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