First month of the fall quarter

For the majority of the summer I spent my time trying to assemble a fully programmable RNA nano-particle that was shaped like a cube and  could possibly be used as a scaffold for drug delivery.  It would serve a medical purpose because one would be able to attach a quantified dosage to the clean geometrical shape of a cube that could have good potential to easily pass through the body to its target and then it would biodegrade naturally within the body as your own RNA does usually.  In addition exploring the different folding patterns and interactions of the RNA motifs used to make the cube has led us to discover more information on the folding morphologies and language of RNA.  Through running various assembly experiments of my cubic nano-structure I discovered that some interactions were not as favorable as they seemed on the computer model I initially made.  I found that the RNA pieces were not combining into the clean cut looking cube I had designed using Swiss Protein Data Base Viewer on the computer.  After running a plethora of polyacrylimide gel electrophoresis experiments and finding that a no distinct cube band was forming, only the half cubic square structures were able to be seen as a band, I decided to run another experiment to see if there were any unwanted interactions taking place.  In my “dimer” experiment I tested how each of the eight cubic pieces interacted with each other piece and found that some motifs were interacting to form dimers when they should not have been connecting at all.  At this point I realized that while a computer model can look nice, it can also not predict everything and it takes multiple different approaches to figure out how to get the final product that you want.  I am now working on forming a semi-programmable cube that combines two of the same half square species in a step-wise fashion so as to try and eliminate any mismatched pairings from occurring.

Posted in 2010-2011, EUREKA

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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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