strange red lines in all of my agarose gels from PCR - (May/10/2007 )
I've been doing research using degraded genomic DNA from bones, and my PCRs have been working in the past, however, a few weeks ago, all of my samples (including my control, which is from contemporary hair) keeps, showing up as red lines on my agarose gels, under blue light. my condidtions are as follows, PCR of samples using, Taq, 10X buffer, dNTPs, water, MgCl, primers and DNA. PCR for 30 cycles, on gradient btw 60-70 degrees, then making up of 1.6% agarose in 1X TAE buffer, including CYBER Green dye, and run at 60 volts for 35 minutes..does anyone have any idea of what's going on...i've exhausted all i know. i've attached a pix
It sounds as if you are doing quantitative PCR. The green is likely from Sybr green. Many of the commercial QPCR mixes also include a reference dye, ROX, which I believe is red. You may have switched to a QPCR mix which includes this reference dye. Regions with both dyes will appear yellow.
to me it also sounds that the cause may be cyber green, you can try once without this dye