title: Recognition of diverse sequences by class I zinc fingers: asymmetries and indirect effects on specificity in the interaction between CF2II and A+T-rich elements.
abstract: The Drosophila CF2II protein, which contains zinc fingers of the Cys2His2 type and recognizes an A+T-rich sequence, behaves in cell culture as an activator of a reporter chloramphenicol acetyltransferase gene. This activity depends on C-terminal but not N-terminal zinc fingers, as does in vitro DNA binding. By site-specific mutagenesis and binding site selection, we define the critical amino acid-base interactions. Mutations of single amino acid residues at the leading edge of the recognition helix are rarely neutral: many result in a slight change in affinity for the ideal DNA target site; some cause major loss of affinity; and others change specificity for as many as two bases in the target site. Compared to zinc fingers that recognize G+C-rich DNA, CF2II fingers appear to bind to A+T-rich DNA in a generally similar manner, but with additional flexibility and amino acid-base interactions. The results illustrate how zinc fingers may be evolving to recognize an unusually diverse set of DNA sequences.
authors.affiliation: The Biological Laboratories, Harvard University, Cambridge, MA 02138, USA.
authors.forename: J A
authors.initials: JA
authors.lastname: Gogos
authors.forename: J
authors.initials: J
authors.lastname: Jin
authors.forename: H
authors.initials: H
authors.lastname: Wan
authors.forename: M
authors.initials: M
authors.lastname: Kokkinidis
authors.forename: F C
authors.initials: FC
authors.lastname: Kafatos
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D017931:DNA Primers / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D029721:Drosophila Proteins; D004331:Drosophila melanogaster; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding; D011994:Recombinant Proteins; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry*; D015533:Transcriptional Activation; D016335:Zinc Fingers
chemical_list: D017931:DNA Primers; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D011994:Recombinant Proteins; D014157:Transcription Factors; C076904:Cf2 protein, Drosophila