DNA sequence-specific recognition of peptides incorporating the HPRK and polyamide motifs.
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.
Chang
Jung-Cheng
JC
Department of Chemistry, Tunghai Christian University, 407, ROC, Taichung, Taiwan.
Yang
Chia Hung
CH
Chou
Ping Yen
PY
Yang
Wan Hsu
WH
Chou
I-Chun
IC
Lu
Ching Tai
CT
Lin
Pei Hsuan
PH
Hou
Rolis Chien-Wei
RC
Jeng
Kee-Ching G
KC
Cheng
Chien Chung
CC
Sheh
Leung
L
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*
D000577:Amides; D001426:Bacterial Proteins; D010455:Peptides; C110847:HPr kinase; D017346:Protein Serine-Threonine Kinases