Winter Quarter Part I

Winter quarter has gotten off to a busy start.  I am taking more units than I was the previous quarter which was also hectic for me; however since I was  able to discover the miraculous ways of time management with a daily planner I have been able to jump into this quarter with the ability to handle a busy schedule.  Luckily I was able to sort out my problems with procrastination and this quarter I have been able to dedicate a steadily increasing amount of time to my research work in the lab.  My graduate mentor had a new baby girl at the beginning of January so I was on my own with synthesizing twenty-one new RNA molecules that I will be working with this quarter.  I ran into a few speed bumps along the way but I knew that I would have some troubles making some of the molecules due to their sequence nature.  When synthesizing RNA we use synthetic DNA that we have purchased and amplify it via PCR.  The cleaner the PCR product of DNA the more easy it is to transcribe the RNA from the complementary DNA.  However many of my molecules were very rich in guanine and cytosine bases which can cause difficulties when performing PCR.  Yet I was able to maneuver around these problems by adjusting my annealing temperatures during PCR incubation.  Now that my molecules have been synthesized I only have to label them radioactively in order to analyze their assembly through gel electrophoresis experiments. For some of the new molecules I have synthesized I will be studying the strength of their ability to fold into a right angle.  This will be done by mixing assembled right angle motifs with a probe molecule that binds most strongly to molecules that are in less rigid right angle structures.  Hence, I can measure the association constant for the probe to various right angle molecules.  We will be testing different molecules that have mutations within the right angle region to test which one folds into a more rigid right angle.  The molecules that fold into a right angle the most strongly will have the smallest association towards the probe.

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Posted in 2010-2011, EUREKA

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Alex Iteen is a second year student majoring in Biology. He is interested in bioengineering and synthetic biology. He is currently working in Dr. Fygenson's lab on DNA nanotubes.
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David Wallace is a third year student majoring in Biochemistry/Molecular Biology. He is currently working in Professor Weimbs's lab studying the pathogenic mechanisms of Autosomal Dominant Polycystic Kidney Disease (ADPKD).
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