qrt-pcr and short fragments
You have to design your primers properly. Usually, in real-time PCR, you don't choose a very long product. Ideal product size is 150-300. 
Next, see what your NRTI is analogous to. For e.g. if I am using AZT (Azathymidie), I would place my reverse primer at or after the last T. 

There are alternate techniques as well. You can use primer extension (radiolabeled) and then quantify different products by scanning the photograph. However, this technique won't be as  quantitative as real-time PCR.