Creating Programs
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5-5
Temperature Control Mode:
This parameter defines the temperature control
algorithm used during the program run. The three different modes include
Calculated
and
Block
. Due to the expected lag of sample temperature behind
block temperature, the DNA Engine Tetrad 2 cycler can use calculated mode to
compensate accordingly. The cycler defaults to
Calculated
mode. Refer to the
section “Choosing a Temperature Control Mode” below for additional information.
Lid Control Mode:
The Hot Bonnet
®
heated lid can be programmed to minimize
condensation by keeping the upper surface of the reaction vessel at a temperature
slightly greater than that of the sample itself. The three available lid modes include
Off
,
Tracking
, and
Constant
. The DNA Engine Tetrad 2 cycler defaults to
Constant
. Refer to the “Choosing a Lid Control Mode” section below for addi-
tional information.
Temperature step:
This sets incubation temperature and duration. The
DNA Engine Tetrad 2 cycler ramps the sample to this temperature at its maximum rate
unless ramp modifying instructions are added to the program (advanced mode only).
The maximum rate of heating is 3°C/sec and cooling is 2°C/sec for all standard Alpha
™
units (maximum rate of heating is 1.2°C/sec for the Slide Chambers
™
Alpha unit).
Gradient step:
This establishes a temperature gradient across a 96-well sample
block. The range of any single gradient can be as great as 24°C or as small as 1°C
from left to right across the block. The maximum programmable temperature is 105°C;
the minimum programmable temperature is 30°C.
GoTo step:
Directs the program to cycle back to an earlier step a specified
number of times.
Lid step:
Directs a Moto Alpha
™
unit to automatically open or close (only available
in advanced programs).
End step:
Automatically included, this instructs the DNA Engine Tetrad 2 cycler
to shut down its heat pump because the program is complete.
Additional program modifications are available with advanced programs (see the
“Types of Programs” section immediately following for more information on
advanced programs):
1. Increment Temp:
Modifies a temperature step to allow a “per cycle” increase
or decrease of temperature (0.1°C to 10.0°C per cycle) each time the step is
executed. This feature is useful when annealing stringency is a consideration
such as in a touchdown program.
In a touchdown program, the annealing temperature begins higher than the cal-
culated temperature, and incrementally decreases each cycle, first reaching, and
eventually falling below the calculated annealing temperature. With the reaction
beginning at a temperature favoring high stringency in hybridization and incre-
menting to lower stringency, the reaction favors the desired product by creating
a high proportion of signal relative to noise in the early amplification cycles.
2. Extend Time:
Modifies a temperature step to allow a “per cycle” lengthening or
shortening of a temperature step hold (by 1–60 sec/cycle) each time a step is exe-
cuted. This capability is useful for slowly increasing (typically by 2 to 5 seconds
per cycle) the hold time during an extension step. The number of bases that a
