TeselaGen's Synthetic Evolution Workflow

TeselaGen's Synthetic Evolution workflow encompasses the Design, Build, Test, and Evolve phases of a rapid prototyping system for synthetic biology.

With TeselaGen's BETA release, the Design level has been made available as a web-enabled bioCAD/CAM tool. TeselaGen's VectorEditor facilitates the creation, visualization, modification, and annotation of DNA sequences. TeselaGen's DeviceEditor facilitates the selection and visual arrangement of biological parts (DNA sequence fragments) to be assembled into new constructs. TeselaGen's j5 automates the design of optimized protocols for DNA assembly.

Here is a representative TeselaGen BETA release workflow:

  • A researcher begins the design process by creating a new DNA design, and visually drafting a prototype arrangement (from 5' to 3') of the DNA part types to be assembled. In DeviceEditor, each column is associated with a DNA part type (indicated by a SBOL visual symbol in the column header) and columns are arranged left to right, from 5' to 3'. For example, a simple design might consist of a vector backbone part type in the first column, followed by a promoter in the second, followed by a 5' UTR in the third, followed by a coding sequence in the fourth, followed by a terminator part type in the last column. The directionality of each column (top or bottom strand) can be set by toggling the left/right arrow in each column header. Note that the resulting abstract prototype does not yet specify the actual DNA parts associated with each of the DNA part types.
  • The researcher then selects the DNA part(s) to be associated with each column of the prototype design, in the row(s) below each column header. If more than one DNA part is selected across multiple rows for the same column, this indicates a combinatorial library design. For example, if a GFP part is selected in the first row and an RFP part in the second row of a coding sequence column, the combinatorial library would consist of constructs with either a GFP or RFP coding sequence at that position. Put in another way, columns left to right correspond 5' to 3', and rows top to bottom correspond to combinatorial complexity. The DNA parts are selected from the researcher's part library. If the desired DNA part does not yet exist in the researcher's part library, new parts can be created by opening in VectorEditor a DNA sequence that contains the sequence for the DNA part, selecting the portion of the sequence that corresponds to the part, and then clicking the create new part button.
  • The researcher can then optionally assign DNA assembly protocol directives (e.g., embed in reverse primer) and design specification rules (e.g., if GFP is in a construct, then RFP should not be) to each DNA part, and to each column, as desired.
  • The researcher then submits the design to the TeselaGen server for mock assembly (a very quick process that does not include DNA assembly protocol design), for visual assessment in VectorEditor of the anticipated resulting construct(s). If the anticipated construct(s) do not match the researcher's intentions, the researcher can iteratively refine the design until intentions are met.
  • After (optionally) setting the parameters that control the DNA assembly protocol design process, the researcher then submits the design to the TeselaGen server for full DNA assembly protocol design. Following inspection of the resulting DNA assembly protocol, the researcher may iteratively refine the design to minimize or mitigate potential assembly issues (e.g., repetitive sequences or incompatible assembly pieces) as desired.
  • Following the DNA assembly protocol design process, the anticipated constructs (to be built) can by deposited into the researcher's sequence library.

Video demonstrations illustrating how to use TeselaGen's platform are provided in the next section.