A NOVEL MATRIX ATTACHMENT REGION DNA-BINDING MOTIF IDENTIFIED USING ARANDOM PHAGE PEPTIDE LIBRARY

SATB1 is a nuclear matrix attachment DNA (MAR)-binding protein which i s predominantly expressed in thymocytes. This protein binds to the min or 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 struct ure was used to identify a MAR binding motif of SATB1. One predominant cyclic peptide C1 of CRQNWGLEGC selected by a MAR-affinity column sho wed 50% identity with a segment in SATB1 (amino acids 355-363). Replac ement of the C1 similarity segment in SATB1 by a random amino acid seq uence or its truncation resulted in more than 80% reduction in MAR bin ding. In contrast, replacement of the same SATB1 segment with the C1 p eptide restored full MAR binding activity and specificity as the wild- type protein. Single amino acid mutation of the conserved Arg or Glu r esidue to Ala greatly reduced MAR binding. Taken together our data sho w that a nine amino acid sequence in SATB1 represents a key MAR bindin g motif. Phage display may provide a general tool for rapid identifica tion of DNA binding peptide motifs.