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DNA devices

In the past two classes we've talked a lot about DNA, what it's made out of, what it looks like, how scientists draw pictures of it, and how we splice it together. Today we'll talk about how genes in the DNA sequence are controlled by the cell to make precise genetic circuits.

Remember the glowing gene from jellyfish that we talked about last week? This is going to be the first component of our gene circuit, the part that makes something happen. Let's add the glowing gene to our registry, it's called GFP, or Green Fluorescent Protein.

But a gene by itself won't do anything, because the cell won't know what to do with it. In front of the gene sequence in the DNA there has to be a spot for the protein that reads the DNA and transcribes it into RNA to bind. This region is called a promoter. Promoters can be constitutive, meaning that the gene they control is always being actively read no matter what, or they can be inducible, meaning that they will only be activated in certain conditions such as increased temperature or the presece of a chemical.

Let's add some promoters to our registry. We want to have some constitutive, and some inducible. What kind of induction do you think would be useful?

There are other genetic elements that control inducible promoters, repressors that stop transcription, and enhancers that promote the promoter activity.

Just like you need a signal to tell the reading and RNA transcription where to start, you need a signal to tell the ribosome where to start translating the RNA into protein. This sequence is called a Ribosome Binding Site, or RBS. RBS's are constitutive, as long as there is a signal there, the ribosome will bind and start making protein. However, the sequence of the RBS can be mutated so that the binding with the ribosome is stronger or weaker. A weaker binding leads to less protein being made. Let's put some RBS's of different strengths in our registry.

The reading and writing machinery in the cell will keep going forever once it's activated unless it reaches a terminator sequence. Protein translation is terminated at something called a stop codon, three letters that signal the ribosome to fall off the RNA and stop making protein. In the DNA sequence, a much larger terminator sequence is required to tell the transcription machinery to stop reading the DNA and transcribing the RNA. Here is our terminator:

Now we know about many of the elements that control whether or not a protein is made in a cell. These elements make up a large sum of the parts that synthetic biologists use to make DNA based devices. The Registry of Standard Biological Parts is filled with promoters, ribosome binding sites, repressors, enhancers, fluorescent proteins and terminators, all with different properties-- strengths, stabilities, speeds.

Let's start mixing together these parts to create biological circuits!