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PMID: 11726523 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate.

The EMBO journal ·Vol. 20 ·No. 23 ·2001-12-03 ·Pages 6877-88

Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T

Abstract

Duplexes of 21-23 nucleotide (nt) RNAs are the sequence-specific mediators of RNA interference (RNAi) and post-transcriptional gene silencing (PTGS). Synthetic, short interfering RNAs (siRNAs) were examined in Drosophila melanogaster embryo lysate for their requirements regarding length, structure, chemical composition and sequence in order to mediate efficient RNAi. Duplexes of 21 nt siRNAs with 2 nt 3' overhangs were the most efficient triggers of sequence-specific mRNA degradation. Substitution of one or both siRNA strands by 2'-deoxy or 2'-O-methyl oligonucleotides abolished RNAi, although multiple 2'-deoxynucleotide substitutions at the 3' end of siRNAs were tolerated. The target recognition process is highly sequence specific, but not all positions of a siRNA contribute equally to target recognition; mismatches in the centre of the siRNA duplex prevent target RNA cleavage. The position of the cleavage site in the target RNA is defined by the 5' end of the guide siRNA rather than its 3' end. These results provide a rational basis for the design of siRNAs in future gene targeting experiments.

MeSH Terms
Animals Base Sequence Drosophila melanogaster/embryology,genetics Gene Silencing Gene Targeting Molecular Sequence Data Oligonucleotides, Antisense/metabolism RNA/metabolism RNA Processing, Post-Transcriptional RNA, Bacterial/genetics,metabolism RNA, Small Interfering RNA, Untranslated/genetics,metabolism
Chemicals
Oligonucleotides, Antisense RNA I RNA, Bacterial RNA, Small Interfering RNA, Untranslated RNA
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Elbashir S M
Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
Martinez J
Patkaniowska A
Lendeckel W
Tuschl T
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Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
DOI
10.1093/emboj/20.23.6877
Published
2001-12-03
Pages
6877-88
Language
English
Region
England
NLM ID
8208664
PMCID
PMC125328
Subset
IM
External Links
PubMed source DOI: 10.1093/emboj/20.23.6877 PMC Full Text View journal details
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