RNAi - vector construction (Jun/05/2007 )

hi,
can anybody help me in RNAi silencing.i am going to silence gene of 1606 base length, in this which sequence do i need to design plasmid vector for effective gene silencing.in one reference article they took502 bp fragments of both sence and antisence. please help me i am new to gene silencing work.
thanks in advance.

I would suggest buying/getting an siRNA vector into which you introduce your siRNA sequence. The siRNA sequence shoul be designed as nicely presented on the ambion website:http://www.ambion.com/techlib/tb/tb_506.html
The description is applicable to any siRNA vector you use. (genscript, Ambion, Invitrogen, etc)

You could use different programs to suggest some sequences in the gene of interest which might be suitable for knocking down.

You need to get a shRNA vector or make one which could be a long route.

After you have identified 3-4 differenr sequences, order the single stranded primers, anneal them and ligate into vector.

There is a lot of literature on how to choose the right sequence for knock down.

Also I think there is a nature protocols paper which describes how to clone shRNA into lenti vectors. You dont have to use a lenti vector you could use any shRNA vector or make one accordingly

Good Luck !!!

Thank you very much JOU and SCOLIX for your valueble suggetions.
thank you very much.