MSUSBC The Basics

The Basics of Engineering Biology for MSU iGEMers

• What does it take to actually design and engineer a biological system?

Well, from some rough experience in trying to come up with ideas, it takes a firm understanding of parts, devices, and systems currently used in synthetic biology. First of all, you must realize that this is not Biology- this is Engineering. Like any other engineering discipline, one must rely on a standard set of fundamental tools and techniques to successfully create things.

Abstraction

• DNA is the most basic abstraction for the information necessary to carry out this thing we call life. Most of this info comes from another page. Basically, we start with DNA, which is like binary in being to difficult and cumbersome to actually manipulate and understand on a creative level. Therefore, we abstract specific sequences of DNA, or nucleotides, that perform a specific known function into a part (RBS, CDS, promoter, terminator). These parts are then abstracted even further, when they can be, into devices that function as a composite of many parts using the same signal (Chetty & Canton). Further up the list is systems. Systems consist of a bunch of devices, or parts operating on the same signal, that cannot be further combined because they use different signals. Therefore, a new device cannot be created. These devices are organized into an operating system that performs a desired task (Chetty & Canton). If you can really grasp this stuff, take a look at the Registry to see all the parts and their technical aspects.

Parts

• A part is simply a piece of DNA in the BioBrick format (Reshema). A BioBrick is set up so that each part has snippets of DNA on each end that allow it to "snap" onto other parts. Thus, one can easily just snap together a few parts and make a new system. It's nowhere near that easy, but hopefully one day it will be close. Anyway, what kinds of parts are there?
• RBS (Binding Sites): The RBS does what it says it does- binds ribosomes to specific site on the genome. Thus, translation is initiated. Think of it as a road sign, it lies upstream from the mRNA sequence signaling the passing ribosome to come in for a stop. For we engineers, here are the basics of the RBS part:

1. "The RBS controls the accuracy and efficiency with which the translation of mRNA begins"
2. An RBS binds a certain ribosome, of which there are many with many efficiencies.
3. In BioBricks, RBS's are separate parts, but can also be found incorportated into parts with protein coding regions.
4. RBS's are chosen for their efficiency and for their optimization of the protein decoding process.

• Promoter: Promoters regulate the binding of RNA polymerase to the DNA molecule. They are the "bouncers", deciding who gets in and when. Most promoters are about 60 base pairs long due to the size of the RNA polymerase. For engineers, it provides a means of control on the transcription of protein coding regions.

1. On Promoters are always on, but their activity can be repressed, thus making them repressible. Ligands are things that attach to the promoter, and in this case, repress its activity. These ligands can be a range of compounds, and they can be used as a control knob to vary the output of the promoted region.
2. Off Promoters are always off, but their activity can be incuced, thus making them inducible. Ligands bind to the promoter region and induce an increased rate of transcription.
3. Of engineering importance is the fact that ligands are often for intracellular use and degrade in the outside environment. Thus, it is difficult to use them for large system control. However, there are a few ligands that work fine intercellularly: Arabinose, ATc, and IPTG.