Choosing A Temperature Control Method; Calculated Control; Block Control - BIO RAD PTC-200 Operation Manual

DNA Engine Operations Manual

Choosing a Temperature Control Method

The DNA Engine cycler can control block temperature in two possible ways, each of
which has different implications for the speed and accuracy of sample heating:
• Calculated control: The DNA Engine cycler adjusts the block's temperature to
maintain samples of a specific volume in a specific vessel type at programmed tem-
peratures. This includes optimized overshoots of the block by a few degrees for a few
seconds, which bring the samples to the programmed temperatures.
• Block control: The DNA Engine cycler adjusts the block's temperature to maintain
the block at programmed temperatures, independent of sample temperature.

Calculated Control

Calculated control is the method of choice for most types of programs, yielding the most
consistent, most reliable, and fastest programs. When using calculated control, the
DNA Engine cycler maintains a running estimate of sample temperatures based on the
block's thermal profile, the rate of heat transfer through the sample tube or slide, and the
sample volume or mass (this information about the samples is provided when a program
is run; see "Setting Up the Temperature Control Method," chapter 5). Since this estimate
is based on known quantities and the laws of thermodynamics, sample temperatures
are controlled much more accurately than with block or probe control.
Hold times can be shortened significantly when protocols are run under calculated
control. In addition to the simple convenience of spending less time running reactions,
shorter protocols also help preserve enzyme activity and minimize false priming.
Cycling denaturations run under calculated control are usually optimal at 5 seconds.
Annealing/extension steps can also be shortened, but the periods for these will be
reaction specific.
Calculated control provides for shorter protocols in three ways:
1. Brief and precise block temperature overshoots are used to bring samples to
temperature rapidly.
2. Incubation periods are timed according to how long the samples, not the
block, reside at the target temperature.
3. The machine automatically compensates for vessel type and reaction volume.

Block Control

Block control provides less accurate control of sample temperatures than calculated
control provides. Under block control, the temperature of samples always lags behind
the temperature of the block. The length of the time lag depends on the vessel type and
sample volume but typically is between 10 and 30 seconds. Block control is chiefly
used to run protocols developed for other thermal cyclers that use block control.
6-4 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com