No Band or Faint Band Due to Thermal Cycling Errors (PCR (Polymerase Chain Reaction))

Question

Accepted Answer

No visible band or very faint band appears on the gel after PCR amplification. This indicates insufficient or failed amplification of the target sequence. Common causes: 1) Too few cycles used (insufficient amplification) 2) Extension time too short (insufficient replication time; generally need 1 min/kb) 3) Annealing time too short (primers need at least 30 sec to bind) 4) Annealing temperature too high (primers unable to bind; should be 5°C below primer Tm) 5) Denaturation temperature too low (incomplete denaturation; use 95°C) 6) Denaturation time incorrect (too long causes DNA degradation; too short prevents complete denaturation; use 3 min initial, 30 sec cycling) Solutions: 1) Use 20–35 cycles (fewer cycles for high template concentration, more for low concentration) 2) Use extension time of 1 min/kb; increase duration for PCR steps, especially extension, for longer targets 3) Use annealing time of at least 30 sec 4) Calculate primer Tm using oligocalc with default salt concentration and 0.2–1 µM primer; set annealing temperature 5°C below lowest primer Tm; optimize using thermal gradient 5) Use denaturation temperature of 95°C 6) Use 3 min at 95°C for initial denaturation to activate polymerase; use 30 sec at 95°C for cycling denaturation