TRINUCLEOTIDE MODELS FOR DNA BENDING PROPENSITY - COMPARISON OF MODELS BASED ON DNASEI DIGESTION AND NUCLEOSOME PACKAGING DATA

DNaseI digestion studies (Brukner et al, EMBO J 14, 1812-1818 1995) an d nucleosome-binding data (Satchwell et al, J. Mol. Biol. 191, 639-659 1986, Goodsell and Dickerson, Nucleic Acids Res. 1. 22, 5497-5503 199 4) provide a possibility to derive bending parameters for trinucleotid es. A detailed comparison of the two models suggests that while both o f them represent improvements with respect to dinucleotide based descr iptions, the individual trinucleotide parameters are not highly correl ated (linear correlation coefficient is 0.53), and a number of moths s uch as TA-elements and CCA/TGG moths are more realistically described in the DNaseI-based model. This may be due to the fact that the DNaseI -based model does not rely on a static geometry but rather captures a dynamic ability of ds DNA to bend towards the major grove. Future refi nement of both models on larger experimental data sets is expected to further improve the prediction of macroscopic DNA-curvature.