DISTINCTIVE DNA CONFORMATION WITH ENLARGED MAJOR GROOVE IS FOUND IN ZN-FINGER DNA AND OTHER PROTEIN-DNA COMPLEXES

We have analyzed DNA conformations in a series of protein-DNA complexe s, and we find that a distinctive conformation-with an enlarged major groove-occurs in a number of different complexes. During this analysis , we also developed a simplified model of DNA structure that illustrat es the relative position of (i) the base pairs, (ii) the phosphate bac kbone, and (iii) the double helical axis. This model highlights the ke g structural features of each duplex, facilitating the analysis and co mparison of structures that are distinct from canonical A-DNA or B-DNA . Comparing DNA conformations in this way revealed that an otherwise u nrelated set of protein-DNA complexes have interesting structural simi larities, including an enlarged major groove. We refer to this class o f structures as B-eg-DNA (where eg means enlarged groove). Since relat ed features occur in such a diverse set of protein-DNA complexes, we s uggest that this conformation may have a significant role in protein-D NA recognition.