The story of how four scientists met the challenge of sequencing the Giant Beaver by Heather Lerner

In a country far, far away, four scientists set forth to capture DNA from an extinct Giant Beaver. George, Heather, Jacob and Mayeesha met in Potsdam, Germany to begin their mission in June 2015. Five fossils of giant beaver teeth were their best hope. They ground the bones to a fine powder, digested them in solution overnight and returned the next morning to finish extracting the DNA. But, no separation column existed that could handle the massive amount of digested Beaver samples. Undaunted, our fearless scientists crammed together pieces from two different kits to make the perfect column system. Early signs were good: four of the extracted bones showed evidence of ancient DNA. That is, short fragments of ~100-200 nucleotides in length.

There was no way to know if that DNA belonged to a Giant Beaver unless they sequenced it. Our scientists knew they would need a lot more copies of each DNA fragment in the samples to be able to sequence them. But this copying process would be risky. At any step, a simple mistake could mean that all of the DNA was lost. Over three days, they attached strings of known DNA (barcodes and adaptors) to the ancient DNA in each tube. Using those known strings as “primers” and a DNA copying enzyme (polymerase), they attempted to copy the ancient DNA. Signs were again good, four of the remaining samples still showed evidence of ancient DNA! An ice cream celebration ensued with much joy.

Our intrepid scientists faced another challenge: DNA sequencing is too expensive to waste time and money on sequences that aren’t Giant Beaver. They would have to somehow pull out only sequences that were likely to be Giant Beaver. “What else might be in that tube?” you might ask. The most likely contaminants are bacteria, any humans who had handled the samples, and any DNA that might have been floating around the lab or in the chemicals they used. They called on another scientist, Johanna, to help them solve this problem. She proposed capturing Giant Beaver DNA with a trap made of modern beaver DNA. Using a similar copying process as before (i.e. PCR), the scientists essentially made a net of modern beaver DNA to capture the Giant Beaver DNA.  When the two types of DNA were mixed, strands of DNA that were similar would be attracted to each other. As the strands paired up, one strand would be made from modern beaver DNA and the other from extinct Giant Beaver.

They faced yet another challenge: to separate the captured beaver DNA from contaminating DNA. Brilliantly, they had modified their original modern beaver DNA by attaching a molecule that sticks to special enhanced magnetic beads (i.e. biotin). By applying a magnet to each tube, they could pull the hybridized strands to the side and pipette everything else away!

One final challenge remained: How would they get their ancient DNA away from the modern DNA, (which would be too expensive to sequence)? Luckily, it is easy to get DNA strands to separate by just heating them up. Again, that magnetic bead came in handy: after heating the tubes, they used the same magnet and pipetted off the ancient DNA that had once been trapped by the modern beaver DNA. It was time to check again to see if they had been successful. This was an important moment after three arduous weeks of challenges, including several mishaps in which they all believed the project had been lost. This time, three of the samples showed evidence of short strands of ancient DNA!

One final step remains in our heroes’ saga: sequence the potential three ancient Giant Beaver samples. And that is where we will leave you…until we hear from our heroes again, we will wonder and dream about if they have recovered the first ever Giant Beaver DNA sequence…

 

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