Antisense oligonucleotides discriminating between two muscular Na+ channel isoforms.

Various 15-mer antisense oligodeoxynucleotides (aODNs) were constructed against RNAs coding for two closely related isoforms of the voltage-dependent Na+ channel, i.e. those of human heart (hH1) and skeletal (hSkM1) muscle. When translated in vitro, either RNA yielded a 220 kDa band on polyacrylamide gels, indicating that the translation product had full length. Of six different aODN constructs developed against hH1 RNA, two each inhibited translation completely, moderately or not at all, depending on the target position. The specificity of the effect (no cross reaction at 10 microM) was confirmed by incubation with 15-mer aODNs against hSkM1 RNA. The most effective aODNs were those hybridizing between bases 3840 and 3880 of hSkM1 RNA and the homologous segment of hH1 RNA. When either of the RNAs was co-injected with its most effective (phospho rothioate-capped) aODN into Xenopus oocytes, the production of Na+ channels was strongly suppressed (relative INa for hSkM1: 0.08 +/- 0.05 times control, n = 14; for hH1: 0.11 +/- 0.08, n = 11). We conclude that aODNs are able to discriminate between closely related RNAs. The efficacy of an aODN depends strongly on its RNA target position.