6-36-3
6-36-3
6-3
Creating Programs
Designing a New Program
Translating a Protocol into a Program
Until you are completely familiar with programming the DNA Engine,
you may find it helpful to first translate the protocol into DNA Engine
program steps and options on paper. Write down the protocol to be pro-
grammed, one step per line. Then write the type of program step that
goes with the protocol steps, at the end of each line. If a protocol step
involves an option as well as a program step, write both names down on
the same line. Finally, write the End step at the bottom of the list; pro-
grams will not run without this step. Number the lines 1 through N, where
N is the final, End line.
Using the GoTo Step to Write Short Programs
The GoTo step allows programs of many repetitious steps to be short-
ened to just a few lines. When the program encounters a GoTo step, it
returns to a specified step, repeats that step, and repeats all steps that
follow, back to the GoTo step. When the program has returned, or cycled,
back to the step a specified number of times, the program moves on to
the step that follows the GoTo step.
For example, consider a basic cycle sequencing protocol consisting of 30
repeats of a denaturation, and an annealing/extension step. Rather than
listing all 60 steps, use a GoTo step to design a short, easy-to-enter pro-
gram:
Raw program:Raw program:
Raw program:Raw program:
Raw program:
1. 92˚ for 30 sec
2. 60˚ for 3 min
3. 92˚ for 30 sec
4. 60˚ for 3 min
5. 92˚ for 30 sec
6. 60˚ for 3 min
7. 92˚ for 30 sec
[continues for total of 60 lines]
Choosing a Temperature Control Method
The DNA Engine can control block temperature in three possible ways,
each of which has different implications for the speed and accuracy of
sample heating:
• Calculated control: The DNA Engine adjusts the block’s tempera-
ture to maintain samples of a specific volume in a specific vessel type
DNA Engine program:DNA Engine program:
DNA Engine program:DNA Engine program:
DNA Engine program:
1. 92˚ for 30 sec
2. 60˚ for 3 min
3. GoTo step 1, 29 times (i.e.,
cycle back to step 1 and repeat
steps 1and 2, 29 times )
5. End
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