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 06:49:04 EST 2007


>Date: Thu, 30 Aug 2007 08:21:53 +0800
>From: ShiCL <cl_shi from hotmail.com>
>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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>Dear Dr. James J Campanella:
>
>I am not really sure about your question, but 
>the probes you mentioned here seems the region 
>you chosed for plant RNAi. If it is in this 
>case, there are several papers about the length 
>for probes. Simply, dsRNA works well comparing 
>to sense or antisense RNA, and people usually 
>use full length mRNA if it is less than 1kb, 
>300-500bp was really popullar used, and the 
>shortest one should be over 100bp for dsRNA induced RNAi.
>
>For your third question, I think the answer is 
>yes, so far we think the homologues will also be 
>attacked. And there are some publications also 
>showed unspecific RNAi and off-target by dsRNA 
>induced RNAi. In your case, you need conform the 
>expression level of the homologues once you silenced your target gene.
>
>In fact, I think the amiRNA may work better than 
>dsRNA, sense or antisense induced RNAi in your 
>case, the amiRNA was showed really specific 
>silencing in plant. You may have a look at the 
>following paper, if you are intersted in it.
>
><http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16531494>http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16531494
>
>Best wishes!
>Sincerely yours,
>Chunlin Shi
>
>
>
>Laboratory of Microbial Genomics
>
>Systems Microbiology Research Center
>
>KRIBB, Daejeon 305-600
>
>South Korea
>
>
> > Date: Wed, 29 Aug 2007 09:55:30 -0400
> > To: arab-gen from magpie.bio.indiana.edu; 
> plantbio from magpie.bio.indiana.edu; methods from oat.bio.indiana.edu
> > From: james.campanella from montclair.edu
> > CC:
> > Subject: [Arabidopsis] Questions on plant RNAi
> >
> > 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 litera ture 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 k nockdown 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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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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