Biomod/2015/OhioMOD/labbook

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<div id="title">LAB BOOK</div>

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<div id="title2"> Supplemental Information</div> <div id="figure01"><img src="http://openwetware.org/images/a/a0/Supplemental-Information1ohiomod15.jpg"></div> <div id="figure01copy"> <b>FIGURE 1:</b> (A) gel of B’C’ open. (B) gel of each lead band and each lag band of B’C’ open. </div> <div id="figure02"><img src="http://openwetware.org/images/e/e5/Supplemental-Information2ohiomod15.jpg"></div>

<div id="figure02copy"> <p><br><b>FIGURE 2:</b> (A) gel of AB open without EDTA dye. (B) gel using tilibit scaffold. </br></p>

<p><br>In <b>FIGURE 1A</b> B’C’ open was purified through gel electrophoresis. Each lag band (red) was combined, and each lead band (yellow) was combined. All of the lag bands and lead bands were then purified again shown in <b>FIGURE 1B</b> to determine if there was a difference or band shift. The results concluded that there was no difference between the double bands.</br></p>

<p><br>In <b>FIGURE 2A</b> AB open was purified in a gel without containing any EDTA to test whether the double bands were an effect of salt concentration. EDTA chelates magnesium ions which causes a decrease in salt concentration. This could potentially cause aggregation of the structure. Alternatively, when EDTA chelates magnesium ions it also decreases the pH. As shown in the figure EDTA does not affect the structure and thus the bands. </br></p>

<p><br>In <b>FIGURE 2B</b>, CA’ open was tested using a tilibit scaffold. We ordered a quality controlled scaffold from tilibit which eliminated the source of in-house contamination. This scaffold resulted in double bands which indicated there was no quality issue with the scaffold.</br></p>

<div id="citations"><small><p><b>Citations</b><p> <p><br> Udomprasert, Anuttara, Marie N. Bongiovanni, Ruojie Sha, William B. Sherman, Tong Wang, Paramjit S. Arora, James W. Canary, Sally L. Gras, and Nadrian C. Seeman. "Amyloid Fibrils Nucleated and Organized by DNA Origami Constructions." <i>Amyloid Fibrils Nucleated and Organized by DNA Origami.</i> Nature Publishing Group, July 2014. Web.</br></p>

<p><br>Castro, Carlos Ernesto, Fabian Kilchherr, Do-Nyun Kim, Enrique Lin Shiao, Tobias Wauer, Philipp Wortmann, Mark Bathe, and Hendrik Dietz. "A Primer to Scaffolded DNA Origami." <i>Nature Methods Nat Meth</i> 8.3 (2011): 221-29. Web.</br></p>

<p><br>Jiang, Qiao, Chen Song, Jeanette Nangreave, Xiaowei Liu, Lin Lin, Dengli Qiu, Zhen-Gang Wang, Guozhang Zou, Xingjie Liang, Hao Yan, and Baoquan Ding. "DNA Origami as a Carrier for Circumvention of Drug Resistance." <i>J. Am. Chem. Soc. Journal of the American Chemical Society</i> 134.32 (2012): 13396-3403. Web.</br></p>

<p><br>Geng, Yanli, Anthony C. Pearson, Elisabeth P. Gates, Bibek Uprety, Robert C. Davis, John N. Harb, and Adam T. Woolley. "Electrically Conductive Gold- and Copper-Metallized DNA Origami Nanostructures." <i>Langmuir </i>29.10 (2013): 3482-490. Web.</br></p>

<p><br>Amir, Yaniv, Eldad Ben-Ishay, Daniel Levner, Shmulik Ittah, Almogit Abu-Horowitz, and Ido Bachelet. "Universal Computing by DNA Origami Robots in a Living Animal." <i>Nature Nanotech Nature Nanotechnology</i> 9.5 (2014): 353-57. Web.</br></p>

<p><br>Douglas, S. M., I. Bachelet, and G. M. Church. "A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads." <i>Science</i>335.6070 (2012): 831-34. Web.</br></p>

<p><br>Kaur, Harleen, and Lin-Yue Lanry Yung. "Probing High Affinity Sequences of DNA Aptamer against VEGF165."<i> PLoS ONE </i>7.2 (2012): n. pag. Web. 13 June 2015.</br></p>
<p><br>Valigra, Lori. "First Aptamer-Based Drugs Take on Tough Diseases." <i>Drug Discovery & Development</i> 8.3 (2007): n. pag. Web. 8 June 2015.</br></p>

<p><br>Takahashi, Tsuyoshi, Kosuke Tada, and Hisakazu Mihara. "RNA Aptamers Selected against Amyloid β-peptide (Aβ) Inhibit the Aggregation of Aβ." <i>Mol. BioSyst. Molecular BioSystems </i> 5.9 (2009): 986. Web.</br></p>

<p><br>Rahimi, Farid, Kazuma Murakami, Jamie L. Summers, Chi-Hong B. Chen, and Gal Bitan. "RNA Aptamers Generated against Oligomeric Aβ40 Recognize Common Amyloid Aptatopes with Low Specificity but High Sensitivity." <i>PLoS ONE</i> 4.11 (2009): n. pag. Web.
</br></p>

<p><br>Smith, Danielle G., Roberto Cappai, and Kevin J. Barnham. "The Redox Chemistry of the Alzheimer's Disease Amyloid β peptide." <i>Biochimica Et Biophysica Acta (BBA) - Biomembranes</i> 1768.8 (2007): 1976-990. Web. 14 Apr. 2015.</br></p>

<p><br>Lu, Jun-Xia, Wei Qiang, Wai-Ming Yau, Charles D. Schwieters, Stephen C. Meredith, and Robert Tycko. "Molecular Structure of β-Amyloid Fibrils in Alzheimer’s Disease Brain Tissue." <i>Cell</i> 154.6 (2013): 1257-268. Web. 13 Apr. 2015.</br></p></small></div>


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