Abstract
Information encoding and processing in DNA has proved to be an important problem for biomolecular computing, including the well studied codeword design problem. A lower bound is established for the capacity of DNA to encode information using a combinatorial model of DNA homology given by the so-called h-distance. This bound decreases exponentially with a parameter τ that roughly codes for stringency in reaction conditions. We further introduce a new family of near-optimal codeword sets, so-called shuffle codes. This construction, which is optimal in terms of efficiency, can also be used to produce set of codewords with a given constant GC-content. These codes yield estimates of the capacity of DNA oligonucleotides to store abiotic information in DNA arrays as defined in [11]. Finally, we discuss the sensitivity of the corresponding DNA chip encodings to store and discriminate inputs, including the regions of maximum discrimination and uncertainty.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Adleman, L.: Molecular computation of solutions of combinatorial problems. Science 266, 1021–1024 (1994)
Alon, N., Spencer, J.H.: The Probabilistic Method, 2nd edn., p. 91. John Wiley & Sons Publisher, Chichester (2000)
Arita, M., Kobayashi, S.: DNA Sequence Design Using Templates. New Generation Computing 20(3), 263–277 (2002) See also [14], 205-214
Baum, E.: Building an Associative Memory Vastly larger than the Brain. Science 268, 583–585 (1995)
Brenneman, B., Condon, A.: Sequence Design for Biomolecular Computation (2001) (In press), http://www.cs.ubc.edu/~condon/papers/wordsurvey.ps
Deaton, R.J., Chen, J., Bi, H., Garzon, M., Rubin, H., Wood, D.H.: A PCRbased protocol for In Vitro Selection of Non-crosshybridizing Oligonucleotides. In: [14], pp. 105–114 (2002)
Deaton, R.J., Chen, J., Bi, H., Rose, J.A.: A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides. In: [14], pp. 211–220 (2002b)
Deaton, R., Garzon, M., Murphy, R.E., Rose, J.A., Franceschetti, D.R., Stevens Jr., S.E.: The Reliability and Efficiency of a DNA Computation. Phys. Rev. Lett. 80, 417 (1998)
Garzon, M.H., Deaton, R.J.: Codeword Design and Information Encoding in DNA Ensembles. J. of Natural Computing (2004) (in press)
Garzon, M.H., Bobba, K., Hyde, B.P.: Digital information encoding on DNA. In: Jonoska, N., Păun, G., Rozenberg, G. (eds.) Aspects of Molecular Computing. LNCS, vol. 2950, pp. 152–166. Springer, Heidelberg (2003)
Garzon, M., Blain, D., Bobba, K., Neel, A., West, M.: Self-Assembly of DNAlike structures In-Silico. Genetic Programming and Evolvable Machines 4(2), 185–200 (2003)
Garzon, M., Neathery, P.I., Deaton, R., Murphy, R.C., Franceschetti, D.R., Stevens Jr., S.E.: A New Metric for DNA Computing. In: Proc. 2nd Annual Genetic Programming Conference, pp. 472–478. Morgan Kaufmann, San Francisco (1997)
Garzon, M., Deaton, R., Neathery, P., Murphy, R.C., Franceschetti, D.R., Stevens Jr., E.: On the Encoding Problem for DNA Computing. In: Poster at The Third DIMACS Workshop on DNA-based Computing, U of Pennsylvania. Preliminary Proceedings, pp. 230–237 (1997)
Hagiya, M., Ohuchi, A. (eds.): DNA 2002. LNCS, vol. 2568. Springer, Heidelberg (2003)
King, O.: Bounds for DNA codes with constant GC-content. Journal of Combinatorics 10(1) R33, 13 (2003)
Marathe, A., Condon, A., Corn, R.: On Combinatorial DNA Word Design. In: Winfree, E., Gifford, D.K. (eds.) Proceedings 5th DIMACS Workshop on DNA Based Computers, pp. 75–89. American Mathematical Society (1999)
Roman, J.: The Theory of Error-Correcting Codes. Springer, Berlin (1995)
SantaLucia Jr., J., Allawi, H.T., Seneviratne, P.A.: Improved Nearest Neighbor Paramemeters for Predicting Duplex Stability. Biochemistry 35, 3555–3562 (1990)
Wetmur, J.G.: Physical Chemistry of Nucleic Acid Hybridization. American Mathematical Society DIMACS Series 48(1999), 1–23 (1997)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Phan, V., Garzon, M.H. (2005). The Capacity of DNA for Information Encoding. In: Ferretti, C., Mauri, G., Zandron, C. (eds) DNA Computing. DNA 2004. Lecture Notes in Computer Science, vol 3384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11493785_25
Download citation
DOI: https://doi.org/10.1007/11493785_25
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-26174-2
Online ISBN: 978-3-540-31844-6
eBook Packages: Computer ScienceComputer Science (R0)