Design of antisense oligonucleotides stabilized by locked nucleic acids

J Kurreck, E Wyszko, C Gillen… - Nucleic acids …, 2002 - academic.oup.com
J Kurreck, E Wyszko, C Gillen, VA Erdmann
Nucleic acids research, 2002academic.oup.com
The design of antisense oligonucleotides containing locked nucleic acids (LNA) was
optimized and compared to intensively studied DNA oligonucleotides, phosphorothioates
and 2′-O-methyl gapmers. In contradiction to the literature, a stretch of seven or eight DNA
monomers in the center of a chimeric DNA/LNA oligonucleotide is necessary for full
activation of RNase H to cleave the target RNA. For 2′-O-methyl gapmers a stretch of six
DNA monomers is sufficient to recruit RNase H. Compared to the 18mer DNA the …
Abstract
The design of antisense oligonucleotides containing locked nucleic acids (LNA) was optimized and compared to intensively studied DNA oligonucleotides, phosphorothioates and 2′-O-methyl gapmers. In contradiction to the literature, a stretch of seven or eight DNA monomers in the center of a chimeric DNA/LNA oligonucleotide is necessary for full activation of RNase H to cleave the target RNA. For 2′-O-methyl gapmers a stretch of six DNA monomers is sufficient to recruit RNase H. Compared to the 18mer DNA the oligonucleotides containing LNA have an increased melting temperature of 1.5–4°C per LNA depending on the positions of the modified residues. 2′-O-methyl nucleotides increase the Tm by only <1°C per modification and the Tm of the phosphorothioate is reduced. The efficiency of an oligonucleotide in supporting RNase H cleavage correlates with its affinity for the target RNA, i.e. LNA > 2′-O-methyl > DNA > phosphorothioate. Three LNAs at each end of the oligonucleotide are sufficient to stabilize the oligonucleotide in human serum 10-fold compared to an unmodified oligodeoxynucleotide (from t1/2 = ∼1.5 h to t1/2 = ~15 h). These chimeric LNA/DNA oligonucleotides are more stable than isosequential phosphorothioates and 2′-O-methyl gapmers, which have half-lives of 10 and 12 h, respectively.
Oxford University Press