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How to design prime detecting plant methylation?


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#1 luck

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Posted 21 February 2009 - 06:17 AM

Hi
I have a problem for help.If I want to detect the methylated state of a gene in Arabidopsis,should I design degenerate primer set or specific primer set ? And how to design the prime ?

#2 microlight

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Posted 23 February 2009 - 01:42 PM

Hi
I have a problem for help.If I want to detect the methylated state of a gene in Arabidopsis,should I design degenerate primer set or specific primer set ? And how to design the prime ?

You can design specific primers using methylexpress @ABI

#3 luck

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Posted 23 February 2009 - 05:20 PM

You can design specific primers using methylexpress @ABI

Thank you for you answer.But arabidopsis methylation include CG,CNG and CNN pattern. methylexpress @ABI designs primer sets accoding to CG pattern ,if i design specific primer by methylexpress @ABI ,how to design CNG and CNN methylation ? Could you give me more suggestion?
Thanks :)

#4 methdetector

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Posted 24 June 2009 - 05:58 PM

Hi
I have a problem for help.If I want to detect the methylated state of a gene in Arabidopsis,should I design degenerate primer set or specific primer set ? And how to design the prime ?


Hi Luck,

I had the same question. I came across this online tool called Kismeth. It is supposed to help in sequence analysis after bisulfite treatment and generate primers for the input plant DNA sequence considering non-CpG as well.
Hope this helps.




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