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Please help me design MSP primer! - (Nov/07/2008 )

Hi everybody,

You will find promoter sequence of my target gene below. I aim to design MSP primers which are required to cover 3rd CpG site within binding site of a transcription factor either by sense or antisense primer. (Plus, there are 10 CpG sites in total.)

Thanks very much for your assistance!

1 atcctggtgg acaaccccac catgacaccc tgccagagcg cgtctgccac cttccccttg
61 aaaaaaggac agatcgggtg gtctctcaag ctgagaccct gtgtgtacga cagctctcgg
121 ggctggtgac agtggggagg ggaagttgac ggacccgggg gacatgaccc cagaggagga
181 gcgggaacag gatgagtggg aggaggttct aaattatcca ttagcacatg cctgccagtg
241 ggccatgcat aaatgtatag agaaaatagg tgggggcaga gggagagaga agaggccagg
301 gtataaaaag ggcccaaaag ggaccaattc cagaatccca ggacccagct ccccagacca
361 ctcagggacc tgtggacagc tcaccggctg tgatggctgc aggcaagtgc ccctaaaatc
421 ccagtgggct tggtgtgttc tgaagggtga cgtgggggcc atgcagatgg atggggcacc
481 aaccttgggc tttggggttt


For this particular sequence, you probably better do bisulfite sequencing


try out methylprimer express



QUOTE (methylnick @ Nov 19 2008, 05:54 AM)
try out methylprimer express



I'm using MethPrimer for my MSp design is the program good? It always give like 5 sets of primers for each query how do you decide which primer pair is best?



I would strongly suggest you design your primers with methyl primer express, it uses better design criteria.