chip assay primers - chip assay primers (Feb/06/2008 )

hi there!
i want to perform a chip assay but i want to know if the primers have to have some particular features?

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The only consideration that I can think of that would be specific to ChIP is that you make sure that the amplicons aren't larger than your average fragment size after shearing the chromatin. I think that, with the larger your amplicon the more likely you are to get results that are biased towards regions of the genome which are not fragmented as well (if your experiment involves comparing multiple regions of the genome).

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If you intend to use qPCR as your final detection then PCR products should be small, around 100-200bp.

I can also imagine that if you design a large fragment then you may be decreasing your chance of a successful PCR, as there is more chance that the target is fragmented when it is larger.

Dave

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