Nucleic Acids Research, Vol 27, Issue 10 2135-2144, Copyright © 1999 by Oxford University Press
DA Hill, ML Pedulla and R Reeves
Histone H1, HMG-1 and HMG-I(Y) are mammalian nuclear proteins possessing
distinctive DNA-binding domain structures that share the common property of
preferentially binding to four-way junction (4H) DNA, an in vitro mimic of
the in vivo genetic recombination intermediate known as the Holliday
junction. Nevertheless, these three proteins bind to 4H DNA in vitro with
very different affinities and in a mutually exclusive manner. To
investigate the molecular basis for these distinctive binding
characteristics, we employed base pair resolution hydroxyl radical
footprinting to determine the precise sites of nucleotide interactions of
both HMG-1 and histone H1 on 4H DNA and compared these contacts with those
previously described for HMG-I(Y) on the same substrate. Each of these
proteins had a unique binding pattern on 4H DNA and yet shared certain
common nucleotide contacts on the arms of the 4H DNA molecule near the
branch point. Both the HMG-I(Y) and HMG- 1 proteins made specific contacts
across the 4H DNA branch point, as well as interacting at discrete sites on
the arms, whereas the globular domain of histone H1 bound exclusively to
the arms of the 4H DNA substrate without contacting nucleotides at the
crossover region. Experiments employing the chemical cleavage reagent 1,
10- orthophenanthroline copper(II) attached to the C-terminal end of a
site- specifically mutagenized HMG-I(Y) protein molecule demonstrated that
this protein binds to 4H DNA in a distinctly polar, direction-specific
manner. Together these results provide an attractive molecular explanation
for the observed mutually exclusive 4H DNA-binding characteristics of these
proteins and also allow for critical assessment of proposed models for
their interaction with 4H DNA substrates. The results also have important
implications concerning the possible in vivo roles of HMG-I(Y), histone H1
and HMG-1 in biological processes such as genetic recombination and
retroviral integration.
ARTICLES
Directional binding of HMG-I(Y) on four-way junction DNA and the molecular basis for competitive binding with HMG-1 and histone H1
Department of Biochemistry and Biophysics and Department of Genetics and Cell Biology, Washington State University, Pullman, WA 99164-4660, USA.
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