patent Number 5,656,467 (1997)

    Google Scholar 

  25. LaBean, T., Kauffman, S.A.: Design of synthetic gene libraries encoding random sequence proteins with desired ensemble characteristics. Protein Science 2, 1249–1254 (1993)

    Article  Google Scholar 

  26. LaBean, T.H., Winfree, E., Reif, J.H.: Experimental Progress in Computation by Self-Assembly of DNA Tilings. DNA Based Computers V (1999)

    Google Scholar 

  27. LaBean, T.H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, H.J.: The construction, analysis, ligation and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122, 1848–1860 (2000)

    Article  Google Scholar 

  28. Li, X., Yang, X., Qi, J., Seeman, N.C.: Antiparallel DNA double crossover molecules as components for nanoconstruction. J. Amer. Chem. Soc. 118, 6131–6140 (1996)

    Article  Google Scholar 

  29. Loewenstern, Y.: Significantly Lower Entropy Estimates for Natural DNA Sequences. In: DCC: Data Compression Conference, pp. 151–161. IEEE Computer Society TCC, Los Alamitos (1997)

    Chapter  Google Scholar 

  30. Mao, C., LaBean, T.H., Reif, J.H., Seeman, N.C.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000)

    Article  Google Scholar 

  31. Mills Jr., A.P., Yurke, B., Platzman, P.M.: Article for analog vector algebra computation. In: Kari, L., Rubin, H., Wood, D.H. (eds.) Proceedings 4th DIMACS Workshop on DNA Based Computers, University of Pennysylvania, Philadelphia, pp. 175–180 (1998)

    Google Scholar 

  32. Mir, K.U.: A Restricted Genetic Alphabet for DNA Computing. In: Proceedings of the Second Annual Meeting on DNA Based Computers, Princeton University (1996); Landwaber, L., Baum, E. (eds.): DNA based computer II. DIMACS series in Discrete Math. and Theoretical Comp. Sci, vol. 44 (1999)

    Google Scholar 

  33. Nevill-Manning, C.G., Witten, I.H.: Protein is Incompressible. In: IEEE Data Compression Conference, pp. 257–266. IEEE Computer Society TCC, Los Alamitos (1999)

    Google Scholar 

  34. Orlian, M., Guarnieri, F., Bancroft, C.: Parallel Primer Extension Horizontal Chain Reactions as a Paradigm of Parallel DNA-Based Computation. In: Rubin, H., Wood, D. (eds.) DNA based computer III. DIMACS series in Discrete Math. and Theoretical Comp. Sci, vol. 48, pp. 142–158 (1999)

    Google Scholar 

  35. Pease, A.C., Solas, D., Sullivan, E.J., Cronin, M.T., Holmes, C.P., Fodor, S.P.: Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl Acad. Sci. USA 91, 5022–5026 (1994)

    Article  Google Scholar 

  36. Reif, J.H.: Local Parallel Biomolecular Computing. In: Rubin, H., Wood, D. (eds.) DNA based computer III. DIMACS series in Discrete Math. and Theoretical Comp. Sci, vol. 48, pp. 243–264 (1999)

    Google Scholar 

  37. Reif, J.H.: Paradigms for Biomolecular Computation. In: Calude, C.S., Casti, J., Dinneen, M.J. (eds.) Unconventional Models of Computation. Springer, Heidelberg (1998)

    Google Scholar 

  38. Reif, J.H.: Parallel Molecular Computation: Models and Simulations. Algorithmica, Special Issue on Computational Biology (1998)

    Google Scholar 

  39. Roberts, S.S.: Turbocharged PCR. Jour. of N.I.H. Research 6, 46–82 (1994)

    Google Scholar 

  40. Rose, J.A., Deaton, R., Garzon, M., Murphy, R.C., Franceschetti, D.R., Stevens Jr., S.E.: The effect of uniform melting temperatures on the efficiency of DNA computing. In: Rubin, H., Wood, D. (eds.) DNA based computer III. DIMACS series in Discrete Math. and Theoretical Comp. Sci., vol. 48, pp. 35–42 (1999)

    Google Scholar 

  41. Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N.V., Goodman, M.F., Rothemund, P.W.K., Adleman, L.M.: A Sticker Based Architecture for DNA Computation. In: Landwaber, L., Baum, E. (eds.) DNA based computer II. DIMACS series in Discrete Math. and Theoretical Comp. Sci, vol. 44, pp. 1–29 (1999)

    Google Scholar 

  42. Schneier, B.: Applied Cryptography: Protocols, Algorithms, and Source Code in C. John Wiley & Sons, Inc., Chichester (1996)

    MATH  Google Scholar 

  43. Storer, J.A.: Data Compression: Methods and Theory. Computer Science Press, Rockville (1988)

    Google Scholar 

  44. Suyama, A.: DNA chips - Integrated Chemical Circuits for DNA Diagnosis and DNA computers (1998)

    Google Scholar 

  45. Taylor, C.T., Risca, V., Bancroft, C.: Hiding messages in DNA microdots. Nature 399, 533–534 (1999)

    Article  Google Scholar 

  46. Winfree, E.: On the Computational Power of DNA Annealing and Ligation. In: Baum, E.B., Lipton, R.J. (eds.) DNA Based Computers. DIMACS: Series in Discrete Mathematics and Theoretical Computer Science, pp. 187–198. American Mathematical Society, Providence (1995)

    Google Scholar 

  47. Winfree, E.: Complexity of Restricted and Unrestricted Models of Molecular Computation. In: Baum, E.B., Lipton, R.J. (eds.) DNA Based Computers. DIMACS: Series in Discrete Mathematics and Theoretical Computer Science, vol. 27, pp. 187–198. American Mathematical Society, Providence (1995)

    Google Scholar 

  48. Winfree, E.: Simulations of Computing by Self-Assembly. In: Proceedings of the Fourth DIMACS Meeting on DNA Based Computing, pp. 213–242 (1998)

    Google Scholar 

  49. Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and Self-Assembly of Two Dimensional DNA Crystals. Nature 394, 539–544 (1998)

    Article  Google Scholar 

  50. Winfree, E., Yang, X., Seeman, N.C.: Universal Computation via Self-assembly of DNA: Some Theory and Experiments. In: Landwaber, L., Baum, E. (eds.) DNA based computer II. DIMACS series in Discrete Math. and Theoretical Comp. Sci, vol. 44, pp. 191–214 (1999)

    Google Scholar 

  51. Ziv, J., Lempel, A.: A universal algorithm for sequential data compression. IEEE Trans. Inf. Theory IT-23, 337–343 (1977)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Gehani, A., LaBean, T., Reif, J. (2003). DNA-based Cryptography. In: Jonoska, N., Păun, G., Rozenberg, G. (eds) Aspects of Molecular Computing. Lecture Notes in Computer Science, vol 2950. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24635-0_12

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-24635-0_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20781-8

  • Online ISBN: 978-3-540-24635-0

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics