How should I optimize my PCR conditions to eliminate nonspecific bands?
Here are some suggestions for optimizing your PCR under such conditions:
-Make sure primers don't have complementary sequences at the 3' ends.
-Optimize the annealing step by increasing the temperature in 2-5 degrees C increments, and minimizing the annealing time. You can try higher annealing temperatures in the first few cycles and lower annealing temperatures in the subsequent cycles.
-Try hot-start protocols.
-Optimize the magnesium concentration for each template and primer combination.
-To minimize chances of amplifying contaminating DNA, use aerosol-resistant tips and UDG.
-Make sure primers don't have complementary sequences at the 3' ends.
-Optimize the annealing step by increasing the temperature in 2-5 degrees C increments, and minimizing the annealing time. You can try higher annealing temperatures in the first few cycles and lower annealing temperatures in the subsequent cycles.
-Try hot-start protocols.
-Optimize the magnesium concentration for each template and primer combination.
-To minimize chances of amplifying contaminating DNA, use aerosol-resistant tips and UDG.