Thermal Cycler FAQs

Q: Why is a temperature gradient required?

A: The annealing temperature of the specific primers used in DNA amplification often requires optimisation. Instead of running multiple experiments with different annealing temperatures and different MgCl2 and primer concentrations the gradient thermal cycler allows the testing of 12 different annealing temperatures (8 different reaction conditions) simultaneously.

Q: What is "Hot start"?

A: The Hot Start step is used to pause the machine at a specific temperature, typically around 70°C, after the initial template denaturation. The reason is to allow the manual addition of unmodified Taq DNA polymerase which may loose activity if added during the initial 5min denaturation. Heat-activated Taq or Hot Start enzymes do not require this step.

Q: How is it possible to connect a single thermal cycler to a computer?

A: If only one cycler is going to be connected then an RS232 cable (part code FGEN232) is required. For the TC-3000X and TC-3000G cyclers a USB cable is required (part code 6205046)

Q: How is it possible to connect multiple thermal cyclers to a computer?

A: The table below indicates which power supply, (when there is no TC-512 in the chain), cables and convertor are required for various set-ups. If further assistance is required please contact the Technical Support team at

TC Model Additional Units No. Extra Units Power Supply Cable Set Convertor Additional cables
TC-3000, TC-312 or TC-412 TC-3000, TC-312 or TC-412 1 FGEN485D FGENTWO FTGEN485 Not required
TC-3000, TC-312 or TC-412 TC-3000, TC-312 or TC-412 3 FGEN485D FGENFOUR FTGEN485 Not required
TC-3000, TC-312 or TC-412 TC-3000, TC-312 or TC-412 9 FGEN485D FGENTEN FTGEN485 Not required
TC-3000, TC-312 or TC-412 TC-3000, TC-312 or TC-412 10 FGEN485D FGENTEN FTGEN485 FGENONE
TC-512 TC-512 1 Not required 6103557 FTGEN485 Not required
TC-512 TC-512 2 Not required 6103557 FTGEN485 6103557
TC-512 TC-3000, TC-312 or TC-412 1 Not required FGENONE FTGEN485 Not required
TC-512 TC-3000, TC-312 or TC-412 2 Not required FGENTWO FTGEN485 Not required
TC-512 TC-3000, TC-312 or TC-412 3 Not required FGENTWO FTGEN485 FGENONE

Q: What is the incremental function?

A: Incremental timing and temperature are used to increase or decrease either the time or temperature incrementally over the number of cycles in a stage. Incrementation of extension time is used with "Long PCR" which is when large template fragments are to be amplified (e.g. 27kb lambda DNA, 40kb genomic DNA). Decremental temperature is used for protocols such as "Touchdown PCR" where the first cycle starts with a high annealing temperature and over the number of cycles there is a gradual decrease in the temperature. This ensures that only the specific product is amplified.

Q: What is a gradient thermal cycler?

A: Gradient blocks enable a particular temperature step in a protocol to be altered so that the temperature varies across the block. By specifying a temperature and the gradient to be applied, each column will achieve a different temperature, with the set temperature in the middle block, the lowest on the left and the highest on the right. The gradient is the total difference across the block, for example if the set temperature was 60°C and the gradient 10°C then the temperatures would range from 55°C to 65°C from left to right.

Q: What is the 'Pause' function at the start of the program used for?

A: Some users prefer to preheat the heated lid before placing the samples into the unit. The pause feature is used to stop the unit after the 4 minute heated lid preheat step. It will also sound an audible alarm indicating that the machine is ready for the sample tubes or plate to be added. Pressing the "Pause" key followed by the "Enter" key will commence the remaining program.