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Nucleic Acids Symposium Series 2006 50(1):295-296; doi:10.1093/nass/nrl147
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© 2006 Oxford University Press

Correlation of structure and activity of short hairpin RNA

Slawomir Antoszczyk1,2, Kazunari Taira3 and Yoshio Kato2

1 Department of Bioorganic Chemistry, Center of Molecular and Macromolecular Studies, Polish Academy of Science, Sienkiewicza 112, 90-363 Lodz, Poland, 2 National Istitute of Advanced Industrial Science and Technology (AIST), Central 4, 1-1-1 Higashi, Tsukuba Science City 305-8562, Japan, 3 Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Tokyo 113-8656, Japan

To explore the relationship between the structure of the precursor of short hairpin RNA (shRNA) and the activity of the shRNA-expression vector, 32 kinds of vectors, which expressed shRNAs with different flanking sequences, were tested. Addition of the poly(A) enhanced the activity of shRNA driven by U6 promoter. The activity of poly (A) tagged U6 promoter driven shRNA was lower than that of the CMV promoter driven constructs, in spite of the identical sequence of both transcripts. The result indicated that it is not only the structure but also the cascade of the transcripts that affects the RNAi activity.


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