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How to design primers for CpG, CpNpG, CpHpH methylation


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#1 WU18

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Posted 08 March 2005 - 08:58 PM

hi all,
I am gonna do some methylation analyis of my gene in arabidopsis, I designed primer using MthPrimer program, but this program can only dedign primer for cpG island, if I want to check the mehylation status of C in the whole sequence, such as CpNpG, CpHpH island , which program should I use?
Thanks a lot.
Best,
Marshal Wu

#2 methylnick

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Posted 08 March 2005 - 09:21 PM

Hi Marshall,

You can give Perlprimer a go, as it can design bisulfite seqeuncing primers irrespective of whether there is a island or not.

The link is herePerlprimer Link.

You can also design them by eye, the old fashioned way :-)

Good luck!

Nick

#3 WU18

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Posted 09 March 2005 - 07:36 PM

Nick, Thanks a lot for your reply.
Best




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