title: DNA sequence-specific recognition of peptides incorporating the HPRK and polyamide motifs.
abstract: Three peptide amides, HPRK(Py)(4)HPRK-NH(2) (PyH-12), HPRK(Py)(3)HPRK-NH(2) (PyH-11) and HPRK(Py)(2)HPRK-NH(2) (PyH-10), incorporating two HPRK motifs and various 4-amino-1-methylpyrrole-2-carboxylic acid residues (Py) were synthesized by solid-phase peptide methodology. The binding of these three peptides to a 5'-32P-labeled 158-mer DNA duplex (Watson fragment) and to a 5'-32P-labeled 135-mer DNA duplex (complementary Crick fragment) was investigated by quantitative DNase I footprinting. On the 158-mer Watson strand, the most distinctive DNase I blockages seen with all three peptides occur around positions 105-112 and 76-79, corresponding to the sequences 5'-GAGAAAAT-3' and 5'-CGGT-3', respectively. However, on the complementary Crick strand, only PyH-12 strongly discriminates the 5'-TTT-3' site around positions 108-110 whereas both PyH-11 and PyH-10 have moderate binding around positions 102-112 comprising the sequence 5'-ATTTTCTCCTT-3'. Possible bidentate and single interactions of the side-chain functions and alpha-amino protons of the peptides with DNA bases are discussed.
authors.affiliation: Department of Chemistry, Tunghai Christian University, 407, ROC, Taichung, Taiwan.
authors.forename: Jung-Cheng
authors.initials: JC
authors.lastname: Chang
authors.forename: Chia Hung
authors.initials: CH
authors.lastname: Yang
authors.forename: Ping Yen
authors.initials: PY
authors.lastname: Chou
authors.forename: Wan Hsu
authors.initials: WH
authors.lastname: Yang
authors.forename: I-Chun
authors.initials: IC
authors.lastname: Chou
authors.forename: Ching Tai
authors.initials: CT
authors.lastname: Lu
authors.forename: Pei Hsuan
authors.initials: PH
authors.lastname: Lin
authors.forename: Rolis Chien-Wei
authors.initials: RC
authors.lastname: Hou
authors.forename: Kee-Ching G
authors.initials: KC
authors.lastname: Jeng
authors.forename: Chien Chung
authors.initials: CC
authors.lastname: Cheng
authors.forename: Leung
authors.initials: L
authors.lastname: Sheh
mesh_terms: D000577:Amides / Q000378:metabolism*; D020816:Amino Acid Motifs; D001426:Bacterial Proteins; D001483:Base Sequence; D001665:Binding Sites / Q000502:physiology; D018983:DNA Footprinting / Q000379:methods; D008969:Molecular Sequence Data; D010455:Peptides / Q000138:chemical synthesis / Q000235:genetics / Q000378:metabolism*; D017346:Protein Serine-Threonine Kinases / Q000138:chemical synthesis / Q000235:genetics / Q000378:metabolism*
chemical_list: D000577:Amides; D001426:Bacterial Proteins; D010455:Peptides; C110847:HPr kinase; D017346:Protein Serine-Threonine Kinases