Trinucleotide Models for DNA Bending Propensity: Comparison of Models Based on DNaseI Digestion and Nucleosome Packaging Data

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Abstract
DNaseI digestion studies (Brukner et al, EMBO J 14, 1812–1818 1995) and nucleosome-binding data (Satchwell et al, J. Mol. Biol. 191, 639–659 1986, Goodsell and Dickerson, Nucleic Acids Res. 1. 22, 5497–5503 1994) provide a possibility to derive bending parameters for trinucleotides. A detailed comparison of the two models suggests that while both of them represent improvements with respect to dinucleotide based descriptions, the individual trinucleotide parameters are not highly correlated (linear correlation coefficient is 0.53), and a number of motifs such as TA-elements and CCA/TGG motifs 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 refinement of both models on larger experimental data sets is expected to further improve the prediction of macroscopic DNA-curvature.