When are primer dimers a problem? - (May/06/2011 )

Hi

Moved from another section

I am preparing for the oral defence of my undergrad. project and I am strugglinf to find the answers to two questions I am guessing I may be asked.

1) When are primer dimers a problem?
(Is it when your aimed for product is small in size? - I basically disregarded them with my project as my product was 350 bp and I cut it out of gel, although they did make my picutres less pretty )

2)When using PCR to test for a pathogen in tissue (mine was fungal) are there any problems with using fresh post mortem tissue verus biopsy materila?
(I don't think this would matter too much as there may be enzymatic auto digestion of tussue but I broke tisse down in my extraction anyway- but I don't know if this changes the concentration of DNases??)

Thank you for your help

1) When are primer dimers a problem?
(Is it when your aimed for product is small in size? - I basically disregarded them with my project as my product was 350 bp and I cut it out of gel, although they did make my picutres less pretty )

Certainly when your intended product is small, dimmer could be problematic. If you are going to run qPCR, primer dimmers could be a problem because they will appear as amplification signal. If you want to assess the template amount, dimmers could interfere with data interpretation.


2)When using PCR to test for a pathogen in tissue (mine was fungal) are there any problems with using fresh post mortem tissue verus biopsy materila?

genetic materials may get degraded in postmortem tissues.