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Nat Struct Mol Biol. 2006 Sep;13(9):849-51. Epub 2006 Aug 20.

Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions.

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Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, Howard Hughes Medical Institute, 701 W. 168th Street, New York, New York 10032, USA.


We use Caenorhabditis elegans to test proposed general rules for microRNA (miRNA)-target interactions. We show that G.U base pairing is tolerated in the 'seed' region of the lsy-6 miRNA interaction with its in vivo target cog-1, and that 6- to 8-base-pair perfect seed pairing is not a generally reliable predictor for an interaction of lsy-6 with a 3' untranslated region (UTR). Rather, lsy-6 can functionally interact with its target site only in specific 3' UTR contexts. Our findings illustrate the difficulty of establishing generalizable rules of miRNA-target interactions.

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