Abstract
We use combinatorial analysis to transform a special case of the computational problem of designing RNA base sequences with a given minimal free energy secondary structure into a coding theory question. The function of RNA molecules is largely determined by their molecular form,wh ich in turn is significantly related to the base pairings of the secondary structure. Hence,thi s is crucial initial work in the design of RNA molecules with desired three-dimensional structures and specific functional properties. The biological importance of RNA only continues to grow with the discoveries of many different RNA molecules having vital functions other than mediating the production of proteins from DNA. Furthermore,RNA has the same potential as DNA in terms of nanotechnology and biomolecular computing.
This material is based upon work supported by the U.S. National Science Foundation under Grant No. 0130108,by the National Sciences and Engineering Research Council of Canada,a nd by GenTel Corp.
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References
K. Komiya, K. Sakamoto, H. Gouzu, S. Yokoyama, M. A. A. Nishikawa, and M. Hagiya. Successive state transitions with I/O interface by molecules. In Preliminary Proc. 6th Intl. Meeting on DNA Based Computers,pages 21–30, June 2000.
D. Mathews, J. Sabina, M. Zuker, and D. Turner. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol.,288:911–940, 1999.
J. SantaLucia Jr. A unified view of polymer,dum bbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA,95:1460–1465, 1998.
P. Schuster, W. Fontana, P. Stadler,and I. Hofacker. From sequences to shapes and back: a case study in RNA secondary structures. Proc R Soc Lond B Biol Sci,255( 1344):279–284, 1994.
N. Seeman. De novo design of sequences for nucleic acid structural engineering. Journal of Biomolecular Structure and Dynamics,8( 3):573–581, 1990.
M. Serra, D. Turner, and S. Freier. Predicting thermodynamic properties of RNA. Meth. Enzymol.,259:243–261, 1995.
R. P. Stanley. Enumerative combinatorics. Vol. 2. Cambridge University Press, Cambridge,1999. With a foreword by Gian-Carlo Rota and appendix 1 by Sergey Fomin.
E. Winfree, F. Liu, L. Wenzler,and N. Seeman. Design and self-assembly of 2D DNA crystals. Nature,394:539–544, August 1998.
H. Yan, X. Zhang, Z. Shen,and N. C. Seeman. A robust DNA mechanical device controlled by hybridization topology. Nature,415:62–65, 2002.
M. Zuker, D. Mathews, and D. Turner. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In J. Barciszewski and B. Clark,editors, RNA Biochemistry and Biotechnology,NATO ASI Series, pages 11–43. Kluwer Academic Publishers,1999.
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Heitsch, C.E., Condon, A.E., Hoos, H.H. (2003). From RNA Secondary Structure to Coding Theory: A Combinatorial Approach. In: Hagiya, M., Ohuchi, A. (eds) DNA Computing. DNA 2002. Lecture Notes in Computer Science, vol 2568. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36440-4_19
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DOI: https://doi.org/10.1007/3-540-36440-4_19
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