How Different DNA Sequences Are Recognized by a DNA-binding Protein: Effects of Partial Proteolysis

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1989 Nov 11

PMID 2685746

Citations 7

Authors

P C Supakar

X Y Zhang

S Githens

R Khan

K C Ehrlich

M Ehrlich

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

The major histocompatibility complex class II promoter-binding protein RFX (NF-X) is a methylated DNA-binding protein.

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PMID: 8413274 PMC: 364743. DOI: 10.1128/mcb.13.11.6810-6818.1993.

RFX1 is identical to enhancer factor C and functions as a transactivator of the hepatitis B virus enhancer.

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PMID: 8413236 PMC: 364696. DOI: 10.1128/mcb.13.10.6375-6384.1993.

Increasing binding of a transcription factor immediately downstream of the cap site of a cytomegalovirus gene represses expression.

Zhang X, Ni Y, Saifudeen Z, Asiedu C, Supakar P, Ehrlich M Nucleic Acids Res. 1995; 23(15):3026-33.

PMID: 7659527 PMC: 307145. DOI: 10.1093/nar/23.15.3026.

Highly repeated sites in the apolipoprotein(a) gene recognized by methylated DNA-binding protein, a sequence-specific DNA-binding protein.

Ehrlich K, Ehrlich M Mol Cell Biol. 1990; 10(9):4957-60.

PMID: 2388631 PMC: 361120. DOI: 10.1128/mcb.10.9.4957-4960.1990.

Binding sites in mammalian genes and viral gene regulatory regions recognized by methylated DNA-binding protein.

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PMID: 2173824 PMC: 332489. DOI: 10.1093/nar/18.21.6253.

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