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MSP Primer Sets (Herman Papers) - (May/23/2006 )

I've been trying to utilize some of the published p16 primer set in JG Hermans methylation paper (Carcinogenesis, vol 24 no. 2 pp 193-198, 2003) but have been running into a very odd problem. I've done my bisulfite treatment and tried to run the nested PCR, but although I get the desired product I also get a lot of "junk" bands and smearing. I've tried to adjust the annealing temperature up and down by running a gradient, but at all annealing temperatures that I tested from 55-65 I got the same "junk" my no template control has nothing. Has anyone encountered problems like this with primers in published papers?

I noticed that almost none of the antisense primers which Herman lists ends on the 3' end with a conversion event or is this something that is more important on the sense primer? Could I be seeing some sort of unspecific binding due to that? Also I saw in his paper that Herman does his bisulfite treatment with 1 ug of DNA. Runs his first round PCR with 1 ul for 30 cycles, and dilutes his first round product 1:1000 to run his nested MSP. Is this typical?

I do my bisulfite treatment with 1 ug of DNA, then run my first round of PCR, then take 1 ul of the first product and run the nested PCR. Could it be that I'm somehow using TOO MUCH template?

-cancergeek-

cancergeek,

it is possible you could be using too much template, if you are using Herman's protocol/primers it would be wise to follow exactly what Herman did.

I have tried some published primers in the past, and I have encountered typos and sequence errors that could be easily overlooked when publishing a paper, but can be devestating to someone who wants to replicate the data. A simple check to see that the primers match the p16 promoter region will tell you if the primers are correct or not.

Good luck!

Nick

-methylnick-