I am studying this protocol described below. I am confused about "ramp-down PCR cycling method" as mentioned by authors. Are touchdown and ramp-down PCR cycling method the same?
"We used a ramp-down PCR cycling method. There was an initial denaturing
step (96 C for 5 min), followed by 5 cycles of high-temperature PCR
(96 C for 45 sec, 55 C for 30 sec, 72 C for 1 min), then 35 cycles of
low-temperature PCR (96 C for 45 sec, 47 C for 30 sec, 72 C for 1
min), and a final step of 72 C for 7 min."
Thanks for your time.
What you are saying seems to be touch down PCR and i have done this several times however i am not sure whether these two are same or not. see this attachment , it may help you.https://www.thermofisher.com/content/dam/LifeTech/global/life-sciences/PCR/pdfs/Thermal-Cycler-Ramp-Rates-AppNote.pdf
Hi there,
Ramp down is playing with the rate of cooling between denaturation and annealing step in order to possibly allow slow annealing event to occur whereas step down in decreasing the temperature of annealing in order to apply very stringent condition for annealing during the first cycles to improve specificity.
The program you described in the question is rather a touchdown pcr program.
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