I'm doing a protocol that includes the capture of sonicated DNA fragments (previously 1% formaldehyde-fixed) with a complimentary biotinylated oligonucleotide.
After incubating with streptavidin-linked magnetic beads and enriching for my target sequence (and subsequent de-crosslinking), I can amplify that sequence very nicely with traditional, agarose-gel endpoint PCR.
However, if I use those same samples for qPCR (SYBR green) instead of traditional PCR, I see no amplification above background noise.
Is there any reason that PCR would work as expected, but qPCR would not?
Edited by Jestr22, 09 October 2014 - 10:02 AM.