Primers, templates and another class act!

Our first attempt at classroom Synthetic Biology is on track as we completed the first stage of our attempt to develop a controlled system for peptide synthesis using Synechocystis genomic data and the help of Sarah, a graduate student in Professor Neil Hunter's research group at the University of Sheffield. The inspiration for the project grew out of discussions with scientists at Croda, one of our commercial partners. Last week, we worked through the first principles of PCR and following this success, we set out to develop a robust method for genomic DNA extraction to generate a supply of PCR template. The class demonstrated that addition of low concentrations of SDS dramatically improved DNA yield prior to boiling, but that these high yields did impact on successful PCR. (We shall revisit the DNA extraction methodology later in the project, since we wanted to produce the most efficient way of going from cells to PCR product). As you can see (top left), amplification of a control Synechocystis gene,was a success for the majority of the class (80 students on 20 groups: Y12s will be able to access their own data via Edmodo). One of the most important aspects of this experiment is the value of a group approach to solving an experimental problem. I will discuss this in a separate Blog, but suffice to say, Sarah had warned us that PCR success with Synechocystis is more sensitive to enzyme buffer and conditions than most colony PCRs; so, I am even more delighted by the results!

The aim of the class today was two-fold. The first was to establish the methodology for the second half of the project: amplifying target Synechocsytis genes and cloning them. But the other aim was to teach everyone how to design PCR primers. Last week, I made my first attempt to explain the logic behind primer design at the end of the day in the lab, but 15 minutes in, with lots of blank expressions, I thought, this needs thinking through more carefully. I was also wrestling with explaining the concept of pi to the younger class (more on this later), and how to move away from from the widely held idea that p is the name of a button on a calculator! I took a small group aside and asked them to design two primers for a short duplex. Those of you who teach this will know that virtually everyone gets the orientation wrong first time. So this week, I went through the background that I felt that was necessary: DNA base pair complementarity rules, the linkage of 5' and 3' to the orientation of the sugar phosphate backbone, the nomenclature behind the numbering of atomic centres in organic ring structures, the sensitivity of the active site of DNA Polymerases to strand orientation etc. Then asked them to have a go. Yes everyone got it wrong the first time. Then, after explaining why they had got it wrong....60% got it right the second time! By the end of the session, everyone I spoke to in the group (60%) had got it. 

So what did I learn from this session. Asking a large lab class to develop a method (in this case for DNA extraction) to meet a set of criteria is a great way to speed up scientific discovery. That concepts like primer design can provide an opportunity to teach pattern recognition, chemical nomenclature and elements of active site chemistry as well as molecular genetics. In summary, synthetic biology is proving to be an excellent vehicle for teaching science in schools and I hope to report on the next stage of the project in about six weeks time.