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This is the first draft of my paper. It's not completed yet, either, and it's not exactly what I wanted by the end of this weekend. I was having some problems finding mathetical papers on DNA condensation polymerization until about an hour ago. I need to put in what information pertains to my results from these articles. I will be getting to that within the week. The large spaces are where I have diagrams, AFM images, and graphs. I couldn't copy and paste it to this document. Right now, this paper is about 8 pages single spaced. I think I will double up the pictures (i.e. have two side-by-side) in order to save room. I will probably do the same with the graphs. This way, I'll have just around 9 pages, so that when I double space the paper, it will be just under 18 pages.

This is what I have so far:

Deposition of DNA Rafts on Mica Resulting in Polymerization The interest in DNA research has escalated in recent years due to the properties of DNA. High specificity in the self-assembly of DNA, rigidity, and the ability to create arbitrary sequences of DNA has allowed researches to consider it as a platform in the creation of new technologies, specifically circuit boards. In order to be used as platforms, DNA rafts must be able to bind in predictable ways. My question, then, pertains to what molarity of a DNA solution can be used to observe the presence of DNA rafts, and when observed, how many rafts are in chains, and what is the number of rafts per chain? Through seeking the answer to this question, a model can be drawn from the data in order to predict the number of DNA rafts in a chain, and the number of chains. This, then, will aid in the creation of DNA platforms. Research in this field of study has been active. A research group at the University of Notre Dame published a paper explaining the effects of DNA oligonucleotides assembling into rafts and binding on silicon wafers with trenches. APTES (aminopropyltriethoxysilane), a substance that binds the DNA to the silicon surface, was deposited in these trenches. The DNA did, indeed, bind to the “stripes” of APTES, resulting in a patterning of the silicon surface (source). Additionally, a research team at Duke University explains the significance of using computer science in the development of nanostructures (Autonomous Programmable Biomolecular Devices Using Self-Assembled DNA Nanostructures). Mathematical literature on condensation polymerization, too, has pertinent information… Prior Works and Contributions of Others on This Project Awaiting to hear from Dr. Sarveswaran on her particular contribution to the project. Methodology Outside Help For my research, I had access to a lab and mentors. Therefore, I was fortunate to be able to obtain and use a lab, Atomic Force Microscope (AFM), and any necessary materials for my project, which included DNA strands, buffer solutions, nitrogen gas, mica chips, desiccators, etc. In order to create my samples, the ds (double-stranded) DNA had to be ordered (from where?) The different strands are represented in the finished raft below. Each Red, Green, Blue, and Yellow strands in the A, B, C, and D tiles are separate. This is a double crossover molecule with "sticky-ends" at the 3' and 5'. Explain how each was mixed with water and placed into separate Eppendorff tubes. These tubes were stored in a freezer until further use. So, when the stock solution was made, I used a vortex to liquefy each oligonucleotide solution. To create the stock solution, then, 5 ul of each of the 16 oligonucleotides was added to 20 ul of Mg 2+/TAE (Tri-acetate) 10x buffer (which balanced the pH of the negative solution) and to 100 ul of 18 mega ohm H20. After the stock solution was created, it had to be annealed in the thermal cycler for 12 hours, so this was executed overnight. The machine heats the solution to 90 degrees Celsius, and then cools it to 20 degrees Celsius, by steps of ___ degrees per hour. The annealing process allows for the renaturation of the DNA strands. It allows for the complementary strands to bind together, and in the case, for the formation of DNA rafts. After the annealing process is complete, 2 ul of the stock solution and 8 ul of the Mg 2+/TAE (1x) buffer were pippetted into an Eppendorff tube. This substances was gently mixed. The remaining stock solution was placed in a refrigerator if it was going to be used within 1-3 days. If not, then it was placed in the freezer. Next, the approximately 1 cm2 mica was cleaned by peeling off 2 surface layers with single-sided tape (the mica, in technical terms, was "cleaved"). After this, it “vigorously” rinsed (i.e. rinsed with about 20 drops of H20) with 18 mega ohm H20 and then dried completely with nitrogen gas. Next, the 10 ul of the DNA solution was deposited onto the surface, with a deposition time of 3 minutes. After the allotted time, the sample was “vigorously” rinsed with 18 mega ohm water and dried thoroughly with nitrogen gas. The sample was then placed on a puck that had a piece of double-sided tape attached to it. This sample was then viewed under the AFM. If, however, the sample was not going to be viewed the same day it was created, it was placed in a desiccator until use. The desiccator helps to prevent the creation of moisture-induced contaminants. Obtaining the right mixture of DNA and the buffer solution was a matter of trial and error. At first, the stock solution contained 80 ul of DNA, 10 ul of Mg2+/TAE (10x) buffer, and 10 ul of 18 mega ohm water. The resulting images under the AFM produced networks and web-like structures, and no clear images of DNA were identified. In essence, the solution was too concentrated, even when the buffer solution was added and the deposition time decreased. Images such as the following were obtained.

20 ul of 0.1mM solution on mica; 5 minute deposition time 10 ul of 0.1 mM solution on mica; 3 minute deposition time 0.1 mM solution diluted further- used 5 ul of solution + 5 ul of Mg 2+/TAE 1x buffer 3 minute deposition time *Didn’t make a homogenous solution of the buffer and DNA before deposition So, when a new, diluted stock solution, a 0.05mM solution, was created, the large clumps of DNA were eliminated. However, a different problem arose in the formation of network and web-like structures on the sample surface. Some examples are presented in the following images. 10 ul 0.05 mM solution; 3 minute deposition time 10 ul 0.05 mM solution; 3 minute deposition time Eventually, these networks were eliminated by rinsing the mica with 18 mega ohm water and drying it completely in the cleaning process before the deposition of DNA. So, from this point onward, every mica sample was “vigorously” rinsed with water before DNA deposition. The next variable that was changed was the mixture of different levels of DNA and the buffer in a homogenous solution before deposition on the mica surface. 0.05 mM solution further diluted- this is 3 ul of DNA solution + 7 ul of Mg 2+/TAE 1x buffer 3 minute deposition time After obtaining this image, and seeing structures resembling DNA chains, or necklaces, I decide to dilute the solution further, in order to spread the molecules farther apart. So, for the next set of samples, I made a new 0.05 mM stock solution, and created the samples using 2 ul of the new stock solution and 8 ul of the buffer. The following images were obtained. So, in order to verify that the particles in these images were, indeed, DNA rafts, section analysis was conducted on the lengths and heights of the DNA rafts. Length and height measurements were conducted on 102 particles. The horizontal measurements added up to a total of ~3780 nm. This was then divided by 102 to obtain ~37 nm, which is the accepted length of a DNA raft (source). The vertical distance measurements added to ~132 nm, when, divided by 102, equals ~1.3 nm, which, too, is within the range of the known height (source). Therefore, upon certifying this information, I was able to plot the length of the DNA raft chains formed v. the number of chains. The histograms for these data are as follows: