Estimation of wedge components in curved DNA

There are growing indications that the inherent curvature of DNA is important in protein–DNA recognition (for reviews see refs 1–3). The 10.5-base-pair (bp) periodicity of some dinucleotides first found in eukaryotic DNA sequences4,5 was interpreted as the expression of curvature of periodic segments of double-stranded DNA, the curvature resulting from co-orientation of periodically spaced 'wedges' between stacked base pairs. The wedge can be decomposed into roll and tilt components, opening towards a groove and a backbone respectively (Fig. 1a), both contributing to DNA curvature (Fig. 1b and c). The largest wedge was estimated to belong to the AA·TT dinucleotides. Recent work6,7 provided new experimental data on synthetic curved DNA. The authors tried to apply the wedge model to their results and met problems in doing so. We have found that taking into account both roll and tilt components of the AA·TT wedge, in the correct ratio, leads to remarkable consistency between the wedge model and the data.

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