Genetic designs that include multiple DNA molecules

There are a number of occasions when it's appropriate to distribute - basically, split up - a design across more than one physical DNA molecule.

Here's just one scenario where that might happen: if you're working with a bacterial system, you may want to integrate part of a design with the host chromosome and house the remainder on a plasmid. For example, many T7 RNA polymerase-dependent genes are housed on plasmids. However, the necessary T7 RNAP is typically expressed from a single copy of the gene on the chromosome. In some cases like this a separate plasmid may even be used for each piece of the design.

Splitting up a design in GenoCAD is easy, and they can easily be distributed across multiple DNA molecules. To indicate that a sequence is a circular DNA molecule like a plasmid, simply enclose the included parts in parentheses. If a design includes two plasmids, then use two sets of (non-nested) parentheses. Here are examples for single-and dual-plasmid designs.



You will run into problems with designs that include multiple molecules if you don't use delimiters – parentheses, as in the example above, and/or curly brackets. In contrast to parentheses, use curly brackets to denote a linear DNA sequence. If you only have a single linear DNA sequence, you don't necessarily have to use delimiters. You can see an example of that below, along with a couple of designs that are invalid because they are multi-molecule designs that don't use delimiters across the entire design.



If you miss a set of delimiters and try to export an invalid design, you'll get the following error message: 

In an upcoming release, these grammatical rules will be enforced at the grammar level. That way, GenoCAD users won't be able to develop grammars that break these rules for multi-molecule designs.