Protocols FAQ

Q: When I use a protocol that contains a 30∞C hold, the processing block turns off a few minutes after the run is started.

A: The acceptable temperature range is 40∞C-98∞C. If the specified temperature is not reached in 5 minutes the site will automatically stop. The lowest temperature in the protocol must be above the internal temperature of the instrument.

Q: Can I add more cycle repeats while an experiment is in progress?

A: Although the software does not allow for the addition of cycle repeats while a run is progress, it is possible to program an excess of cycle repeats and stop the run or sites when appropriate.

Q: Can I read optics during multiple steps in a single stage?

A: No, only one optical read per stage can be programmed.

Q: Can I use the SmartCycler® II System as a tradition PCR instrument?

A: Yes, you can use the SmartCycler® II System as a traditional thermocycler by turning the optics OFF during the cycling protocol.

Q: Can I perform a melt from a high temperature to a low temperature?

A: Yes. The lowest temperature must be greater than internal temperature of the instrument.

Q: How many first derivative peaks are displayed on the melt graph?

A: Multiple first derivative peaks indicate that multiple products were amplified during the PCR. Generally, primer-dimers melt before specific products. Refer to Smart Note 6.4 Intercalating Dye Assay on the Smart Cycler® System for more details on reducing primer-dimer formation. To change the number of melt peaks that are displayed on the graph or to change the qualifying height for the first derivative peaks, click Setup menu>System Defaults>Melt Settings. If the melt curve appears noisy (jagged), try smoothing the melt curve by averaging 3 –5 points. Click the Setup menu>System Defaults>Melt Settings.