Modelling DNA Structure from Sequence
Biological thinking in recent years has been profoundly influenced by the idea of local structural polymorphism in DNA. DNA is no longer considered as a featureless polymer but rather as a series of individual domains differing in flexibility and curvature. Local structural polymorphism is expected to contribute to the specificity of various biological events as gene regulation, packaging, for example, through regulating the affinity of protein binding (Travers and Klug, 1990). In contrast to traditional structural polymorphism (e,g, B, A or Z structures), here we deal with a localised micropolymorphism in which the original B-DNA structure is only distorted but is not extensively modified. The DNA segments involved in protein-induced and inherent DNA-bending are 10–50 base pairs in length (Olson and Zhurkin, 1996) i.e. they are longer than what can be easily handled by atomic resolution molecular modelling or quantum mechanical approaches. Traditional elastic models of DNA, that represent DNA as an ideally elastic, homogeneous cylindrical rod, were used to model macroscopic behaviour of long DNA segments, such as supercoiling (Langowski et al., 1996; Olson, 1996). However, local DNA conformations and recognition by DNA-binding proteins are clearly sequence-dependent, so conventional elastic rod models of DNA, which do not explicitly represent the dependence of the elasticity on the base sequence, cannot say much about them. Here we attempt to briefly review advantages and limitations of the rod-models of DNA with particular regard to elastic modelling of local bending phenomena.
KeywordsEntropy Anisotropy Phenol Rubber Electrophoresis
Unable to display preview. Download preview PDF.
- Gabrielian, A., Vlahovicek, K., Munteanu, M. G., Gromiha, M. M., Brukner, I., Sanchez, R. and Pongor, S., 1998, Prediction of Bendability and Curvature in Genomic DNA. In Tenth conversation in biomolecular stereodynamics, pp. 117–132.Google Scholar
- Gromiha, M. M., Munteanu, M. G., Simon, I. and Pongor, S., 1997, The Role of DNA Bending in Cro Protein-DNA Interactions. Biophysical Chemistry, in press.Google Scholar
- Langowski, J., Olson, W. K., Pedersen, S. C., Tobias, I., Westcott, T. P. and Yang, Y., 1996,DNA Supercoiling, Localized Bending and Thermal Fluctuations [Letter]. TrendsBiochem.Sci. 21:50.Google Scholar
- Olson, W. K. and Zhurkin, V. B., 1996, Twenty Years of DNA Bending, In Biological Structure and Dynamics, (Sarma, R. H. and Sarma, M. H., Eds), Adenine Press, Schenectady, pp. 341–370.Google Scholar
- Travers, A. A. and Klug, A., 1990, Bending of DNA, In DNA Topology and Its Biological Effects, (Cozzarelli, N. R. a. W., J.C., Ed.), Cold Spring Harbor laboratory, Cold Spring Harbor, pp. 57–106.Google Scholar
- Zienkiewicz, O. C. a. T., R.L., 1991, The Finite Element Methods. McGraw-Hill.Google Scholar