Very quick and very dirty: remove an aliqot of the reaction after every cycle and run a gel. You will be able to rougly distinguish different concentrations.

Very accurate, given an well-optimized PCR, but also laborious and difficult is a limitting-dilution PCR. Using lower numbers of replicates and dilution steps the quantification becomes more feasable but less precise. Maybe there is an acceptable trade-off point between precision and workload for you.

Quite accurate is the quantitative competitive PCR, but for this you will need good competitor and the instrumentation to accurately quantify the mix of target and competitor.

There is a lot of literatur availabe for limiting-dilution PCR and quantitative competitive PCR. You can find a lot in Google and Medline.

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CDoQFjAB&url=http%3A%2F%2Fwww.researchgate.net%2Fpublication%2F6872167_Real-time_polymerase_chain_reaction_and_melting_curve_analysis%2Ffile%2Fe0b4951e73f093cdac.pdf&ei=msN7Uva_Hs2y7Aaq6IHQBA&usg=AFQjCNEV62Ew8dgJ4aGYVLvPSBDvX05WsA&bvm=bv.56146854,d.ZGU&cad=rja

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=7&ved=0CG8QFjAG&url=http%3A%2F%2Fwww.biotechniques.com%2Fmultimedia%2Farchive%2F00011%2F96212rv01_11496a.pdf&ei=j8F7UtyRAeGR7AbcpIDADw&usg=AFQjCNFPFCjiD-Tq4PUVG2_RgSD7GeX9yQ&bvm=bv.56146854,d.ZGU&cad=rja

https://www.researchgate.net/publication/21766890_Quantitation_of_targets_for_PCR_by_use_of_limiting_dilution

Article Quantitation of targets for PCR by use of limiting dilution

Tqvm

You mean You cannot perform qPCR? Try a semi-quantitative PCR. Start with an equal amound of DNA-digested RNA, reverse-transcribe it and use as a tamplate for PCR. Run 25, 27, 30 cycles and verify it against internal control (reference gene, for instance EF1a, actin and so on). This method works well and was used many times in lots of publications.

Przemyslaw Wieczorek , ya, we have only a conventional thermal cycler in our lab. Thanks for your suggestions, can you provide some publications regarding your suggested methods?

Hi, just skipping throught the www: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000347 (Fig. 7) , http://www.sciencedirect.com/science/article/pii/S0885576513000404 or http://link.springer.com/article/10.1007/s00299-010-0830-z#page-1 (fig. 2). Sometimes interpretation of the obtained results is straightforward, but sometimes there is a need to do additional densitometry measurments so the band density could be converted into accurate computational values. Remember to always use the internal standard. It is really important here.