Synthesis and structural characterization of PNA-DNA quadruplex-forming chimeras

The synthesis and structural characterization of four PNA-DNA chimeras - (5')TGGG(3')-t (C1), (5')TGG(3')-gt (C2), t-(5')GGGT(3') (C3) and tg-(5')GGT(3') (C4), where lower and upper case letters indicate PNA and DNA residues, respectively are reported. The oligomers were synthesized through the use of commercially available Bhoc/Fmoc PNA monomers and 3'- or 5'-phosphoramidite nucleosides as building blocks. All the molecules were studied by H-1 NMR, CD and UV spectroscopy and by molecular modelling. The CD spectra and NMR spectroscopic data of C1 and C3 are typical of quadruplexes involving four parallel strands. Moreover, the UV melting profiles indicate that their thermal stabilities are quite similar to that observed for the reference quadruplex [d(TGGGT)](4). The H-1 NMR spectra of C2 and C4 show that these oligomers are not able to fold into a single, well defined species. (C) Wiley-VCH Verlag GmbH Co.