Synthesis and DNA nicking studies of a novel cyclic peptide: Cyclo[Lys-Trp-Lys-Ahx-]

Two novel cyclic tetrapeptides: cyclo[Lys-Tyr-Lys-Ahx-] 7a and cyclo[Lys-Tr p-Lys-Ahx-] 7b were synthesized by coupling protected amino acid in solutio n and the subsequent cyclization effected by the pentafluorophenyl eater me thod as described in previous papers. These cyclic peptides were designed a nd synthesized to study their interaction with DNA, based on previous repor ts that linear peptides Lys-Tyr-Lys and Lys-Trp-Lys could bind to various f orms of DNA and cleaved supercoiled DNA at apurinic sites. Ethidium bromide displacement assay showed that the apparent DNA binding constant of linear Lys-Tyr-Lys and cyclic peptide 7a are far below 1 x 10(3) M-1, whereas tho se of cyclic peptide 7b and linear Lys-Trp-Lys are 1.9 x 10(4) M-1 and 9.5 x 10(3) M-1, respectively. Kinetic studies using agarose gel electrophoresi s showed that cyclic peptide 7b and Lys-Trp-Lys possessed DNA nicking activ ity on natural supercoiled phi X174 DNA. with nicking rate of 50.7 and 75.6 pM min(-1) at 65 degreesC, respectively, whereas cyclic peptide 7a and line ar Lys-Tyr-Lys were devoid of the corresponding activity. The DNA nicking r ate increased significantly with increase in reaction temperature. At react ion temperatures lower than 65 degreesC, the DNA nicking rate of cyclic pep tide 7b exceeded that of linear Lys-Trp-Lys. The addition of 1 muM ferrous ion did not give significant enhancement effect on the DNA nicking rate by the peptides. UV irradiation gave a marked rate enhancement on the DNA nick ing rate of linear Lys-Trp-Lys and a moderate enhancement on the DNA nickin g rate of cyclic peptide 7b. (C) 2001 Elsevier Science Ltd. Ail rights rese rved.