Digital production, transmission and storage have revolutionized how we access and use information but have also made archiving an increasingly complex task that requires active, continuing maintenance of digital media. This challenge has focused some interest on DNA as an attractive target for information storage because of its capacity for high-density information encoding, longevity under easily achieved conditions and proven track record as an information bearer. Previous DNA-based information storage approaches have encoded only trivial amounts of information or were not amenable to scaling-up, and used no robust error-correction and lacked examination of their cost-efficiency for large-scale information archival. Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2 × 10(6) bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade.

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

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Molecular Biology of the Gene.

: Significant progress has been made with solution of location problems and in preprocessing and decomposition for discrete optimization. There has also been research on the application of techniques from combinational optimization to nonlinear problems.

http://www.dtic.mil/dtic/tr/fulltext/u2/a273552.pdf

Discrete Applied Mathematics

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Computation in Living Cells: Gene Assembly in Ciliates

This paper provides an overview of existing approaches to encoding information on DNA strands for biocomputing, with a focus on the notion of Watson---Crick (WK) palindromes. We obtain a closed form for, as well as several properties of WK palindromes: The set of WK-palindromes is dense, context-free, but not regular, and is in general not closed under catenation and insertion. We obtain some properties that link the WK palindromes to classical notions such as that of primitive words. For example we show that the set of WK-palindromic words that cannot be written as the product of two nonempty WK-palindromes equals the set of primitive WK-palindromes. We also investigate various simultaneous Watson---Crick conjugate equations of words and show that the equations have, in most cases, only Watson---Crick palindromic solutions. Our results hold for more general functions, such as arbitrary morphic and antimorphic involutions.

Watson---Crick palindromes in DNA computing

This paper is a theoretical study of notions in combinatorics of words motivated by information being encoded as DNA strands in DNA computing. We generalize the classical notions of conjugacy and commutativity of words to incorporate the notion of an involution function, a formalization of the Watson-Crick complementarity of DNA single-strands. We define and study properties of Watson-Crick conjugate and commutative words, as well as Watson-Crick palindromes. We obtain, for example, a complete characterization of the set of all words that are notWatson-Crick palindromes. Our results hold for more general functions, such as arbitrary morphic and antimorphic involutions. They generalize classical results in combinatorics of words, while formalizing concepts meaningful for DNA computing experiments.

Watson-Crick conjugate and commutative words

The set of all sequences that are generated by a biomolecular protocol forms a language over the four letter alphabet Δ={A,G,C,T}. This alphabet is associated with a natural involution mapping θ, A↦ T and G↦ C which is an antimorphism of Δ*. In order to avoid undesirable Watson-Crick bonds between the words (undesirable hybridization), the language has to satisfy certain coding properties. In this paper we build upon the study initiated in [11] and give necessary and sufficient conditions for a finite set of “good” code words to generate (through concatenation) an infinite set of “good” code words with the same properties. General methods for obtaining sets of “good” code words are described. Also we define properties of a splicing system such that the language generated by the system preserves the desired properties of code words.

Languages of DNA Based Code Words

For an involution ? : ?* ? ?* over a finite alphabet ? we consider involution codes: ?-infix, ?-comma-free, ?-k -codes and ?-subword-k-codes. These codes arise from questions on DNA strand design. We investigate conditions under which both X and X+ are same type of involution codes. General methods for generating such involution codes are given. The information capacity of these codes show to be optimized in most cases. A specific set of these codes was chosen for experimental testing and the results of these experiments are presented.

Kalpana Mahalingam

Papers

Watson---Crick palindromes in DNA computing

Watson-Crick conjugate and commutative words

Languages of DNA Based Code Words

Involution codes: with application to DNA coded languages

Generating DNA Code Words.