designed primer more powerful? - (Oct/19/2004 )
hi, I am doing methyaltion of one tumor supressor gene, and to my interest, I design a pair of primer according the methprimer web online, I determine the methylation status with both primer from the reference and prime I design, and I found the positivity is obvious high with desighed primer than that with primer from reference, is it possible?
Are you doing MSP? Do you mean you got more methylated amplifications with methprimer designed primers than primers from references?
The problem is which result is closer to the reality. Generally speaking, software designed primers are better than manually picked primers because primers are screened by the program against many criteria and only those that pass the test are returned to the user. For MSP, I would say all MSP primers should be tested by sequencing before they are used for sample screening.