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Does phenol extraction have effect on DNA methylation?


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4 replies to this topic

#1 jacinthe

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Posted 02 February 2009 - 12:20 PM

Has anyone heard if the Phenol/chlorophorm extraction of the DNA could have an effect on the methylation? Would it interfere with the bisulfit traitment? (I'm using the Epitect-BS from Qiagen)

#2 methylnick

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Posted 02 February 2009 - 01:23 PM

Hi there,

it doesn't have an effect, if FFPE treated samples don't alter the methylation patterns then I would say phenol chloroform wouldn't either.

nick

#3 ForEpi

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Posted 03 February 2009 - 09:07 AM

Hi,

PC extraction should indeed have no effect as Weber (Weber, 2005) uses it to clean up his methylated DNA after his MeDIP procedure ...

B
I believe in the power of Selenium!!

#4 jacinthe

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Posted 03 February 2009 - 11:27 AM

Thank you both! I feel more confortable now using phenol/chloro for my DNA extraction (because I'm not very happy with my Qiagen kit!)

Jacinthe

#5 et2b

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Posted 02 March 2009 - 06:30 AM

Thank you both! I feel more confortable now using phenol/chloro for my DNA extraction (because I'm not very happy with my Qiagen kit!)

Jacinthe



He you....CpG methylation is a covalent modification to the cytosine....it wont fall off :rolleyes: , No really it wont..... :D --> chemistry is a nice thingy, sometimes
Cells can actively Demethylated with some thingies (enzymes).....so when cells are death and protein denaturated you wont be risking your Cytosine methylation. So no worries
Hope it helps...




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