First Week Update!

Hello everyone! Andresen Lab Crew Summer 2022 here! We are here to give you guys a rundown of our first  week of research. For starters, we are working with DNA (I know right!!). Aisha and Sofia will be collaborating on the same projects; Measuring the Kinetics of the Disassembly of Mononucleosomes and Measuring Zn2+ binding to DNA, while Tam will be independently working on The Entropy and Enthalpy of DNA systems.

The Golden Trio at Golden Hour

On our first day, we learned the basic skill of pipetting. We pipetted water in order to get a grip on the basics of pipetting before proceeding to pipette different solutions and liquids. Professor Andresen wanted us to use each pipette to measure the same amount three times, with the hopes of eventually getting a percent error below 5%.

On Tuesday we started the day by making DNA stock, which we would be using in all of our samples. We started out by measuring 0.08 grams of DNA. We put the DNA aside and pipetted (with our recently mastered pipetting skills) 7840 microliters of water into a 50mL tube. We then pipetted 80 microliters of TRIS solution and 20 microliters of EDTA solution into the tube, in order to make a TE buffer. We put the DNA in the tube and mixed it in the vortex mixer for a while, in order to break up most of the DNA. After that, to make sure the DNA was really broken up, we put it in the sonicator for several rounds. Now we had a 8mL sample of 10mg/mL of DNA, which we then diluted into a 1mg/mL sample so its concentration could be double checked in our spectrophotometer. After several rounds of checking the concentration, we got around 0.8 mg/mL, which is considerably less than what we theoretically had. However, the next morning we repeated the process and measured our concentration to be around 1mg/mL, so success!

On Wednesday, we started by mixing our DNA stock with NaCl and MgCl2 solutions. Our goal was to make 5mg/mL of DNA in different concentrations of NaCl and MgCl2. We used the formula M1V1= M2V2 (which looks the same as the momentum conservation formula) to find the amount of NaCl and MgCl2 we needed to get the right concentration for our solutions. After that, we had to dilute all of our samples by a factor of 5 because that was the concentration that our spectrophotometer can measure. Most of our results were within a reasonable range (the expected values of DNA’s concentration was 1000 ng/microLiter).

Today (Thursday), we spent the day in our collaborator, Dr, Buettner’s lab, using the CD machine to measure how long it’ll take for the DNA to unwrap, (the nucleic acid inside the DNA). After measuring all 11 of our samples, professor Andresen gave us a coding crash course, so we could start interpreting and graphing our results using Jupyter. However, we realized that we measured our DNA samples within a range that was too narrow, so we have to go back tomorrow and do it all over again. Nonetheless, we will not be taken aback by a small setback, we will come back stronger than ever tomorrow! 

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