Pushing the Limits of the Electrophoresis Lab

For the second year now, we've been using Bio-Rad's forensic electrophoresis lab. My schedule is different than last year, so when I could prep for this lab had to be shifted. I poured the agarose gels on the Thursday of the week before we were going to do the lab and put them in the fridge with some buffer. I had planned to run the gels that Tuesday, so the gels would only be 5 days old.

I emailed the company about the feasibility of rehydrating the DNA samples and aliquoting them on Friday because I wasn't confident that I'd have enough time to do it Monday morning before we did the restriction digest. A Bio-Rad scientist confirmed that it would be fine.

Monday morning my students did the restriction enzyme digest. An hour later, we received the announcement that school would be closed on Tuesday because of how many students were out sick with the flu. On Tuesdays and Thursdays, we have 80 minutes for class, but on Wednesdays we only have 38 minutes. I knew 38 minutes wasn't long enough, so I called Bio-Rad and asked if our DNA would still be "runnable" if we waiting until Thursday. They confirmed that yes, it was possible and we could stick the samples in the freezer to be even safer.

Wouldn't you know it, we had a snow day on Thursday! Both Friday and Monday were only 38 minute periods for us, so I decided we'd just put it off until the next Tuesday. I figured even if it was a bust, I have pictures of successful gels and at least they would have the experience of filing the wells and watching the dye move through the gels as they were in the chambers.

The next Tuesday, 13 days after I had poured the gels and 9 days after we had done the restriction enzyme digest we ran our crime scene samples.

Although I followed Bio Rad's directions for running the gels in 20 minutes, I let them go for 45 minutes since the year before the bands hadn't moved very far. I think it's my power source. Anyway, by then my students had left for their next class, so I stained and destained their gels. I saw nothing right after. I figured the time lag was too long and I'd just show them pictures. I didn't toss the gels though since I wanted my students to see them anyway. I happened to take a look about 30 minutes later, and viola! There were the DNA bands. They weren't fabulous, but I think it has more to do with trying to run them rapidly. Next year I'll try the agarose concentrations for the longer running time and see how that goes.

Restriction Enzymes and Washi Tape

We're going to do the gel electrophoresis lab in AP Biology this coming week. I love for students to have a visual of what is happening when we get DNA ready for electrophoresis. This visual also helps them as we discuss why some pieces of DNA move faster than others and therefore give us distinct bands.

For our pre-lab conceptual practice we use toilet paper to represent DNA, washi tape to represent the location of specific palindromic restriction sites, and scissors labeled with specific washi tape to represent the restriction enzymes. Students take turns using the restriction enzymes to cut the DNA and then we determine the number and placement of bands on a gel using the number of toilet paper squares that are in each cut piece of DNA. The idea for this came this video on Vimeo.

 

For students to represent their electrophoresis gels, I made a template in Google Slides that I can project onto the whiteboard in the classroom.  Students can mark where they think the toilet paper DNA will migrate to.  Then I switch to the second slide that will reveal the banding pattern of the "criminal".  I like to wait to show that until last, otherwise they figure out who the criminal is before they finish getting all the bands up.  This way, the suspense lasts until all the bands are drawn on the board.

The template in Google Slides also includes the sketch of locations of each of the restriction sites.