Nucleic Acids Research, Vol 25, Issue 17 3523-3531, Copyright © 1997 by Oxford University Press
DA Hill and R Reeves
High mobility group proteins HMG-I(Y) and HMG-1, as well as histone H1, all
share the common property of binding to four-way junction DNA (4H), a
synthetic substrate commonly used to study proteins involved in recognizing
and resolving Holliday-type junctions formed during in vivo genetic
recombination events. The structure of 4H has also been hypothesized to
mimic the DNA crossovers occurring at, or near, the entrance and exit sites
on the nucleosome. Furthermore, upon binding to either duplex DNA or
chromatin, all three of these nuclear proteins share the ability to
significantly alter the structure of bound substrates. In order to further
elucidate their substrate binding abilities, electrophoretic mobility shift
assays were employed to investigate the relative binding capabilities of
HMG-I(Y), HMG-1 and H1 to 4H in vitro. Data indicate a definite hierarchy
of binding preference by these proteins for 4H, with HMG-I(Y) having the
highest affinity (Kd approximately 6.5 nM) when compared with either H1 (Kd
approximately 16 nM) or HMG-1 (Kd approximately 80 nM).
Competition/titration assays demonstrated that all three proteins bind most
tightly to the same site on 4H. Hydroxyl radical footprinting identified
the strongest site for binding of HMG-I(Y), and presumably for the other
proteins as well, to be at the center of 4H. Together these in vitro
results demonstrate that HMG-I(Y) and H1 are co-dominant over HMG-1 for
binding to the central crossover region of 4H and suggest that in vivo both
of these proteins may exert a dominant effect over HMG-1 in recognizing and
binding to altered DNA structures, such as Holliday junctions, that have
conformations similar to 4H.
ARTICLES
Competition between HMG-I(Y), HMG-1 and histone H1 on four-way junction DNA
Department of Biochemistry/Biophysics, Washington State University, Pullman, WA 99164-4660, USA.
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