The "Slider" below describes the design process with screen captures from the Oligo Maker app. Refresh the page if slider is not moving on it's own.
The oligo type is chosen and the target mRNA seqeunce is entered.
We chose to design DNA oligos against this target mRNA.
We choose a range of values for three critical oligo properties.
Oligo length (min/max) %GC (min/max) Tm (min/max)
Default oligo, mRNA target, and salt concentrations are shown.
Changing these parameters will affect Tm calculations (*Salt for DNA and RNA only)
Once we are happy with the parameters chosen we click 'Generate'.
We can always come back and change a few parameters to optimize design.
The generated oligos get an Oligo Grade and are listed from best to worst.
The position and length of each oligo is shown
By the third page we see the oligos dipping into the "yellow" zone.
We like to avoid yellow and red zone oligos ...
There are still more oligos!
We would have seen fewer if we tightened up ranges for critical properties.
Half of the oligos on the last page are red!
The whole list can be saved with a tap of 'Save'.
I choose the five best oligos!
With another tap on the "box with arrow" in the blue bar at the bottom...
We have generated an email with all five oligos listed in order...
Best to Worst
The data is nicely formatted
From Oligo Expert