Shear Joy

On Tuesday the 24th, we tried to shear our modern beaver DNA into pieces about 150-200 base pairs long so that we could continue making our baits. Shearing DNA involves putting the sample into a machine called a sonicator that uses ultrasonic waves to break up the DNA. Think of an ultrasonic jewelry cleaner, but much more powerful. The sonication machine was brand new, so we didn’t know for sure how long to run it for or what intensity to use. Our first try was a conservative 3 minutes at 30% intensity, which worked nicely; the DNA got down to about 900 base pairs. After this, we ran into trouble. We sheared the DNA again to get it down to the size we wanted it, but it seemed like no matter how long or on what intensity we ran the sonicator, we couldn’t get the DNA below about 300 base pairs. We ran the sonicator five times on Tuesday, and after calling the company for troubleshooting on Wednesday morning, we ran it three more times. Finally we got the DNA down to about 200 base pairs. On Thursday, we used the sheared DNA to finish creating the baits. We used the Nanodrop machine to see how many baits were present, and the result was incredibly high. So high, in fact, that we were very suspicious about how true that was. We plan to run a more accurate test later to see how successful we actually were.

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The sonicator  makes an ear-splitting noise

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Up close and personal with the sonicator. We had to maintain the water level exactly at the level of the samples in the tubes. If it got to high, the samples would jump up the sides of the tube and escape shearing. 

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Shearing is a three-person job

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