Email updates

Keep up to date with the latest news and content from BMC Research Notes and BioMed Central.

Open Access Open Badges Research article

Improvement of the design and generation of highly specific plant knockdown lines using primary synthetic microRNAs (pri-smiRNAs)

Sandra Niemeier1, Leonardo Alves12 and Thomas Merkle1*

Author Affiliations

1 Institute of Genome Research and Systems Biology, RNA-based Regulation, Faculty of Biology, University of Bielefeld, D-33594 Bielefeld, Germany

2 Current address: John Innes Centre, Dept. of Cell and Developmental Biology, Norwich Research Park, Colney, Norwich NR4 7UH, UK

For all author emails, please log on.

BMC Research Notes 2010, 3:59  doi:10.1186/1756-0500-3-59

Published: 4 March 2010



microRNAs (miRNAs) are endogenous small non-coding RNAs that post-transcriptionally regulate gene expression. In plants, they typically show high complementarity to a single sequence motif within their target mRNAs and act by catalyzing specific mRNA cleavage and degradation. miRNAs are processed from much longer primary transcripts via precursor miRNAs containing fold-back structures. Leaving these secondary structures intact, miRNAs can be re-designed experimentally to target mRNAs of choice.


We designed primary synthetic miRNAs (pri-smiRNAs) on the basis of the primary transcript of the Arabidopsis MIR159A gene by replacing the original miR159a and the corresponding miR159a* with novel sequences, keeping the overall secondary structure as predicted by the program RNAfold. We used the program RNAhybrid to optimize smiRNA design and to screen the complete Arabidopsis transcriptome for potential off-targets. To improve the molecular cloning of the pri-smiRNA we inserted restriction sites in the original MIR159A primary transcript to easily accommodate the smiRNA/smiRNA* DNA fragment. As a proof-of-concept, we targeted the single gene encoding chalcone synthase (CHS) in Arabidopsis. We demonstrate smiRNA(CHS) expression and CHS mRNA cleavage in different transgenic lines. Phenotypic changes in these lines were observed for seed color and flavonol derivatives, and quantified with respect to anthocyanin content. We also tested the effect of mismatches and excess G:U base pairs on knockdown efficiency.


RNAhybrid-assisted design of smiRNAs and generation of pri-smiRNAs using a novel vector containing restriction sites greatly improves specificity and speed of the generation of stable knockdown lines for functional analyses in plants.