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Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions.

Abstract：

:Contradictory reports in the literature have emphasised either the sequence of small interfering RNAs (siRNA) or the structure of their target molecules to be the major determinant of the efficiency of RNA interference (RNAi) approaches. In the present study, we analyse systematically the contributions of these parameters to siRNA activity by using deliberately designed mRNA constructs. The siRNA target sites were included in well-defined structural elements rendering them either highly accessible or completely involved in stable base-pairing. Furthermore, complementary sequence elements and various hairpins with different stem lengths and designs were used as target sites. Only one of the strands of the siRNA duplex was found to be capable of silencing via its respective target site, indicating that thermodynamic characteristics intrinsic to the siRNA strands are a basic determinant of siRNA activity. A significant obstruction of gene silencing by the same siRNA, however, was observed to be caused by structural features of the substrate RNA. Bioinformatic analysis of the mRNA structures suggests a direct correlation between the extent of gene-knockdown and the local free energy in the target region. Our findings indicate that, although a favourable siRNA sequence is a necessary prerequisite for efficient RNAi, complex target structures may limit the applicability even of carefully chosen siRNAs.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Schubert S,Grünweller A,Erdmann VA,Kurreck J

doi

10.1016/j.jmb.2005.03.011

keywords:

subject

Has Abstract

pub_date

2005-05-13 00:00:00

pages

883-93

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(05)00269-X

journal_volume

348

pub_type

杂志文章

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