Experiment: Round 2

The experiment Paul and I have been working on finally worked!  This was exciting, but the data was very disappointing.  We were testing an idea that we hoped would shed some light on how this type of DNA nanotube forms by attempting to make very long nanotubes (above 20 micrometers).  The idea was that we would keep the individual strands of DNA that make up a nanotube at a temperature where they couldn’t form but also wouldn’t melt.  One group would be diluted 10 times and another 100 times. Then, we would “seed” half the samples with tubes that had already formed hoping that they would jump-start long tube formation.  In technical terms this is called nucleation.  One is probably most familiar with it in terms of Mentos and Coke.  The surface of a Mentos is not very smooth on a microscopic scale.  So, when it is dropped into Coke the dissolved carbon dioxide gathers on the surface of the mint forming a bubble and eventually reaches a volume where it can no longer stay on the mint or in the soda.  In this case it happens very fast, hence the exploding Coke.  That is essentially what we were trying to do.  On top of that, we were also testing how the rate of cooling after seeding would affect the length.  If you’re keeping track thats three variables; seeding, concentration, and rate of cooling.  When we looked at our tubes we were pleased to find that we had made very long tubes (almost 20 micrometers).  However, when we looked at all our data it turned out that we couldn’t make any solid conclusions and we didn’t make the tubes the length we wanted.  So, after talking with Dr. Fygenson we decided that our temperature was probably melting the “seeds” and that we should run the experiment again.  This time we will keep the design simpler.  We are not going to test concentration or cooling rate.  However, we will do the experiment three times at different temperatures and we will test to see if the “seeds” are doing their job by dying them a different color than the other tubes.  Hopefully, this works.  Bring on the data.

~Alex

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Posted in 2010-2011

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Student Contributors
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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Eneida Chesnut is a senior majoring in chemical engineering. She transferred from SBCC, where she studied chemistry. She works with organic materials for solar cells and is very interested in renewable energy research.
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Erzsebet is a second year chemical engineering major. She is interested in biotechnology and biophysics, and is working in Professor David Awschalom's lab investigating how cephalopod skin responds to different types of stimulation by light.
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Madison Cornwell is a second year student majoring in Biochemistry and Spanish. She is a EUREKA intern through the California NanoSystems Institute and the Resident Assistant of the Women in Science and Technology House in Manzanita Village. She will be working closely with Dr. Kosik and graduate student Israel Hernandez for the remainder of her time at UCSB.
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