MJ Research PTC-0200, Operation Manual

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DNA Engine & DNA Engine Tetrad Operations Manual
The Elements of a Program
DNA Engine programs consist of a series of steps encoding a protocol.
These steps are run using one of three possible temperature control meth-
ods: calculated control, block control, and probe control.
Programs may contain five types of steps. Two of the steps are manda-
tory, and two are optional:
1. Temperature step (mandatory): Sets a temperature for the block and
the length of time it is held at that temperature. The DNA Engine
brings the block to this temperature at its maximum rate of heating
or cooling, unless modifying instructions are added to the program.
(The maximum rate of heating and cooling is up to 3˚C/sec for all
single- and dual-block Alpha units; 1.2˚C/sec for the Twin Tower.)
2. Gradient step (optional): allows you to program a temperature gra-
dient across the sample block. The range of any single gradient can
be as great as 24
°
C from left to right. The maximum programmable
temperature is 105
°
C; the minimum programmable temperature is
30
°
C.
3. Ramp step (optional): Sets a slower-than-maximum rate of heating
or cooling.
4. GoTo step (optional): Causes the program to cycle back to an earlier
step for a specified number of times (up to 9,999 times).
5. End step (mandatory): Instructs the DNA Engine to shut down its
heat pump because the program is complete.
Additional instructions, termed “options,” can be added to certain pro-
gram steps to modify their effects:
1. Increment: Modifies a temperature step to allow a progressive increase
or decrease of temperature (0.1˚–10.0˚C per cycle) each time the step is
executed in a cycle. This is useful in “touchdown” programs, when the
annealing temperature of an oligonucleotide is not known.
2. Extend: Modifies a temperature step to allow progressive lengthen-
ing or shortening of a temperature step hold (by 1–60 sec/cycle) each
time a step is executed in a cycle. This is useful for accommodating
an enzyme with diminishing activity.
3. Beep: Modifies a temperature step or ramp step to make the machine
beep when the target temperature is reached.