Nucleic Acids Research, Vol 25, Issue 14 2888-2896, Copyright © 1997 by Oxford University Press
R Bravieri, T Shiyanova, TH Chen, D Overdier and X Liao
The hepatocyte nuclear factor 3 (HNF-3)/fork head (fkh) family contains a
large number of transcription factors which recognize divergent DNA
sequences via a winged-helix binding motif. In this report we present
studies on the DNA binding properties of winged-helix HNF-3/fkh homologues
1 (HFH-1) and 2 (HFH-2) which recognize a shared DNA binding site with
different affinities. To explore how HFH-1 and HFH-2 proteins recognize
this DNA binding sequence, the binding affinities of these two HFH proteins
toward a series of DNA sites containing a single strand trimer loop
insertion at different positions were studied. This insertion induces a
bend of approximately 80 degrees in the DNA binding site (prebending).
HFH-1 and HFH-2 were shown to recognize DNA sites prebent at many
nucleotide positions on both strands of the DNA sequence. Both HFH-1 and
HFH-2 were more sensitive to mismatch insertions on the sense strand of the
DNA binding site, especially within the AAAATAAC sequence. Our data suggest
that the recognition helix (helix 3) recognizes the AAAATAAC sequence and
that the helix 3/DNA interaction results in bending of the DNA which
narrows the major groove in the AAAATAAC sequence. Furthermore, the binding
affinities of HFH-1 and HFH-2 toward DNA binding sites with base-pair
reversion in the AAAATAAC sequence was also investigated. Different
patterns of response from HFH-1 and HFH-2 to both prebent and base-pair
reverted binding sites was observed. Our results demonstrate that even two
highly conserved members of the winged-helix family may contact the same
DNA sequence differently.
ARTICLES
Different DNA contact schemes are used by two winged helix proteins to recognize a DNA binding sequence
Department of Biochemistry, College of Medicine, University of Illinois, 1819 West Polk Street, Chicago, IL 60612, USA.
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