Help: Check my MSP primers - is my MSP primer correct??? (Jun/29/2005 )

Hey:
I design three MSP primer sets by myself. The gene sequence and bisulfite modificated sequence and primer sets are in the attachment. Would you so kind to check My MSP promer sets ? Is there any problem in My primer sets?

hi rockysofar,

ideally you want your MSP and USP primer sets to have equivalent Tm.

I have checked your primer Tm for your seqeunces using perlprimer

Gene 1 MSP-Sense 73.3
Antisense 77.0

USP- Sense 66.1
Antisense 70.1

I think for gene 1 at least the variation of Tm between sense and antisense primers as well the between MSP and USP is too great and you should adjust it so they have equivalent Tms

The variation is not so bad for gene 2.

You can either trim back seqeunces with a high Tm or add seqeunces to primers with a low Tm, modify the 5' end of course.

Good luck

Nick