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(2′‐ O ‐Methyl‐RNA)‐3′‐PNA Chimeras: A New Class of Mixed Backbone Oligonucleotide Analogues with High Binding Affinity to RNA
Author(s) -
Greiner Beate,
Breipohl Gerhard,
Uhlmann Eugen
Publication year - 2002
Publication title -
helvetica chimica acta
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.74
H-Index - 82
eISSN - 1522-2675
pISSN - 0018-019X
DOI - 10.1002/1522-2675(200209)85:9<2619::aid-hlca2619>3.0.co;2-7
Subject(s) - rna , chemistry , oligonucleotide , dna , linker , chimera (genetics) , microbiology and biotechnology , biochemistry , stereochemistry , gene , biology , computer science , operating system
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 ‐( ω ‐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′‐ O ‐methyl‐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 ‐(4‐hydroxybutyl)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‐oligonucleotide‐mediated correction of aberrant splicing of pre‐mRNA.