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.
KeywordsMajor Groove Isotropic Elastic Model Strand Symmetry Simple Elastic Model Hydrophobic Moment Plot
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