Biomod/2013/CUMC/Intro.html

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     <td width="47%" rowspan="2" style="min-width:20px;"><a class="fancybox" href="http://www.cumc.columbia.edu/"><img src="http://i920.photobucket.com/albums/ad48/himynameisparth/columbia_logo_zpse5bce01f.jpg" width="215" height="100" align="top"></a></td>
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<nav id='menu'> <input type='checkbox'/> <label>&#8801;<span>Navigation</span></label> <ul class="fluid"> <li><a href='http://openwetware.org/wiki/Biomod/2013/CUMC'>Home</a></li> <li><a href='about.html'>About Us</a></li> <li><a href='Intro.html'>Project<font size='1'>&#9660;</font></a> <ul class='menus'> <li><a href='Intro.html'>Abstract and Introduction</a></li> <li><a href='Methods.html'>Materials and Methods</a></li> <li><a href='Results.html'>Results and Discussion</a></li> <li><a href='Conclusion.html'>Conclusion</a></li> <li><a href='https://skydrive.live.com/view.aspx?resid=6006BCA28B2E2BAF!123&app=OneNote&authkey=!AC3_eA_y21JncjE'>Lab Notes</a></li> <li><a href='Images.html'>Images</a></li> <li><a href='../lts_website/vid.html'>Video</a></li> </ul> </li> <li><a href='Intro.html'>Related Sites<font size='1'>&#9660;</font></a> <ul class='menus'> <li><a href='http://www.cumc.columbia.edu/dept/medicine/BasicResearchers/Stojanovic.html'>Stojanovic Research Site</a></li> </ul> </li>

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</table> <div id="div3.1" class="clearfix"> <h1>Introduction</h1> <h2><span class="mw-headline" style="font-size: 20px">DNA Origami</span></h2> <p style="text-align: left; font-size: 16px;"> The specificity of Watson-Crick binding offers DNA molecules as a promising candidate for highly customizable programming and structural design. One method, DNA origami, calls for a long single stranded scaffold (usually 7249 bp) along with ~200 shorter oligonucleotides that complement to specific regions of the scaffold. By doing so, the scaffold folds up into various 2D and 3D nanostructures. These DNA Origami structures offer the field of nanotechnology various novel applications including enzyme immobilization, drug delivery systems, and self-assembly. </p>

<h2><span class="mw-headline" style="text-align: left; font-size: 20px;">DNA Barrel structure</span></h2> <p style="font-size: 16px; text-align: left;"; text-align: left;">This study investigates the self-assembly of three distinct structures: a bundle, inner barrel, and outer barrel. The bundle is highly dense in the shape of a bullet with a 400 bp single stranded loop at the end. It is designed to be able to bind to numerous different drugs, in essence “soaking up” the drugs like a sponge. The following two structures are the inner-outer barrel pair that makes a capsule structure when assembled. A basket weave like pattern is investigated at the end cap of each barrel. This pattern consists of staples running perpendicular to the scaffold every 6 bp to account for the nature of DNA helical turn -- hypothesizing the interweaving nature of the scaffold and staple. </p> <p style="font-size: 16px; text-align: left;">Previous research was limited to the assembly of 2D basic building block and tile shapes. Here, this study demonstrates the assembly of three independent 3D origami nanostructures. This difficulty lies within the electrostatic barrier that each structure poses on one another. Each DNA molecule holds the same negative charge which builds up and presents an overall repulsion, hence no stochastic insertion of the bundle inside either of the barrel structures. The goal is to be able to draw the inner bundle into the barrel by the usage of extended staples acting as toehold strands that complement to the 400 bp loop. The outer barrel structure is also designed with a 400 bp loop to be able to follow identical protocols for post-fold assembly as of the bundle. These structures show to be optimal for cell nuclear pore intake in both shape and size. The ultimate aim is to assemble a nano-capsule to optimize drug delivery to selected sites, primarily for cancer therapy. </p>

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<h2><span class="mw-headline" style="text-align: left; font-size: 20px;">Goals</span></h2> <p>-Create a 3 pieces to a barrel structure using the method of DNA origami</p> <p>-Assemble all 3 pieces into a single structure</p> <p>

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