Dave Gray's Build-A-Gene Experience Notes

These are some notes regarding the Build-A-Gene class experience. More technical class notes can be found here.

Motivation

I was thrilled to here that the class was available. The thought that I could have the experience of artificially introducing a gene into a living organism during my lifetime without taking a college course in advanced biology was amazing. It's not that I had a wierd urge to make bacteria fluoresce under UV light. But genetics is up there with the theory of relativity and quantum mechanics in offering a peek into how the universe works, and this was an opportunity to get hands-on experience which should massively increase my understanding of this important field.

The Instructor

Lisa Scheifele, a professor at Loyola is conducting the course. She is doing a fine job. Clearly, she has spent quite a bit of time in preparation for each class, ensuring we had the right materials and notes to complete each successive session. The process has many steps and each one is a learning experience. Lisa has also made herself available via email to answer questions that we don't think to ask during class, and I will include links to my emails and her responses below.

The Sessions

In each session, Lisa provides us with written instructions describing what to do, coaches us as needed and answers questions that we raise. The process involves a lot of, as she says, moving around tiny bits of clear liquid. That's because the DNA is so invisible to the naked eye and are the other molecules we work with. The results can be seen at several steps as we use a procedure called gel electrophoresis to sort out the DNA strands by size. This allows us to see if they are as long as expected.

In Session 1, we covered the basics of using the pipettes and tiny plastic "test tubes" (about the size of a pen cap). We learned about a process called "PCR" which allows DNA to be rapidly replicated into a very large number of copies. We then followed instructions to copy some DNA components that we will be working with. You can read the instructions for that session here. Afterwards, I sent an email with some questions for Lisa. My questions and here responses are here.

In Session 2, we used gel electrophoresis to check the results of our PCR from session 1. (My results were not stellar, but still something I could work with. This was my first time, after all!) We also used a technique called PCA to assemble short lengths of artificially produced DNA into a complete strand. Then we used PCR to create many copies of the fully assembled strands. (The process actually leaves a lot of incomplete fragments, but the way PCR works ensures that only the complete strands get copied. By the time PCR is done, there are many more complete strands than fragments.). My emailed questions to Lisa after Session 2 and her answers are here.

In Session 3, we used gel electrophoresis to check the results of our PCA/PCR in Session 2. (My results were zilch, but no matter. It's a learning experience!) In this case, we mixed our own gel for electrophoresis, so that was interesting. Next, we purified our DNA from sessions 1 and 2 to remove everything other than the DNA itself, added restriction enzymes to snip off the sections we want to join and put them into an incubator. (There they float in foam in a hot water bath.) I sent a few questions to Lisa after this session which we discussed in class. My questions and notes regarding her responses are found here.

In Session 4,

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