Questions on plant RNAi

Dr. James J. Campanella via methods%40net.bio.net (by james.campanella from montclair.edu)
Wed Aug 29 08:55:30 EST 2007


Dear Colleagues,

I have several questions about practical plant RNAi to which I have 
been unable to find the answers in the literature. I suspect that 
these questions are mostly naive, but I since none of my colleagues 
here on my own campus work with plant RNAi, I thought I may be able 
to find the answers out here.

First, are there any good practical guides or reviews out there on 
plant RNAi? Most of the literature that I have been able to dig up is 
on animal RNAi which is quite different in terms of RNAi probe design 
and activity. So far, the most practical advice has come from the 
Methods in Enzymology volume on RNAi.

Second, again, there is a great deal of literature on designing the 
short RNAi probes for animals. There are even computer programs to 
help design those short sequences. However, I have been unable to 
come across any advice on choosing the long (300-500 bp) sequences 
needed for plant RNAi.

Third, I am working with a family of plant genes, and I want to be 
able to knock down specific members of that family. What is the 
breakpoint percentage of homology at which you need no longer worry 
about cross-over inhibition against homologues? If the probe is 50% 
homologous to another family member which is not the target, will you 
get knockdown of the homologue? 40%? 30%? Is this even common 
knowledge, or does it come down to finding out these answers by 
practical experiments with your own species and gene family?

Thanks for the help,

Jim Campanella


James J. Campanella,
Associate Professor,
Department of Biology and Molecular Biology
Montclair State University
1 Normal Avenue
Montclair, NJ 07043

Alternate email address: jcamp from alumni.uchicago.edu

Ph: 973-655-4097
Fax: 973-655-7047 



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