RM's+Siemens+Outline

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General Notes: eliminate names, spell out all acronyms and give brief description  ** I.  **     **Purpose of Research** a.  The goal is to CONTRIBUTE TOWARD THE DEVELOPMENT OF, NOT "UTILIZE" the development of smaller circuit boards by utilizing DNA rafts. RAFTS CONNECT TO "NECKLACES" HOW? b. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> My question, specifically, is what is the ideal molarity of the DNA solution for which we can observe the growth of DNA necklaces? And is that growth random, or ordered? Specifically, I'm also discovering the relationship between the number of beads in a necklace v. the number of DNA necklaces. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** II. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** **Rationale for Research** a. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> DNA nanotechnology is one of the fastest growing technological fields. The use of DNA is especially important due to its reliability, nano-size structures, and ability to self-assemble. In the age of smaller electronics, DNA nanotechnology will be at the forefront. DNA rafts, in particular, are the building blocks for new nanotechnology. They are the platforms which can be built upon. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** III. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** **Pertinent Scientific Literature** a. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> DNA oligonucleotides self-assemble into rafts and bind onto silicon wafers. These wafers have trenches, in which APTES, a substance binding to both silicon and DNA, was deposited. The DNA rafts bind to these “stripes” of APTES, resulting in a patterning of the silicon surface (“**<span style="font-weight: normal; font-family: 'Calibri','sans-serif'">Deposition of DNA rafts on cationic SAMs on silicon [100]”). ** b. Reif and Labean (recent paper from ~ 3 weeks ago in //Science)// c. P. Rothemund (Nature, 2006 or 2007) d. mathematical ref's about modeling condensation polymerization

<span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** IV. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** **Prior Works and Contributions of Others on This Project** (will depend on outcome of histograms) a. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> MY MENTOR'S  group at MY HOST UNIVERSITY “are studying fundamental materials issues for the integration of self-assembling DNA nanostructures (DNA lattices, tiles, or origami) with top-down CMOS fabrication methods.” <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> i. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal">  Koshala’s research using gold particles  --ONLY IF AVAILABLE OUTSIDE OF YOUR LAB (PUBLISHED OR PRE-PUBLISHED). THIS REPORT MUST BE FREE OF NAMES THAT COULD IDENTIFY YOU, YOUR MENTOR, OR YOUR INSTITUTION b. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal">  Professor Reif and Associate Professor LaBean at Duke University. Their work focuses on DNA tiling lattices, biomolecular computing, and DNA robotics. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> i. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal">  ? c. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal">   ?? <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** V. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** **Methodology (how to make DNA necklaces)** a. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> <span style="font-family: Arial,Helvetica,sans-serif"> Outside help: the specific tiles were ordered for me, and the annealing was done by one of my mentors. - lab equiment, materials (AFM and software, mica chips, forceps, nitrgoen tanks, fume hoods, safety-wear, computers, etc.) - lab set-up in general - annealing (what is it? how did they do it? did I help at all? - ordering the specific sequences <span style="font-family: Arial,Helvetica,sans-serif">b.  <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"><span style="font-family: Arial,Helvetica,sans-serif">  <span style="font-family: Arial,Helvetica,sans-serif"> Prepare DNA stock solution (what's the dna sequence, provide diagram) <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> i. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> 5 ul of each of the 16 oligonucleotides (specific names…A, B, C, and D tiles, each with Red, Green, Blue, and Yellow strands) <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ii. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> 20 ul of Mg 2+/TAE 10x buffer (adjusted from 10 ul in first stock solution) <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> iii. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> 100 ul of 18 mega ohm H20 (adjusted from 10 ul in first solution) c. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Anneal solution (heat solution to 90 degrees Celsius, then cool to 20 degrees Celsius overnight) d. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Pipette 2 ul of DNA solution and 8 ul of Mg 2+/TAE 1x buffer into Eppendorff tube and mix e. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Clean mica f. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Peel off 2 layers with tape g. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> “Vigorously rinse” with 18 mega ohm water (show images of "vigorous" v. "non-vigourous" washing) h. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Dry with nitrogen gas i. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Deposit the 10 ul from Eppendorff tube onto surface j. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Deposition time: 3 minutes k. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> “Vigorously rinse” with 18 mega ohm water l. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Dry completely with nitrogen gas m. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Place on puck with double-sided tape and view under AFM n. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> If the sample cannot be viewed the within a few hours of preparation, place in the desiccator. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** VI. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> **** Results (include optimization of sample prep- rinsing of mica, deposition time, and DNA concentration were all variables) ** a. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> After overcoming many obstacles, such as blurry images, web-like structures forming on the surface, dirty samples, and the lack of DNA rafts on the surface, I had successive images that showed a formation of DNA necklaces. (Where do I include the adjustments made to the procedure before obtaining images of DNA necklaces? In the methodology?) I WOULD THINK SO. YOU COULD PROVIDE A BIT OF HISTORY, RATIONALE IN YOUR METHODOLOGY. b. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> The raft-like particles’ measurements match with the accepted length and height of DNA rafts (37 nm long, 8 nm tall). Include the measurements of the DNA particles. c. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Over the course of a couple days, the increase in necklaces formed seemed to increase. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** VII. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** **Discussion- Interpretation of results** RECALL 2-PART QUESTION a. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> After experimenting with different concentrations of DNA, I struck upon a concentration that yielded the best results (2 ul of the DNA solution, 8 ul of TAE/Mg 2+ 1x buffer). This answered the first part of the question. HAS THIS RESULT BEEN DETERMINED, PUBLISHED BEFORE? b. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal">  Regarding the second part of the question….I need to make the histograms and do the analysis. a. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal">  (Based on the data I put together for the histogram, I will see if any other questions need to be answered) b. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal">  The basis of this research for future work? Is it for utilizing the pattern/randomness to predict (if the chain length is ordered) how the rafts will arrange, and to use this pattern to create DNA platforms for technological devices? <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** IX. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> ** **References** a. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal">  Works Cited in the paper (will probably include many of the papers from Lieberman group, as well as those by Professor Reif and Associate Professor LaBean at Duke). REMEMBER, REFERENCES MUST MAP 1-1 AND ONTO THE WORKS YOU ACTUALLY SITE, i.e., USE, IN YOUR REPORT.
 * VIII. <span style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal"> Conclusions **