MJ Research PTC-0200, Operation Manual

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DNA Engine & DNA Engine Tetrad Operations Manual
at programmed temperatures. 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 adjusts the block’s temperature to
maintain the block at programmed temperatures, independent of
sample temperature.
• Probe control: The DNA Engine adjusts the block’s temperature to
maintain the probe at programmed temperatures.
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 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 thermody-
namics, 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 activ-
ity 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 proto-
cols developed for other thermal cyclers that use block control.