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J. Biol. Chem., Vol. 279, Issue 40, 42230-42239, October 1, 2004

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Structural Features of MicroRNA (miRNA) Precursors and Their Relevance to miRNA Biogenesis and Small Interfering RNA/Short Hairpin RNA Design^*

Jacek Krol, Krzysztof Sobczak, Urszula Wilczynska, Maria Drath, Anna Jasinska, Danuta Kaczynska, and Wlodzimierz J. Krzyzosiak

From the Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland

We have established the structures of 10 human microRNA (miRNA) precursors using biochemical methods. Eight of these structures turned out to be different from those that were computer-predicted. The differences localized in the terminal loop region and at the opposite side of the precursor hairpin stem. We have analyzed the features of these structures from the perspectives of miRNA biogenesis and active strand selection. We demonstrated the different thermodynamic stability profiles for pre-miRNA hairpins harboring miRNAs at their 5'- and 3'-sides and discussed their functional implications. Our results showed that miRNA prediction based on predicted precursor structures may give ambiguous results, and the success rate is significantly higher for the experimentally determined structures. On the other hand, the differences between the predicted and experimentally determined structures did not affect the stability of termini produced through "conceptual dicing." This result confirms the value of thermodynamic analysis based on mfold as a predictor of strand section by RNAi-induced silencing complex (RISC).

Received for publication, May 4, 2004 , and in revised form, July 30, 2004.

^* This work was supported by the State Committee for Scientific Research, Grant 2PO5A08826, PBZ/KBN/040/P04/12, and the Foundation for Polish Science, Grant 8/2000. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. 1–5.

To whom correspondence should be addressed. Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704, Poznan, Poland. Tel.: 48-61-8528503; Fax: 48-61-8520532; E-mail: wlodkrzy{at}ibch.poznan.pl.

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