Problems with RNA extraction or QPCR for AI

[deki]

Can somebody help me,
When I test samples (alantoic fluid) on Avian Influenza, using QIAamp Viral RNA Kit for extraction and Taqman Influenza A/H5 detection kit version 1.0 for QPCR detection, I have no problem.
I am having problems with RNA extraction or Q-RT-PCR when I test samples that are inactivated with formaldehyde. The results are always negative, and when I test the same sample without inactivation with formaldehyde, results are positive. Where is the problem, in extraction or in Q-RT-PCR reaction?

[PeterScherp]

Hi Deki,

you found the answer yourself: It is the formaldehyde. This is know to be a great inhibitor of your enzymes. That is why you kill you transcriptase and your polymerase and you do not get a signal in real-time PCR. The same is true for ethanol and other organic solvents.
My tip: Remove as much Formaldehyde from your RNA sample as possible. Even traces of FA will negatively affect your PCR reactions.
This is crucial and as you mentioned it does not happen with samples that are FA free. So wash wash wash that Formaldehyde out !!!!
Hope that solves the problem.

[tsunami]

Hi Deki,
try other inactivation. I used many inactivated antigens, which are allontoic fluids inactivated and freeze dried (avian flu) and never had this problem!