title: A novel matrix attachment region DNA binding motif identified using a random phage peptide library.
abstract: SATB1 is a nuclear matrix attachment DNA (MAR)-binding protein which is predominantly expressed in thymocytes. This protein binds to the minor groove specifically recognizing an unusual DNA context exhibited by a specific MAR region with strong base-unpairing propensity. A phage library displaying nonamer random peptides without any built-in structure was used to identify a MAR binding motif of SATB1. One predominant cyclic peptide C1 of CRQNWGLEGC selected by a MAR-affinity column showed 50% identity with a segment in SATB1 (amino acids 355-363). Replacement of the C1 similarity segment in SATB1 by a random amino acid sequence or its truncation resulted in more than 80% reduction in MAR binding. In contrast, replacement of the same SATB1 segment with the C1 peptide restored full MAR binding activity and specificity as the wild-type protein. Single amino acid mutation of the conserved Arg or Glu residue to Ala greatly reduced MAR binding. Taken together our data show that a nine amino acid sequence in SATB1 represents a key MAR binding motif. Phage display may provide a general tool for rapid identification of DNA binding peptide motifs.
authors.affiliation: Cancer Research Center, La Jolla Cancer Research Foundation, California 92037, USA.
authors.forename: B
authors.initials: B
authors.lastname: Wang
authors.forename: L A
authors.initials: LA
authors.lastname: Dickinson
authors.forename: E
authors.initials: E
authors.lastname: Koivunen
authors.forename: E
authors.initials: E
authors.lastname: Ruoslahti
authors.forename: T
authors.initials: T
authors.lastname: Kohwi-Shigematsu
mesh_terms: D000595:Amino Acid Sequence; D001435:Bacteriophages / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D015723:Gene Library; D006801:Humans; D036961:Matrix Attachment Region Binding Proteins; D008969:Molecular Sequence Data; D010455:Peptides / Q000235:genetics; D013601:T-Lymphocytes / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D036961:Matrix Attachment Region Binding Proteins; D010455:Peptides; C076189:SATB1 protein, human; D004247:DNA