visualizing unknown DNA with linkers and PCR - (Jul/14/2006 )
Since I don´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.
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