A mammalian high mobility group protein recognizes any stretch of six A.T base pairs in duplex DNA.
alpha-Protein is a high mobility group protein originally purified from African green monkey cells based on its affinity for the 172-base-pair repeat of monkey alpha-satellite DNA. We have used DNase I footprinting to identify 50 alpha-protein binding sites on simian virus 40 DNA and thereby to determine the DNA binding specificity of this mammalian nuclear protein. alpha-Protein binds with approximately equal affinity to any run of six or more A X T base pairs in duplex DNA, to many, if not all, runs of five A X T base pairs, and to a small number of other sequences within otherwise (A + T)-rich regions. Unlike well characterized sequence-specific DNA binding proteins such as bacterial repressors, alpha-protein makes extensive contacts within the minor groove of B-DNA. These and related findings indicate that, rather than binding to a few specific DNA sequences, alpha-protein recognizes a configuration of the minor groove characteristic of short runs of A X T base pairs. We discuss possible functions of alpha-protein and the similarities in DNA recognition by alpha-protein and the antibiotic netropsin.
Solomon
M J
MJ
Strauss
F
F
Varshavsky
A
A
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002522:Chlorocebus aethiops; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D006147:Guanine / Q000378:metabolism; D006609:High Mobility Group Proteins / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000378:metabolism; D013329:Structure-Activity Relationship
D004268:DNA-Binding Proteins; D006609:High Mobility Group Proteins; D010710:Phosphates; D006147:Guanine; D004247:DNA