The enzymes ate my homework!

Edgar Allan Poe was pretty good at what he did but I’m fairly convinced that his stories would have been enhanced had he spent time in a molecular biology lab. No joke. It can be truly frightening because things will just go wrong. Horribly wrong. And you might not know why. In fact—in my case at least—you almost never know why. And to figure it out takes time and then by that point you’re both behind in the work you were meant to do and late to re-do whatever it was that didn’t work.

As you may have guessed, I feel a bit like I’ve been in a Poe-esque story for the last couple of weeks (granted we had a lovely Queen’s Birthday weekend holiday in the middle of it—look for an upcoming post).

Essentially I thought I was all set to send off DNA samples to be sequenced. I had done all the build-up work and I felt really good about the work I’d done. Thiw was likely my first mistake, since the Molecular Biology Gods (MBGs) can smell satisfaction and to them it smells like skunks. Just to be cautious I tested a few of my samples to make sure they were high enough concentration to sequence. They weren’t really. Well, technically they were too low. But I thought, “well, my sequences worked before and not much has changed so maybe it’s just a mistake and it will work.”

Nope. Sequencing didn’t work. The next logical step was to test all the other samples I had waiting to get sequenced. Their concentrations were also too low. At this point I was pretty upset because we’re talking about 80 samples that I thought I was basically done with.

So what happened to the DNA? My theory is that the enzymes I added to “clean” my PCR reaction—the ExoSAP that I talked about in my “scientific waste” entry—was inexplicably eating double stranded DNA in addition to the other stuff it is meant to eat. I’m currently trying to prove this but the little mini-experiments I’m setting up to test it are on the back burner as I try to redo essentially a month or more of work in a couple of weeks—using a different clean-up protocol, of course. It’s a new art called “Turbo Science!”

Hesitantly, I will report that it’s going okay but I refuse to be satisfied with my work thus far lest I upset the MBGs again.

Today, a number of samples went off to be sequenced. So, if you want to do me a favor, cross you fingers and hope that they come out okay! =)

Thanks friends,

Ellie