Codeword design and information encoding in DNA ensembles

  • Authors:

  • Max H. Garzon;Russell J. Deaton

  • Affiliations:

  • Computer Science, The University of Memphis, Memphis, TN 38152-3240, USA (Author for correspondence, e-mail: mgarzon@memphis.edu);Computer Science and Engineering, The University of Arkansas, Fayetteville, AR 72701, USA

  • Venue:
  • Natural Computing: an international journal
  • Year:
  • 2004

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Abstract

Encoding of information in DNA-, RNA- and other biomolecules is animportant area of research in fields such as DNA computing,bioinformatics, and, conceivably, microbiology and genetics. This surveyfocuses on two fundamental problems, the codeword design problemand the representation problem of abiotic information, formassively parallel processing with DNA molecules. The first problemrequires libraries of DNA sequences to be designed so that specificduplexes are formed during annealing while simultaneously preventingother undesirable hybridizations from occurring in the course of acomputation in the tube. The second involves a search for efficient andcost-effective methods of representing non-biological information in DNAsequences for storage and retrieval of large amouns of data (tera- andpeta-byte scales). Two approaches are treated, namely thermodynamic andcombinatoric-computational. Both experimental and theoretical resultsare described. A reference list of major works in the area is given.Finally, some open problems deemed important for their possible impacton encoding of abiotic information representation and processing arediscussed.