primer design: end-point vs. RT - (Nov/15/2004 )

dear all,

this is the very first time that I'm designing RT primers and I'd like to find out what the main differences are between conventional and quantitative PCR primer design.

As of right now I have my target sequence (a catalytic site) in an exon, I have the neighboring exons too, so hopefully at least one primer will be spanning an exon-exon junction...

My questions are:
Do I decide if the probe is on the F or the R primer?
Do I use the online program provided by the company making my primers or do I hand-design them (for the end-point PCR I usually designed them manually)?
Is there anything else to look out for that I haven't thought about myself?

thank you so much.

dear all,

this is the very first time that I'm designing RT primers  and I'd like to find out what the main differences are between conventional and quantitative PCR primer design.

As of right now I have my target sequence (a catalytic site) in an exon, I have the neighboring exons too, so hopefully at least one primer will be spanning an exon-exon junction...

My questions are:
Do I decide if the probe is on the F or the R primer?
Do I use the online program provided by the company making my primers or do I hand-design them (for the end-point PCR I usually designed them manually)?
Is there anything else to look out for that I haven't thought about myself?

thank you so much.