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From a brief survey of the literature, it seems Kawasaki and Taira have been largely vindicated by the community before and since their paper. The retraction was by Taira alone, Kawasaki refused to co-sign because he maintained the data were valid. From the retraction it seems the reason for the retraction was a lost lab book. Prior to the Kawasaki and ...


3

If gene B makes a protein product, you can try designing a morpholino against the 5'-UTR of gene B. This can prevent translation initiation at the ribosome as the morpholino occludes mRNA entry into the ribosome. You can detect this by western blotting. If gene B makes some sort of regulator RNA, you will need to target expression of gene B at the DNA ...


3

How well is gene A annotated? Do you have the gene A sequence (after post-transcriptional modifications)? If you do, you can order it from a company like DNA2.0 and they will synthesize it for you for like $0.35/base. Then you can transform the cells with this plasmid and do a knockout of gene B by inserting some sequence at the ~200bases overlap. Also, I ...


3

First you should decide whether you want to design an shRNA or use siRNAs. If you want to use shRNA you should look at the rules that "Mad Scientist" mentioned. You can insert mismatches but make sure not to disrupt the secondary structure. You can use RNAFold to verify. shRNA always has issues and you have to optimize your design, test it by realtime ...


1

The answer is in the slides you provided a link to. The key fact is that Craig & Andy did careful controls to show that it was the presence of dsRNA in both the sense control, and in the anti-sense experimental sample that was responsible for the RNAi-mediated knock-down. Actually, Ken Kemphues showed this earlier in a Nature paper (the control also ...



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