Abstract
Among techniques for conformational analysis of DNA molecules, restrained molecular dynamics and distance geometry are, up to now, most widely used. Both techniques are essentially based on local search strategies which use evaluation criteria that are simplified for pragmatic reasons. In practice, this approach appears to be decreasingly adequate when increasingly complex conformational spaces are dealt with.
These shortcomings can be largely circumvented by employing large-scale search techniques based on non-linear adaption. In particular, we wish to bring into attention the potential of genetic algorithms for conformational analysis of aqueous DNA. It appears that this approach, as compared to aforementioned “traditional” conformational techniques, exhibits significantly better sampling of conformational space, leads to conformations that are not biased by the expert chemist's intuition, and, as a rule, manages to satisfy all experimental constraints imposed within experimental error.
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References
Blommers, M.J.J. Aspects of Loopfolding in DNA Hairpins. PhD thesis, Catholic University of Nijmegen, 1990.
Caruana, R.A. and Schaffer, J.D. Representation and hidden bias: Gray vs. binary coding for genetic algorithms. In Laird, J., editor, Proceedings of the Fifth International Conference on Machine Learning, page 153, San Mateo, CA, 1988. Morgan Kaufmann.
Goldberg, D.E. Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley, Reading, MA, 1989.
Holland, J.H. Adaptation in Natural and Artificial Systems. University of Michigan Press, Ann Arbor, MI, 1975.
Lucasius, C.B., Blommers, M.J.J., Buydens, L.M.C, and Kateman, G. A genetic algorithm for conformational analysis of DNA. In Davis, L., editor, The Genetic Algorithms Handbook. Van Nostrand-Reinhold, 1990. In press.
Macura, S. and Ernst, R.R. Elucidation of cross relaxation in liquids by two-dimensional NMR spectroscopy. Molecular Physics, 41(1):95, 1980.
Metzler, W.J., Hare, D.R., and Pardi, A. Limited sampling of conformational space by the distance geometry algorithm: implications for structures generated from NMR data. Biochemistry, 28:7045, 1989.
Saenger, W. Principles of Nucleic Acid Structure. Springer-Verlag, New York, NY, 1984.
van de Ven, F.J.M. and Hilbers, C.W. Nucleic acids and nuclear magnetic resonance. European Journal of Biochemistry, 178:1, 1988. Review.
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© 1991 Springer-Verlag Berlin Heidelberg
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Lucasius, C.B., Werten, S., van Aert, A.H.J.M., Kateman, G., Blommers, M.J.J. (1991). Conformational analysis of DNA using genetic algorithms. In: Schwefel, HP., Männer, R. (eds) Parallel Problem Solving from Nature. PPSN 1990. Lecture Notes in Computer Science, vol 496. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0029737
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DOI: https://doi.org/10.1007/BFb0029737
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