Genetic Design: Writing DNA with GenoCAD

Genetic design is a rule-based process for writing DNA. We capture design rules in GenoCAD grammars that biologists can use to develop plasmids for various applications.

Rule-based genetic design

For a reader to understand a text written in English, it needs to comply with the rules of the English language. Similarly, DNA sequences need to follow a set of biological rules for a cell to make sense of it. Since the rules of DNA are not completely understood, part of our research program aims at deciphering this high-level genetic code.

We are developing rule-based genetic design strategies using GenoCAD. We formulate hypotheses and test them experimentally.

Writing DNA with GenoCAD

Preparing a letter is an iterative process.  First, you use an application like Microsoft Word to write the document. When you need a physical copy of the letter, you print the document. Today there is a clear distinction between writing and printing because hardly anything is handwritten. Back in the days where handwriting was still the primary way of putting a text on paper, writing a letter meant both developing sentences that conveyed a message and putting them on paper.

A similar transition is happening in the life sciences. In the first 30 years of molecular biology, the techniques to manipulate DNA molecules in vitro were limiting to copying and pasting DNA fragments. Molecular biologists focused their attention on cloning these DNA fragments. Since 2000, a growing number of services providers have been offering de novo DNA synthesis services. It is now possible for genetic engineers to print almost any DNA molecule they can imagine. This creates the need for a new generation of software tools for writing DNA.

GenoCAD grammars

GenoCAD grammars are datasets that include libraries of genetic parts and sets of rules describing how to combine these parts in synthetic DNA molecules.
We described several GenoCAD grammars in peer-reviewed publications: