Preferential binding to DNA sequences of peptides related to a novel XPRK motif.
Two dodecapeptide amines: (WPRK)(3)NH(2)[WR-12] and (YPRK)(3)NH(2)[YR-12], and a 30-mer polypeptide amide (SP-30) were synthesized by solid-phase peptide methodology. DNase I footprinting studies on a 117-mer DNA showed that WR-12 and YR-12 bind selectively to DNA sequences in a manner similar to SP-30 which has a repeating SPK(R)K sequence. The most distinctive blockages seen with all three peptides occur at positions 26-30, 21-24 and 38-45 around sequences 5'-GAATT-3', 5'-TAAT-3' and 5'-AAAACGAC-3', respectively. However, it appears that YR-12 is better able to extend its recognition site to include CG pairs than is SP-30. At low concentrations YR-12 was able to induce enhanced rates of DNase I cleavage at regions surrounding some of its binding sites. To obtain further quantitative data supplementary to the footprinting work, equilibrium binding experiments were performed in which the binding of the two peptides to six decanucleotide duplexes was compared. Scatchard analyses indicated that WR-12 may be more selective for oligomers containing runs of consecutive purines or pyrimidines. On the other hand, YR-12 binds better to d(CTTAGACGTC)- d(GACGTCTAAG) than to the other oligomer duplexes, denoting selectivity for evenly distributed C/G and A/T sequences.
Yang
Chia-Hung
CH
Department of Chemistry, Tunghai Christian University, Taichung, Taiwan 407.
Chou
Ping-Jen
PJ
Luo
Zhen Long
ZL
Chou
I Chun
IC
Chang
Jung-Cheng
JC
Cheng
Chien-Chung
CC
Martin
Christopher R H
CR
Waring
Michael J
MJ
Sheh
Leung
L
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001483:Base Sequence; D004247:DNA / Q000378:metabolism*; D018983:DNA Footprinting; D008969:Molecular Sequence Data; D010455:Peptides / Q000138:chemical synthesis / Q000378:metabolism*; D011485:Protein Binding; D020449:Repetitive Sequences, Amino Acid; D017422:Sequence Analysis, DNA / Q000379:methods
D010455:Peptides; D004247:DNA