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TeselaGen’s partition tool is a feature that allows you to divide DNA sequences into fragments. This can identify if those fragments are available on your physical inventory (Build Module) to reuse them or provide potential synthesis fragments. Using this tool, you can
To start working with this tool, go to the landing page of the Design Module, and click on the “Tools” option in the upper menu. There, you will see this screen, where you can select “Create Parts from Digest Parts” to select your restriction enzymes. In this case, we will select “Create Design from Partition Tool” to obtain the optimal fragments using the Partition Tool.
As you can see, this will create a design by partitioning a DNA sequence. To start the process, make sure your digest parts are already available in your libraries, and click on “Launch Tool” to see this screen:
Before starting the partition process, change the design and part names if needed (you can use variables to indicate from which part or sequence your new design comes). Then, click on “Select Sequences” or “Select DNA part”, and notice that any parts or sequences under 100 base pairs long will be ignored. Next, you will see the list of your sequences or parts registered in your library, where you will select the ones you want to use with the partitioning tool.
Once you have selected them, you will see a confirmation screen with the names of the parts or sequences you selected:
If the selection is correct, click on “Next”. On the next screen, you will be asked to indicate your design parameters:
Partitioning tool parameters: Indicate the minimum and maximum length size for your fragments (this depends on the DNA synthesis capacity)
Assembly strategy - Select between:
Flanking homology (Gibson/SLIC/CPEC): if you select this option, you will be asked to indicate the overlap size and GC content (indicating minimum, maximum, and optimal ranges in bp), as well as the partitioning constraints (such as non-tandem repeats, duplicated overlap sequences, etc.)
Type II endonuclease (Golden Gate/MoClo): In this case, you have to select the restriction enzymes being used.
Inventory parameters: By turning on/off this option, the software automatically checks the inventory you have registered on the Build module and prioritizes the aliquots you already have in your laboratory.
After you adjusted your parameters, click on “Submit” to start the process:
Once the process is started, a new task will be created, so you can keep track of your progress on the “Tasks” section on the upper menu. There, you should be able to see if your design has any problems that are not allowing its completion, or if it is in progress or completed.
On the case of your design having trouble, on the “Status” section you will see that it can’t be completed (this may be caused by your design parameters, so you may retry the task paying attention to and changing them if necessary). Once your design shows the “Complete” status you can check it on the “Designs” section of the upper menu. There, you can open your design and add tags.
When the task is complete, it will be shown as a typical design. The amount of parts and complexity of your design will also depend on the parameters you established at the beginning. With this done, you can work with it as with any other design.
If one of the parts generated is available in your inventory, PCR will be automatically selected as the assembly strategy, and it will show a small gray square on the left upper corner; on the other hand, if the option is direct synthesis, it will show a blue square on the same position.
You can click on “Submit for Assembly” to run a J5 report assembly. This tool of TeselaGen’s software carries out a detailed analysis of your design to give you some insights about your assembly.
Some of the information you will receive from this analysis is:
Cost-effectiveness of the assembly direct synthesis
Design of the DNA sequences required for that synthesis
Design of the DNA oligos to amplify the created pieces
Details on the PCR reactions, including incompatibilities between pieces and the condensation of multiple assembly designs