Protocol Online logo
Top : Forum Archives: : Macroarray and Microarray

visualizing unknown DNA with linkers and PCR - (Jul/14/2006 )

Hi there,
Since I donĀ“t have sequence information for PCR I need to label genomic DNA after ChIP to show that there is DNA coming down with my protein of interest. I thought about using linkers and subsequently PCR to show presence of DNA.
Any suggestions for protocols I can use? Or maybe an alternative way?
Thanks in advance.


you can hybridize a promoter microarray if you got enough funding. an alternative is to sequence all the ChIPed DNA. but before all the steps, you have to amplify your DNA.


hi ackl-d
well if you only want to know if you have DNA just measure the OD260 (nanodrop) (first prot K and Rnase treatment, purify with DNA silica column Qiagen).
if you also wanna know what sequence it has, then use a promotor array or sequence it (like wop168 says), but it's quit expensive

good luck