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

Proc Natl Acad Sci U S A. 1996 Mar 5;93(5):2159-64. doi: 10.1073/pnas.93.5.2159.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Composition
  • Base Sequence
  • Binding Sites
  • DNA Primers / chemistry
  • DNA-Binding Proteins / chemistry*
  • Drosophila Proteins*
  • Drosophila melanogaster
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Protein Binding
  • Recombinant Proteins
  • Sequence Alignment
  • Transcription Factors / chemistry*
  • Transcriptional Activation
  • Zinc Fingers*

Substances

  • DNA Primers
  • DNA-Binding Proteins
  • Drosophila Proteins
  • Recombinant Proteins
  • Transcription Factors
  • Cf2 protein, Drosophila