Design and Synthesis of Imidazole Conjugated PNA and Polypeptides as Nuclease Mimics

Abstract

The imidazole moiety is incorporated on PNA monomers by replacing the base with imidazole. All monomers were characterized by 1H & 13C NMR spectroscopy, mass spectral analysis and other appropriate analytical data. The rationally designed modified PNA monomers have been incorporated into 10-mer pyrimidine and, 9-mer and 12-mer mixed purine- pyrimidine PNA sequence. The PNA oligomers after cleavage were purified by RP-HPLC and characterized by MALDI-TOF spectrometry. Duplexes from all imidazolyl PNAs with complementary antiparallel DNA showed significant destabilisation with all natural nucleobases in cDNA. In case of antiparallel PNA:PNA duplexes, these imidazolyl PNAs showed more stability with complementary G and A PNAs PNAs whereas, T and C PNAs showed significantly less stable duplexes. In case of parallel PNA:PNA duplexes, all imidazolyl PNAs showed G to be more compatible against imidazole modifications and stabilise corresponding duplex better than other three nucleobases A, C and T. The NH-Boc-aminoethyl-N-(imidazole-N1-acetamido) ethyl glycinate and NH-Boc-aminoethyl-N-(imidazole-C4-acetamido) ethyl glycinate monomers showed selective metal complex with Cu2+ and Zn2+ respectively and the thermal stability (Tm) of PNA:PNA duplexes of Im(N1)-PNA 1 and Im(C4)-PNA 2 are significantly increased 5 ºC specifically in presence of Cu2+ and Zn2+ respectively. In triplex and half duplex (UImT10-PNA 4)2:RNA 1, (γCImT10-PNA 5)2:RNA 1 and Bis-Im- PNA 6:RNA 1, the imidazole modified PNAs cleaved 10% RNA 1 in the absence of metal salts and in presence of metal salt cleavage increased upto the 20%. With duplexes UIm-PNA 7:RNA 1/RNA 2 and γCIm-PNA 8:RNA 2/RNA 3, the imidazole modified PNAs did not cleave RNA 2/ RNA 3 in presence or absence of Zn2+ metal ions, but RNA 2/ RNA 3 partial degradation was observed only in presnsce of only Zn2+ ion. Further, the imidazolyl-4-aminoproline peptides were studied for the RNA hydrolysis in presence and absence of metal; however, they did not cause any significant degradation (observed degradation less than 10%) of RNA 1 in the absence or in presence of Zn salt.