Digital Information Encoding on DNA

  • Max H. Garzon
  • Kiranchand V. Bobba
  • Bryan P. Hyde
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2950)


Novel approaches to information encoding with DNA are explored using a new Watson-Crick structure for binary strings more appropriate to model DNA hybridization. First, a Gibbs energy analysis of codeword sets is obtained by using a template and extant error-correcting codes. Template-based codes have too low Gibbs energies that allow cross-hybridization. Second, a new technique is presented to construct arbitrarily large sets of noncrosshybridizing codewords of high quality by two major criteria. They have a large minimum number of mismatches between arbitrary pairs of words and alignments; moreover, their pairwise Gibbs energies of hybridization remain bounded within a safe region according to a modified nearest-neighbor model that has been verified in vitro. The technique is scalable to long strands of up to 150-mers, is in principle implementable in vitro, and may be useful in further combinatorial analysis of DNA structures. Finally, a novel method to encode abiotic information in DNA arrays is defined and some preliminary experimental results are discussed. These new methods can be regarded as a different implementation of Tom Head’s idea of writing on DNA molecules [22], although only through hybridization.


Gibbs Energy Strand Length Template Code Base Strand Biomolecular Computation 
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.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Max H. Garzon
    • 1
  • Kiranchand V. Bobba
    • 1
  • Bryan P. Hyde
    • 2
  1. 1.Computer ScienceThe University of MemphisMemphisU.S.A.
  2. 2.SAIC-Scientific Applications International CorporationHuntsvilleU.S.A.

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