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 06:49:15 EST 2007

>Date: Wed, 29 Aug 2007 20:35:59 -0700 (PDT)
>From: seyed javad davarpanah <jdavarpanah from yahoo.com>
>Subject: Re: [Arabidopsis] Questions on plant RNAi
>To: "Dr. James J. Campanella" <campanellj from mail.montclair.edu>
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>Original-recipient: rfc822;james.campanella from montclair.edu
>Dear Dr. Campanella
>I think designing 300-500 probe for RNAi is somehow strange. I 
>myself use 20-30 nucleotide  specific primers for the gene of interest.
>for specific downregulation ,3'-utr of the m-RNA can be a fine 
>target to downregulate your gene of interest expression.
>I am just a PhD student. I hope you find what I wrote useful.
>Sincerely yours
>"Dr. James J. Campanella" <james.campanella from montclair.edu> wrote:
>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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>Seyed Javad Davarpanah
>Plant Genomics Center
>Korea Research Institute of Bioscience and Biotechnology(KRIBB)
>52, Oun-dong, Yusong-gu, Daejon, 305-333, Korea
>TEL. 042-860-4465, FAX. 042-861-
>Seyed Javad Davarpanah
>Plant Physiology Lab.
>Department of Bioscience
>School of Bioscience and Biotechnology
>Chungnam National University (CNU)
>TEL. 042-821-7536,
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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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