title: Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes.
abstract: 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 key 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 Beg-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.
authors.affiliation: Howard Hughes Medical Institute, Cambridge, MA.
authors.forename: L
authors.initials: L
authors.lastname: Nekludova
authors.forename: C O
authors.initials: CO
authors.lastname: Pabo
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016335:Zinc Fingers
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA