DIY DNA Extraction

Hello SANDS followers, we had an exciting day at SANDBOX (our unofficial name for the space) last week because we were trying out a new DNA extraction protocol for the first time. As you may know, one of our projects focuses on interactive platforms for DIY biology.

Earlier in the semester, we’ve been developing a few interfaces. We have designed an acoustic-based interactive table and the iPad web application as education and outreach tools for performing bio experiments outside of professional labs. Recently, we got our lab sink installed (thank you!), and today was the first day for us (Pat & Jennifer) to get our hands wet!

Here is all of the material that we used for the DNA extraction. Most of the stuff beside some chemicals from the DNA extraction kit are just regular off-the-shelf things. For example, the pot and hot plate to incubate our samples.

For this DNA extraction, we used a protocol from Carolina’s barcoding kit. Barcoding is a process by which you can identify the species present in your sample and it can be very useful for studying biodiversity and local ecology. DNA extraction is the first step for this type of analysis. To test out this protocol, we used the unknown plant as a sample. As you can see below, Jennifer was using a plastic pestle to chop down some plant tissue in order to increase the surface area that came in contact with the lysis buffer. This process is the very important because DNA is found in the nucleus of the cell, so the DNA yield depends on the amount of cell that we can break.

 Normally, after we break down the tissue we need to incubate our samples in a water bath. However, to make it DIY, we decided to use just a warm water in the pot instead because the purpose of having a tube in the warm temperature is just to speed up the lysis process (lysis is a process of breaking down the cell membrane), so any way that can warm up the tube is good to go.

Here is another exciting part, centrifuge (a process for separating solid particles from the liquid solution by rapidly spinning a sample). Again, we used a dremel instead of a real centrifuge, but the result is pretty acceptable. However, the dremel generates a lot of noise and is a little bit distracting.

At the end we used almost three eppendorfs (small tubes) in order to extract a DNA of a plant that we picked. The process is really fun because we got to use a lot DIY tools. We spent around one hour for this extraction, but we have learned a lot for our project. We will keep blogging as we do more exciting things at the sandbox, so keep checking this out!