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PMID: 15811921 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

The contributions of dsRNA structure to Dicer specificity and efficiency.

RNA (New York, N.Y.) ·Vol. 11 ·No. 5 ·2005-05-00 ·Pages 674-82

Vermeulen A, Behlen L, Reynolds A, Wolfson A, Marshall WS, Karpilow J, Khvorova A

Abstract

Dicer processes long double-stranded RNA (dsRNA) and pre-microRNAs to generate the functional intermediates (short interfering RNAs and microRNAs) of the RNA interference pathway. Here we identify features of RNA structure that affect Dicer specificity and efficiency. The data presented show that various attributes of the 3' end structure, including overhang length and sequence composition, play a primary role in determining the position of Dicer cleavage in both dsRNA and unimolecular, short hairpin RNA (shRNA). We also demonstrate that siRNA end structure affects overall silencing functionality. Awareness of these new features of Dicer cleavage specificity as it is related to siRNA functionality provides a more detailed understanding of the RNAi mechanism and can shape the development of hairpins with enhanced functionality.

MeSH Terms

Base Sequence Cell Line DEAD-box RNA Helicases Endoribonucleases/metabolism Humans Molecular Sequence Data Nucleic Acid Conformation RNA Helicases/metabolism RNA, Double-Stranded/chemistry,genetics,metabolism RNA, Small Interfering/chemistry,genetics,metabolism Ribonuclease III Substrate Specificity

Chemicals

RNA, Double-Stranded RNA, Small Interfering Endoribonucleases DICER1 protein, human Ribonuclease III DEAD-box RNA Helicases RNA Helicases

Authors & Affiliations

7 authors, click to expand affiliations / ORCID

Vermeulen Annaleen

Dharmacon Inc., 2650 Crescent Dr., Suite #100, Lafayette, CO 80026, USA.

Behlen Linda

Reynolds Angela

Wolfson Alexey

Marshall William S

Karpilow Jon

Khvorova Anastasia

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Article Info

Journal

RNA (New York, N.Y.)

Abbr.

RNA

ISSN

1355-8382

DOI

10.1261/rna.7272305

Published

2005-05-00

Epub

2005-00-05

Pages

674-82

Language

English

Region

United States

NLM ID

9509184

PMCID

PMC1370754

Subset

External Links

PubMed source DOI: 10.1261/rna.7272305 PMC Full Text View journal details

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