So I have scoured the boards trying to find someone else who had had a similar issue, but I came up empty-handed.
I am doing simple phenol chloroform extractions with EtOH precipitation. My yields are pretty good for environmental samples and I was pleased, until today.
I decided nanodrop the positive control that shows up on gel after PCR (as you would hope), and got some really strange results: the numbers were very similar to those of the negative control.
negative: 2.07 (260/280) 0.10 (260/230) 1.6 (ng/ul)
positive: 1.81 (260/280) 0.03 (260/230) 1.2 (ng/ul)
my sample: 1.94 (260/280) 0.41 (260/230) 82.5 (ng/ul) (I know that the second ratio is way low, but I can fix that)
Last time I nanodropped (verb?) the positive in September, the numbers were very similar to my current sample (what you would expect).
The PCR blanks come up negative, so I know I'm not having a contamination problem. I am blanking the Nanodrop with the correct solvent. So why would DNA show up on a gel and not on a Nanodrop? (The reverse of the normal problem.)
Thank you so much for your help!