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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 ...


2

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 ...



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