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Nucleic Acids Research, 1989, Vol. 17, No. 21 8611-8629
© 1989

MOLECULAR BIOLOGY

How different DNA sequences are recognized by a DNA-binding protein: effects of partial proteolysis

Prakash C. Supakar, Xing-Yang Zhang, Sherwood Githens1, Rana Khan, Kenneth C. Ehrlich2 and Melanie Ehrlich

Department of Biochemistry, Tulane Medical School New Orleans, LA 70112, USA 1Department of Biological Sciences, University of New Orleans New Orleans, LA 70148, USA 2Southem Regional Research Center, US Department of Agriculture, New Orleans LA 70179, USA

Received July 5, 1989. Revised September 22, 1989. Accepted September 22, 1989.

MDBP is a sequence-specific DNA-binding protein from mammals that recognizes a variety of DNA sequences, all of which show much homology to a partially palindromic 14 base-pair consensus sequence. MDBP subjected to limited proteolysis and then incubated with various specific oligonucleotide duplexes yielded two types of complexes. The relative concentrations of these complexes varied greatly depending on how closely the MDBP site matched the consensus sequence. No such DNA sequence-specific differences in the types of complexes formed were seen with intact MDBP. Partial proteolysis also changed the relative affinity of MDBP for several of its binding sites. The nature of the two types of complexes formed from fragmented MDBP and DNA was studied by DNA competition assays, protein titration, site-directed mutagenesis, and dimethyl sulfate and missing base interference assays. The results suggest that, for some specific DNA sequences, half-site interactions with one MDBP subunit predominate and for others, strong interaction of two subunits with both half-sites readily occur.


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