title: Binding of A/T-rich DNA by three high mobility group-like domains in c-Abl tyrosine kinase.
abstract: The c-Abl tyrosine kinase has been shown previously to bind DNA. Using polymerase chain reaction-based binding site-selection methods, no consensus high affinity binding site for c-Abl was found. Instead, oligonucleotides with runs of A/T sequences were isolated, and purified c-Abl was shown to bind A/T-containing oligonucleotides better than those without A/T sequences. DNA binding of c-Abl was dependent on three high mobility group 1-like boxes (HLBs), which bound cooperatively to the A/T-rich oligonucleotides. To distinguish binding to A/T sequences per se from binding to nonspecific DNA with a bend at the A/T-rich region, two oligonucleotides were compared for binding to c-Abl. Both oligonucleotides contained A/T sequences. In one, the A/T motif was part of an 80-mer duplex DNA. In another, the A/T motif was in the duplex arm of an 80-mer "bubble DNA" containing an internal unpaired 20-mer region to provide a flexible hinge. Interestingly, the HLBs of c-Abl bound better to the oligonucleotide containing the bubble, suggesting a higher affinity for bent DNA rather than A/T sequences per se. Taken together, these observations define a new class of DNA binding domains, the HLBs, which do not bind DNA with a high degree of sequence specificity, but may selectively bind to bent DNA or to sequences that are easier to distort.
authors.affiliation: Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0347, USA.
authors.forename: Y J
authors.initials: YJ
authors.lastname: Miao
authors.forename: J Y
authors.initials: JY
authors.lastname: Wang
mesh_terms: D000241:Adenosine / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002460:Cell Line; D004247:DNA / Q000378:metabolism*; D006609:High Mobility Group Proteins / Q000378:metabolism*; D051379:Mice; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016315:Proto-Oncogene Proteins c-abl / Q000378:metabolism*; D016415:Sequence Alignment; D013936:Thymidine / Q000378:metabolism
chemical_list: D006609:High Mobility Group Proteins; D004247:DNA; D016315:Proto-Oncogene Proteins c-abl; D000241:Adenosine; D013936:Thymidine