Advertisement

Cellular DNA Computing

  • Zoya Ignatova
  • Karl-Heinz Zimmermann
  • Israel Martínez-Pérez
Chapter

Abstract

Cellular DNA computing investigates computational properties of DNA in its natural environment: the living cell. This chapter reviews some recent DNA computing models which are proposed to work at the cellular level. The first model describes gene synthesis during sexual reproduction in ciliates, while the other models focus on logical control or manipulation of cellular expression patterns.

Keywords

Transition Rule Gene Assembly Input String Computational Gene Signed Graph 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Anderson JC, Magliery TJ, Schultz PG (2002) Exploring the limits of codon and anti-codon size. Chem & Biol 9:237–244CrossRefGoogle Scholar
  2. 2.
    Alton E (2007) Progress and prospects: gene therapy clinical trials (part 1). Gene Ther 14:1439–1447CrossRefGoogle Scholar
  3. 3.
    Bayer T, Smolke C (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotech 23:337–343CrossRefGoogle Scholar
  4. 4.
    Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) An autonomous molecular computer for logical control of gene expression. Nature 414:430–434CrossRefGoogle Scholar
  5. 5.
    Condon A Automata make anti-sense (2004) Nature News Views 429:351–352CrossRefGoogle Scholar
  6. 6.
    Drude I, Drombos V, Vauleon S, Müller S (2007) Drugs made of RNA: development and application of engineered RNAs for gene therapy. Mini Rev Med Chem 7:912–931CrossRefGoogle Scholar
  7. 7.
    Ehrenfeucht A, Harju T, Petre I, Prescott D, Rozenberg G (2003) Formal systems for gene assembly in ciliates. Theoret Comp Sci 292:199–219MATHCrossRefMathSciNetGoogle Scholar
  8. 8.
    Ehrenfeucht A, Harju T, Petre I, Prescott D, Rozenberg G (2004) Computing in Living Cells. Springer, HeidelbergGoogle Scholar
  9. 9.
    Ehrenfeucht A, Harju T, Petre I, Rozenberg G (2002) Characterizing the micronuclear gene patterns in ciliates. Theory Comput Syst 35:501–519MATHCrossRefMathSciNetGoogle Scholar
  10. 10.
    Ehrenfeucht A, Petre I, Prescott D, Rozenberg G (2001) String and graph reduction systems for gene assembly in ciliates. Math Struct Comp Sci 12:113–134MathSciNetGoogle Scholar
  11. 11.
    Freund R, Martin-Vide C, Mitrana V (2002) On some operations on strings suggested by gene assembly in ciliates. New Gen Comp 20:279–293MATHGoogle Scholar
  12. 12.
    Ehrenfeucht A, Harju T, Petre I, Rozenberg G (2002) Gene assembly through cyclic graph decomposition. Theoret Comp Sci 281:325–349MATHCrossRefGoogle Scholar
  13. 13.
    Harju T, Rozenberg G (2003) Computational processes in living cells: gene assembly in ciliates. LNCS 2450:1–20MathSciNetGoogle Scholar
  14. 14.
    Harju T, Li C, Petre I, Rozenberg G (2006) Parallelism in gene assembly. Nat Comp 5:203–223MATHCrossRefMathSciNetGoogle Scholar
  15. 15.
    Hohsaka TY, Ashizuka H, Taira H, Murakami H, Sisido (2001) Incorporation of non-natural amino acids into proteins by using four-base codons in an E. coli in vitro translation system. Biochem 40:11060–11064Google Scholar
  16. 16.
    Hohsaka TY, Ashizuka H, Murakami H, Sisido (2001) Five-base codon for incorporation of non-natural amino acids into proteins. Nucleic Acids Res 29:3646–3651Google Scholar
  17. 17.
    Kari L, Kari J, Landweber LF (1999) Reversible molecular computation in ciliates. In: Karhum J, Maurer H, Păun, Rozenberg G (eds.) Jewels are Forever. Springer, Heidelberg 353–363Google Scholar
  18. 18.
    Landweber LF, Kari L (1998) The evolution of cellular computing: nature’s solution to a computational problem. LNCS 2950:207–216Google Scholar
  19. 19.
    Landweber LF, Kari L, (1999) Universal molecular computation in ciliates. In: Landweber LF, Winfree E (eds.) Evolution as computation. Springer, HeidelbergGoogle Scholar
  20. 20.
    Landweber LF (1999) The evolution of cellular computing. Biol Bull 196:324–326CrossRefGoogle Scholar
  21. 21.
    Martinez-Perez I, Ignatova Z, Gong Z, Zimmermann KH (2007) Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype. BMC Bioinform 8:365CrossRefGoogle Scholar
  22. 22.
    Nakagawa H, Sakamoto K, Sakakibara Y (2006) Development of an in vivo computer based on E. coli. LNCS 3892:203–212Google Scholar
  23. 23.
    Prescott D, Rozenberg G (2002) How ciliates manipulate their own DNA. Nat Comp 1:165–183MATHCrossRefMathSciNetGoogle Scholar
  24. 24.
    Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R, Benenson Y (2007) A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotech 25:795–801CrossRefGoogle Scholar
  25. 25.
    Salmons B, Gunzburg WH (1993) Targeting of retroviral vectors for gene therapy. Human Gene Ther 4:129–141CrossRefGoogle Scholar
  26. 26.
    Tamm I, Wagner M (2006) Anti-sense therapy in clinical oncology: preclinical and clinical experiences. Mol Biotechnol 33:221–238CrossRefGoogle Scholar

Copyright information

© Springer-Verlag US 2008

Authors and Affiliations

  • Zoya Ignatova
    • 1
  • Karl-Heinz Zimmermann
    • 2
  • Israel Martínez-Pérez
    • 2
  1. 1.Cellular BiochemistryMax Planck Institute of BiochemistryMunichGermany
  2. 2.Institute of Computer TechnologyHamburg University of TechnologyGermany

Personalised recommendations