Fwd: Re: [Arabidopsis] Questions on plant RNAi

Dr. James J. Campanella via arab-gen%40net.bio.net (by james.campanella from montclair.edu)
Thu Aug 30 06:48:52 EST 2007


>Date: Wed, 29 Aug 2007 22:19:10 +0000
>From: Vicki Vance <vance from biol.sc.edu>
>Subject: Re: [Arabidopsis] Questions on plant RNAi
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>To: "Dr. James J. Campanella" <campanellj from mail.montclair.edu>
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>Original-recipient: rfc822;james.campanella from montclair.edu
>
>Jim,
>
>You should really use artificial microRNAs for your experiment 
>instead of RNAi -
>it gives much finer control and you don't have to worry about transitive
>silencing so it is well suited for gene families.
>
>Vicki
>
>Quoting "Dr. James J. Campanella" <james.campanella from montclair.edu>:
>
> > 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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> > Arab-gen from net.bio.net
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> >
> >
>
>
>Vicki Bowman Vance
>Professor
>Department of Biological Sciences
>University of South Carolina
>Columbia, SC 29208
>
>phone: (803) 777-3179
>fax: (803) 777-4002
>phone: (803) 777-3179
>fax: (803) 777-4002
>http://zebra.biol.sc.edu/~vance/index.html

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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