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 complexes, 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 illustrates the relative position of (i) the base pairs, (ii) the phosphate backbone, and (iii) the double helical axis. This model highlights the keg structural features of each duplex, facilitating the analysis and comparison of structures that are distinct from canonical A-DNA or B-DNA. Comparing DNA conformations in this way revealed that an otherwise unrelated set of protein-DNA complexes have interesting structural similarities, including an enlarged major groove. We refer to this class of structures as B-eg-DNA (where eg means enlarged groove). Since related features occur in such a diverse set of protein-DNA complexes, we suggest that this conformation may have a significant role in protein-DNA recognition.