The baker from Boston
I love baking muffins.
Not just baking - specifically baking muffins. Cakes are ok; bread takes too long; cookies never turn out well, but muffins - I can bake muffins.
Muffins are resilient. You can make all sorts of substitutions, vary the ratios, throw in something extra, and they still turn out well. In fact, in grad school, I would make muffins from a banana, crushed-up cereal, baking soda, fruit juice, and flour. They were fluffy and fruity and absolutely delicious.
The polymerase chain reaction (PCR), used for making copies of DNA in the lab, is a lot like baking, but not like baking muffins. It's like baking cookies - you look at the batter the wrong way, and they come out dry and burnt and gross. I suck at baking cookies. And I suck at PCR.
Well, I did.
Over the past several weeks, I have struggled to get even a single PCR to work. My collaborator, Hanny, fielded my frustrated text messages and helped me troubleshoot the process. We thought we had it down to one bad ingredient - the DNA primers - but after we bought new primers, the PCR still failed. I was pretty much at a loss, so Hanny stepped in. She has much more experience with PCR than I do, having run countless reactions during her PhD. She drove down from her home in Boston over the weekend, met me in the lab, and set to work.
Hanny tried three different approaches, and without giving you the gory details, we figured out the PCR was failing because of another bad ingredient. Magnesium chloride is a key reagent for DNA replication, kind of like baking soda in a recipe: you don't need a lot, but you absolutely need it. Hanny had tons of magnesium chloride left over from her past PCRs, and by Murphy's Law, I grabbed the one aliquot that was contaminated. We're not exactly sure what the contaminant is, but it has to be something that digests DNA. The evil enzyme would degrade my sample, the primers, and any DNA copies the PCR managed to make before they could see the light of day. It's like trying to bake with flour-eating bacteria in your batter - not going to work.
With some fresh magnesium chloride on hand, the PCR is now running smoothly. I even had my own successful reaction today! I'm grateful for such a great collaborator and for the progress that we've made.
Not just baking - specifically baking muffins. Cakes are ok; bread takes too long; cookies never turn out well, but muffins - I can bake muffins.
Muffins are resilient. You can make all sorts of substitutions, vary the ratios, throw in something extra, and they still turn out well. In fact, in grad school, I would make muffins from a banana, crushed-up cereal, baking soda, fruit juice, and flour. They were fluffy and fruity and absolutely delicious.
The polymerase chain reaction (PCR), used for making copies of DNA in the lab, is a lot like baking, but not like baking muffins. It's like baking cookies - you look at the batter the wrong way, and they come out dry and burnt and gross. I suck at baking cookies. And I suck at PCR.
Well, I did.
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| An electrophoresis gel showing the successful results of our PCR troubleshooting |
Hanny tried three different approaches, and without giving you the gory details, we figured out the PCR was failing because of another bad ingredient. Magnesium chloride is a key reagent for DNA replication, kind of like baking soda in a recipe: you don't need a lot, but you absolutely need it. Hanny had tons of magnesium chloride left over from her past PCRs, and by Murphy's Law, I grabbed the one aliquot that was contaminated. We're not exactly sure what the contaminant is, but it has to be something that digests DNA. The evil enzyme would degrade my sample, the primers, and any DNA copies the PCR managed to make before they could see the light of day. It's like trying to bake with flour-eating bacteria in your batter - not going to work.
With some fresh magnesium chloride on hand, the PCR is now running smoothly. I even had my own successful reaction today! I'm grateful for such a great collaborator and for the progress that we've made.
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