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DNA Design on TeselaGen Community Edition
DNA Design on TeselaGen Community Edition

Learn about how you can use use the TeselaGen Community Edition designing your assemblies

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Written by Eduardo Abeliuk
Updated over a week ago

Contents of this Article

Getting Started

The TeselaGen Community Edition provides a unified interface and a computing infrastructure for you to design DNA constructs, automate the generation of instructions for building DNA assemblies, design primers, and visualize and edit plasmids for free. After you create an account, your landing page will look like this:

Notice the three lines in the upper left corner; click on them to open the left panel with the Toolkits. Locate the Molecular Biology Toolkit and click on it to display the available libraries and open the "Designs" library.

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A design is a schematic representation of a DNA assembly process in which users specify the biological parts and the order in which they appear in the final assembled construct. On Community Edition, you can access to the Designs Library and work on them.

Next,

Create your Designs

To create a design, click on the “New Design” button and select "Blank Design". At the “Create New Design” page you have the following options: create a new design, upload an existing design, or load an example design.

Give your design a name (this is required), you can add a description and you have the option to select a Design Layout Type i.e. either combinatorial or add the design to a Project, then just click Save. This will take you to the Design editor.

You can add bins according to your DNA Design Assembly and personalize them accordingly:

  1. Right click on the bin and this will open up a pop-up menu through which you can personalize your bin.

  2. You can also personalize the bin icon according to SBOL standards by left clicking on the icon in the Bin Details section. Moreover, you can also add and select additional information for your part such as its:

    1. Direction

    2. Set specific overlap/overhang position between assembly pieces at junctions that occur at the 3' end of the highlighted bin.

    3. Add or remove a specific number of base pairs from the 5' side of the Gibson/SLIC/CPEC overlap for the junction that would occur on the 5' side of this bin.

    4. Add or remove a specific number of base pairs from the 5' side of the Gibson/SLIC/CPEC overlap for the junction that would occur on the 5' side of this bin.

Loading Example Designs

There are two ways to access our provided example designs:

  1. When creating a new design

  2. When inside the design editor

When creating a new design, you are given an option to create a Blank Design or Load Example Design.

Hover over the Load Example Design and select one of the five example Designs available:

  1. Golden Gate

  2. Gibson

  3. Combinatorial Golden Gate*

  4. Combinatorial Gibson*

  5. Gateway

(You can read more about these assembly methods in this article.) Give your design a name and click submit. You will be directed to the Design Editor, which will be loaded with DNA parts that are defined in the selected example design. When you load up an example design, the parts associated with these designs will be automatically saved in the DNA Parts Library, which can be reused in other designs.

The image below is an example of a Combinatorial Golden Gate* design.

*The Combinatorial Designs are available on the paid version of the TeselaGen software. If you want to either use or explore the feature you can request for a demo here and our team will reach back to you.

Another way to access our example designs and data is to click on the Help tab within the design editor, hover over Load Example Design and select the example design of interest.
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Reports
With the TeselaGen Community Edition you can auto-generate reports and protocols for your assembly. Once you've created your design, click on Submit for Assembly. This will run the j5 algorithm which will power the automatic protocol generation step.

You can now view your report from the Reports from:

  • The Reports window by clicking on Reports at the header bar.

  • A notification for creation of report will appear from where you can also access it

    • or you can directly access it from the side information tab in the design editor.

Here you can find:

  • Prebuilt Constructs: Desired sequences that have already been built and are available in your library.

  • Assembled Constructs: Desired sequences to be built in a j5 run.

  • Input Sequences: Sequences that contain the input parts.

  • Input Parts: Segments of a sequence that are being used in a j5 run.

  • Assembly Oligos: List of oligos that need to be directly synthesized.

  • Synthon Sequences: List of DNA pieces that need to be directly synthesized.

  • PCRs: PCR reactions that need to be run to generate the assembly pieces. The software will automatically develop primers and will also provide you the Mean Tm, Delta Tm, Mean Tm3', Delta Tm3'

  • Assembly Pieces: Pieces of DNA that will be put together in a final assembly reaction to give the desired constructs.

  • Assemblies: Assembly pieces that need to be combined to create each reaction.

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