Combinatorial assembly tool: how to open and high through-put limitations

Sakura
Sakura
  • Updated

Within Benchling, you are able to model and design new constructs using the combinatorial assembly tool. Within the combinatorial assembly tool, there are two broad assembly types- cloning and concatenation.

Cloning refers to the creation of an exact copy of a sequence. Using different laboratory techniques, you can clone full sequences or specific parts of sequences. Within Benchling, you are able to model 3 different cloning methods using DNA sequences- Gibson, Golden Gate, and Homology.

Concatenation is a specific technique performed as the final step of cloning protocols or independently of any cloning to join multiple sequences into a single construct. Within Benchling you are able to model the concatenation of the following sequence type- DNA sequences, DNA oligos, RNA sequences, RNA oligos, and Amino Acid sequences.

 

Open the combinatorial assembly tool- cloning based assembly

This section walks through how to open the combinatorial assembly tool to perform Gibson, Golden Gate, or Homology-based assemblies.

From global create

  1. Click the + icon within the left hand tool bar
  2. Under Assembly, select Assemble DNA sequences by cloning. This will open the assembly pop-up modal.
    1. For assembly set-up details, see cloning method specific article
      1. Modeling homology assemblies with the combinatorial assembly tool
      2. Modeling Golden Gate assemblies with the combinatorial assembly tool
      3. Modeling Gibson assemblies with the combinatorial assembly tool

Cloning_Global_Create.gif

 

From a DNA sequence

  1. Open a DNA sequence
  2. In the bottom left corner, click on Assembly
  3. Select Combinatorial cloning. This will open the assembly pop-up modal
    1. For assembly set-up details, see cloning method specific article
      1. Modeling homology assemblies with the combinatorial assembly tool
      2. Modeling Golden Gate assemblies with the combinatorial assembly tool
      3. Modeling Gibson assemblies with the combinatorial assembly tool

Cloning_Sequence.gif

 

Open the combinatorial assembly- concatenation assembly

This section walks through how to open the combinatorial assembly tool to perform concatenation assembly.

From global create

  1. Click the + icon within the left hand tool bar
  2. Under Assembly, select Assemble sequences and oligos by concatenation. This will open the assembly pop-up modal.
    1. For assembly set-up details, see Modeling concatenation assemblies with the combinatorial assembly tool

Concatenation_Global_Create.gif

 

Modeling high-throughput assembly with combinatorial cloning and concatenation

The Benchling combinatorial assembly tool can model cloning and concatenation methods to design and assemble up to 5000 constructs. 

Limitations of the combinatorial tool when modeling high-throughout assembly

Fragments:

  • Up to 5000 total fragments
  • Up to 100kb per fragment
  • 15 fragment bins
    • Exception: only up to 10 fragment bins for Homology-based cloning

Spacers (cloning) / constants (concatenation)

  • Up to 20 bases per spacer/ constants
  • Up to 15 spacers/ constants

Constructs

  • Up to 5000 total constructs
  • Up to 150kb per construct

Primers

  • Up to 100 bases for primers

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