how to reduce the dimer in MSP - (Aug/23/2005 )
I am doing real time MSP, but keep getting dimers. Since I am using sybergreen, so that would interfer a lot. Who can give me some suggetions how to reduced the dimers?
the easy way out of this is to redesign your primers I would think!!
I use methprimer, seems the primers from there always show dimers.
can you design primers without the need of a program? I have been doing this for BSP with no problem at all.
Thanks for the quick reply, Methylink!
But Can you share the critieas when you desing MSP primers, is that same as what Methprimer used?
Some people use IDT to checkthe dimer prolbme after designing the primer. Which one do you use to check the quality of primers?
I have limited experience with MSP primers, but i have used similar criteria to what is described by methprimer, to check for primer dimer and the like I use perlprimer for this, it has a current Tm formula and is able to look for dimers and the like.
It's a handy thing to learn, picking primers by eye, although I have to say there are some really good programs that help you with primer selection, but they can be somewhat spirious at times.
When i use perlprimer to check my primers, it said: warning: reverse primer run found, forward primer run found. what does that mean?
There is an option within perlprimer that looks for runs of nucleotides within a primer, I think it is set to a run of four, meaning within the primer there is a run of 4 T's or 4 A's or more, it shouldn't be a worry unless your primers contain complimentary runs!!!