The Oligo Was a No Go | TS Digest


     Photo of Melanie McConnell

Melanie McConnell conducted her graduate research at the University of Otago. She is now a professor at Victoria University of Wellington.

Victoria University of Wellington

In the mid-1990s, I was a first-year graduate student at the University of Otago in Michael Eccles’ laboratory. Our group studied transcriptional regulation in pediatric kidney cancer, and I was tasked with determining the DNA-binding site of a transcription factor involved in kidney development. 

To do this, we decided to build a large oligonucleotide. My department had just purchased a brand-new oligonucleotide synthesizer—the first one in New Zealand. It was really complicated and took us ages, but we eventually designed a 100 base pair oligonucleotide. As the synthesis was going to take a few days, we programmed the machine to run over the weekend. 

When I arrived in the lab on Monday, I was excited to validate the oligonucleotide. But first, I needed to wash the oligonucleotide to remove the chemicals that were added during synthesis. That’s when it all went wrong. 

I’ll never forget that moment. As soon as I added the wash buffer to the spin column, I watched the tube and my precious oligonucleotide melt into a puddle of plastic. I misread the protocol. Instead of adding the wash buffer containing 0.1% trifluoroacetic acid (TFA), I accidentally added 100% TFA!

I was dumbstruck. The pungent fumes snapped me back to reality, and I sheepishly ventured to my advisor’s office to break the news. I knew that this was an expensive mistake. The synthesis cost NZ $1000, which was a lot of money at the time. After a long slow inhale, he said, “Okay, we can make another one.”

I learned two important lessons that day. First, read protocols and chemical safety sheets very carefully! Second, failure in science is normal and not a reflection of my potential. I wasn’t discouraged. We made more oligonucleotides, but eventually switched to a different technique and went on to discover the binding site for the transcription factor.1 I still study regulation of gene expression in cancer, but now as a professor at Victoria University of Wellington

This interview has been edited for length and clarity. 

Reference

  1. McConnell MJ, et al. Oncogene. 1997;14:2689-2700.

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