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J. Biol. Chem., Vol. 278, Issue 9, 7108-7118, February 28, 2003
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From the GeneTrove Division and Antisense Core Research Department,
Isis Pharmaceuticals, Inc., Carlsbad, California 92008
RNA interference can be considered as an
antisense mechanism of action that utilizes a double-stranded RNase to
promote hydrolysis of the target RNA. We have performed a comparative
study of optimized antisense oligonucleotides designed to work by an
RNA interference mechanism to oligonucleotides designed to work by an
RNase H-dependent mechanism in human cells. The potency,
maximal effectiveness, duration of action, and sequence specificity of
optimized RNase H-dependent oligonucleotides and small
interfering RNA (siRNA) oligonucleotide duplexes were evaluated and
found to be comparable. Effects of base mismatches on activity were
determined to be position-dependent for both siRNA
oligonucleotides and RNase H-dependent oligonucleotides. In
addition, we determined that the activity of both siRNA
oligonucleotides and RNase H-dependent oligonucleotides is
affected by the secondary structure of the target mRNA. To
determine whether positions on target RNA identified as being
susceptible for RNase H-mediated degradation would be coincident with
siRNA target sites, we evaluated the effectiveness of siRNAs designed
to bind the same position on the target mRNA as RNase
H-dependent oligonucleotides. Examination of 80 siRNA
oligonucleotide duplexes designed to bind to RNA from four distinct
human genes revealed that, in general, activity correlated with the
activity to RNase H-dependent oligonucleotides designed to
the same site, although some exceptions were noted. The one major
difference between the two strategies is that RNase H-dependent oligonucleotides were determined to be active
when directed against targets in the pre-mRNA, whereas siRNAs were not. These results demonstrate that siRNA oligonucleotide- and RNase H-dependent antisense strategies are both valid
strategies for evaluating function of genes in cell-based assays.
Efficient Reduction of Target RNAs by Small Interfering
RNA and RNase H-dependent Antisense Agents
A COMPARATIVE ANALYSIS*
,
*
The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
To whom correspondence should be addressed: GeneTrove Division,
Isis Pharmaceuticals, Inc., 2292 Faraday Ave., Carlsbad, CA 92008. Tel.: 760-603-2367; E-mail: tvickers@isisph.com.
Copyright © 2003 by The American Society for Biochemistry and Molecular Biology, Inc.
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