Dedicated to Prof. Dr. Dr. h.c. Wolfgang Pfleiderer on the occasion of his 75th birthday
The automated on-line synthesis of DNA-3'-PNA chimeras 1 ± 4 and (2'-O-methyl-RNA)-3'-PNA chimeras 5 ± 8 is described, in which the 3'-terminal part of the oligonucleotide is linked to the N-terminal part of the PNA via N-(w-hydroxyalkyl)-N-[(thymin-1-yl)acetyl]glycine units (alkyl Et, Ph, Bu, and pentyl). By means of UV thermal denaturation, the binding affinities of all chimeras were directly compared by determining their T m values in the duplex with complementary DNA and RNA. All investigated DNA-3'-PNA chimeras and (2'-Omethyl-RNA)-3'-PNA chimeras form more-stable duplexes with complementary DNA and RNA than the corresponding unmodified DNA. Interestingly, a N-(3-hydroxypropyl)glycine linker resulted in the highest binding affinity for DNA-3'-PNA chimeras, whereas the (2'-O-methyl-RNA)-3'-PNA chimeras showed optimal binding with the homologous N-(4-hydroxybutyl)glycine linker. The duplexes of (2'-O-methyl-RNA)-3'-PNA chimeras and RNA were significantly more stable than those containing the corresponding DNA-3'-PNA chimeras. Surprisingly, we found that the charged (2'-O-methyl-RNA)-3'-PNA chimera with a N-(4hydroxybutyl)glycine-based unit at the junction to the PNA part shows the same binding affinity to RNA as uncharged PNA. Potential applications of (2'-O-methyl-RNA)-3'-PNA chimeras include their use as antisense agents acting by a RNase-independent mechanism of action, a prerequisite for antisense-oligonucleotidemediated correction of aberrant splicing of pre-mRNA.