Biomod/2014/ASU/Design: Difference between revisions

Revision as of 01:28, 23 October 2014

<html xmlns="http://www.w3.org/1999/xhtml" xmlns:v="urn:schemas-microsoft-com:vml" xml:lang="en" lang="en" dir="ltr"> <head>

<title>Nanodevils - OpenWetWare</title> <style type="text/css" media="screen, projection">/*<![CDATA[*/ @import "/skins/common/shared.css?164"; @import "/skins/monobook/main.css?164"; /*]]>*/</style> <link rel="stylesheet" type="text/css" media="print" href="/skins/common/commonPrint.css?164" />

<link rel="stylesheet" href="http://fonts.googleapis.com/css?family=Lato:300,100&subset=latin"> <script src="//ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js" ></script>

<script type"text/javascript"> $(function () { $("style[media*='screen']").remove(); $("link[href*='favicon']").remove(); //fix heading var h1 = $(".firstHeading").text().split("/"); $(".firstHeading").text(h1[h1.length-1]); $("tr:odd").addClass("odd"); }); </script>

<style type="text/css"> /**** Base styles ****/

column-one, #footer, div#sidebar-main, #contentSub, .firstHeading, #siteSub, #jump-to-nav, .printfooter{

   display: none;

content {

   margin: 0;
   padding: 0;

background: #fff;
border: none;
}


html, body, div, span, object, iframe,
h1, h2, h3, h4, h5, h6, p, blockquote, pre,
abbr, address, cite, code, del, dfn, em, img, ins, kbd, q, samp,
small, strong, sub, sup, var, b, i, dl, dt, dd, ol, ul, li,
fieldset, form, label, legend,
table, caption, tbody, tfoot, thead, tr, th, td,
article, aside, canvas, details, figcaption, figure,
footer, header, hgroup, menu, nav, section, summary,
time, mark, audio, video {

 margin: 0;
 padding: 0;
 border: 0;
 font: inherit;

}
article, aside, details, figcaption, figure,
footer, header, hgroup, menu, nav, section {

 display: block;

}
body {

 /*padding: 15px;*/
 font-family: 'Lato', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Arial, sans-serif;
 font-size: 2rem;
 font-weight: 200;
 line-height: 1.4;
 background: #fff;
 color: #000000;
 max-width: 1280px;
 padding-top: 55px;
margin-left: auto;
   margin-right: auto;

}
}
h1, h2, h3, p, ul, ol, pre, dl {

 font-weight: 100;

}
h1, h2, #super-list, .box, .tagline, #index-list {

 font-family: 'Lato', 'Helvetica Neue', Arial, sans-serif;

}
h1, h2, h3 { font-weight: 300; }
h1 {

 font-size: 16px;
 line-height: 1.1em;

}
h2 {

 font-size: 22px;

}


a,
a code {

 color: #FB4;
 text-decoration: none;

}
a:hover,
a:hover code {

 color: #FFCC00;

}
a:active,
a:active code {

 color: #000000;
 /*background: black;*/

}
a img { border: none; }
a.anchor{display: block; position: relative; visibility: hidden;}
p{
	text-align:left;
}
em { color: #00EF00; }
strong { font-weight: bold; }
blockquote {

 padding-left: 1.0em;
 margin-left: 1.0em;
 border-left: 1px solid #333;
 font-style: italic;

}


nav {

 background: rgba(25, 25, 25, 0.85);
 padding: 0px;
 position: fixed;
 top: 0px;
 left: 0px;
bottom: 0px;
 right: 0px;
 z-index: 100;

}
nav ul {

 width: 100%;
 
 margin: 0px auto;
 padding: 0px;
 list-style-type: none;

}
nav ul li {

 float: left;
 line-height:2.5;

}
nav ul li.selected {

 border-bottom: solid 10px #580000;

}
nav ul li.home {

 padding: 0px;

}
nav ul a {

 float: left;
 text-decoration: none;
 color: #F2F2F2;
 text-transform: uppercase;
 font-size: 20px;
 font-weight: 300;
 padding: 0px 20px 0;

content {

   margin-top: 60px;

filters > li{

	margin: 0px;
	display: inline-block;
}
.box.clickable:hover{
	background: none repeat scroll 0 0 #fff;
}
.clickable img {
	transition: 0.3s ease;
}
.clickable img:hover {
	opacity:0.9;
	transition: 0.3s ease;
}
.background {
	left: 0;

   margin: 0;
   max-width: 100%;
   padding: 0;

}
/*the boxes*/
.box.b2x2{
	height: 300px;
	width: 300px;

       position: fixed;

}
.box.b2x2 > img{
	display: block;

   margin-left: auto;
   margin-right: auto;
   margin-top: 10px;
   height: 300px;
   width: 300px;
   position: fixed;

}
.box.b2x1{
	height: 360px;
}
.box.b1x2{
	width: 930px;

       height: 3500px;

}
.box.b1x3{
	width: 700px;
}


/*start page*/	
.box.intro      { font-size:7.2rem;}
.box > p {
	font-size: 16px;

   padding: 0 20px;
   margin-top: 10px;
   text-align: justify;

	font-weight: 300;
}
.box > h2 {
	font-size: 20px;

   font-weight: 100;

	text-align:left;
	margin-left: 20px;

   margin-top: 15px;

}
.tease > h2 {

   font-size: 40px;
   font-weight: 100;
   margin-top: 80px;

}


/*project*/
.project{
	background-attachment: fixed;

   width: 100%;

	padding-bottom: 40px;
}
.project h2 {
	color: #FFFFFF;

   font-weight: 300;
   margin-bottom: 30px;
   margin-left: 180px;
   padding-top: 20px;
   position: relative;

}


.project h3 {

   font-size: 26px;

}
.project .box {
	margin-bottom: 20px;

   margin-top: 0;

}
.interlude{
	background: none repeat scroll 0 0 #2A2A2A;
	box-shadow: 0 0 25px rgba(0, 0, 0, 0.8);
	border: 1px solid rgba(0, 0, 0, 0.3);

   height: 150px;
   position: relative;
   z-index: 3;

}
.interlude *{
	float:left;
}
.interlude h2{
	color: #FFFFFF;

   display: block;
   font-weight: 300;
   line-height: 150px;
   margin-left: 24%;
   margin-right: -14%;
   width: 50%;

}
.interlude img{
	float: left;

   line-height: 150px;
   margin-left: 10%;
   margin-top: 25px;
   vertical-align: middle;

}


.clear{
	clear: both;
	}


.project_box{
	background: none repeat scroll 0 0 #FFFFFF;

   color: #000000;
   display: block;
   float: left;
   font-size: 18px;
   font-weight: 300;
   line-height: 1.6;
   margin-left: auto;
   margin-right: auto;
   overflow: hidden;
   padding: 10px;
   width: 50%;

}
.figure_box{

   display: block;
   float: left;
   margin-left: 20px;
   overflow: hidden;
   width: 230px;

}


/*se*/
.project_box h2{
	color: #1A1A1A;

   display: block;
   font-weight: 300;

   margin-left: 0%;
   margin-right: -10%;
   width: 90%;

}
.project_box p{

   text-align: justify;

	margin-bottom: 18px;
}
.project_box li {
	margin-left:50px
}

pb_mot.project_box{

	height: 350px;
}

pb_dna_scaff.project_box{

	height: 400px;
}

pb_dna_req.project_box{

	height: 250px;
}

pb_poly_intro.project_box{

	/*right: -20%;*/
	height: 200px;
}

pb_poly_pmoxa.project_box{

	/*right: -20%;*/
	height: 600px;
	width:  1000px;
	overflow:scroll;
}

pb_ir.project_box{

	/*right: -20%;*/
	height: 1300px;
	}

pb_poly_cp.project_box{

	/*right: -20%;*/
	height: 600px;
}
/*team page*/
.bio_box {

   background: none repeat scroll 0 0 #E74C3C;
   float: left;
   font-size: 15px;
   height: 440px;
   padding: 15px;
   text-align: justify;
   width: 210px;

}
.bio_box > .name{
	font-size: 24px;

   font-weight: 300;
   margin-bottom: 25px;
   text-align: center;
   width: 100%;

}
.bio_box > p{

   text-align: justify;

	font-weight: 300;
	font-size: 16px;
}
.box.big  img{

   opacity:1;

}
.flag > *{
	float:left;
}
.flag > p{
	font-size: 18px;

   position: relative;
   text-align: center;
   top: -6px;
   width: 75%;

	margin-bottom: 10px;
}

team .big{

	opacity:1;
}
.head{
	width:220px;
	float:left;
}
/*sponsor page*/

sponsors .box {

   background: none repeat scroll 0 0 white;

sponsors figcaption {

   height: 65px;
   width: 100%;

	font-size: 15px;

   font-weight: 300;
   top: auto;
   bottom: 0;
   opacity: 0;
   transform: translateY(100%);

	transition: transform 0.4s, opacity 0.1s 0.3s;
	-webkit-transform: translateY(100%);

   -webkit-transition: -webkit-transform 0.4s, opacity 0.1s 0.3s;

sponsors .descr{

	background: none repeat scroll 0 0 rgba(0, 0, 0, 0.4);

   font-size: 12px;
   font-weight: 300;
   height: 60px;

	margin: 0;

   padding-left: 10px;
   padding-right: 10px;
   padding-top: 10px;
   text-align: justify;
   top: -155px;
   line-height: 1.3;

sponsors .descr p{

	width:90%;
	margin-left:auto;
	margin-right:auto;
}

sponsors figure.clickable:hover figcaption{

   opacity: 1;
   transform: translateY(0px);
   transition: transform 0.4s, opacity 0.1s;

	-webkit-transform: translateY(0px);

   -webkit-transition: -webkit-transform 0.4s, opacity 0.1s;

sponsors figure:hover .descr{

   opacity: 1;
   transform: translateY(155px);
   transition: transform 0.4s, opacity 0.1s;

	-webkit-transform: translateY(155px);
	-webkit-transition: -webkit-transform 0.4s, opacity 0.1s;
}
/*gallery*/

gallery .box img{

	min-height: 220px;

   min-width: 220px;

	}
/*ptocols*/
.protocol_box{
	background: none repeat scroll 0 0 #FFFFFF;

   color: #000000;
   display: block;
   float: left;
   font-size: 18px;
   font-weight: 300;
   line-height: 1.6;
   margin-left: 40px;
   margin-right: auto;
   overflow: hidden;
   padding: 10px;
   width: 66%;

}	
.protocol_box li {
	margin-left:50px
}
.protocol_box p{

   text-align: justify;

	margin-top: 18px;
}
.protocol_box   h1 {
	font-size: 30px;
}
.protocol_box   h2 {
	font-size: 24px;
}
.protocol_box   h3 {
	font-size: 22px;
}
/*Outreach*/
.outreach_box{
	background: none repeat scroll 0 0 #FFFFFF;

   color: #000000;
   display: block;
   float: left;
   font-size: 18px;
   font-weight: 300;
   line-height: 1.6;
   margin-left: 10px;
   margin-right: auto;
   overflow: hidden;
   padding: 10px;
   width: 70%;

}
.outreach_box li {
	margin-left:50px
}


/*Acknowlegement*/
.ack_box{
	background: none repeat scroll 0 0 #FFFFFF;

   color: #000000;

	text-align: center;

   display: block;
   float: left;
   font-size: 18px;
   font-weight: 300;
   line-height: 1.6;
   margin-left: 10px;
   margin-right: auto;
   overflow: hidden;
   padding: 10px;
   width: 80%;

}
.ack_box p {
	text-align: center;
	}
.next, .prev{
	z-index: 99;
	background-image: url("http://openwetware.org/images/5/55/Fancybox_sprite.png");
	width: 36px;
	height: 36px;
	top: 200px;
}


figure.box > .next {
	left: 425px;
	background-position: 0 -72px;
}	
figure.box > .prev {
	background-position: 0 -36px;
}	
/**** Isotope styles ****/
/* required for containers to inherit vertical size from window */
html,
body {

 height: 100%;

container {

 padding: 0px;
 bottom-margin: 10px;

}
.box {

 width: 220px;
 height: 220px;
 margin: 10px;
 float: left;
 overflow: hidden;
 position: fixed;
 background: #fff;
 color: #000000;
 display: table-cell;
 text-align: center;
 vertical-align: middle;
 overflow:hidden;

}
div#b2x2{ position:fixed;}
figure.box > *{
	left: 0;

   position: absolute;
   right: 0;

}
.box figure{
	overflow: hidden;
}
.box figcaption {

   background: none repeat scroll 0 0 rgba(0, 0, 0, 0.4);
   bottom: 0;
   font-size: 20px;

	font-weight: 300;

   padding-left: 5px;
   text-align: center;
   width: 100%;

	z-index: 4;
}
.clickable .box:hover {

 cursor: pointer;

}
/* The Magnificent Clearfix: nicolasgallagher.com/micro-clearfix-hack/ */
.clearfix:before, .clearfix:after { content: ""; display: table; }
.clearfix:after { clear: both; }
.clearfix { zoom: 1; }
/* Start: Recommended Isotope styles */
/**** Isotope Filtering ****/
.isotope-item {

 z-index: 2;

}
.isotope-hidden.isotope-item {

 pointer-events: none;
 z-index: 1;

}
/**** Isotope CSS3 transitions ****/
.isotope,
.isotope .isotope-item {

 -webkit-transition-duration: 0.8s;
    -moz-transition-duration: 0.8s;
     -ms-transition-duration: 0.8s;
      -o-transition-duration: 0.8s;
         transition-duration: 0.8s;

}
.isotope {

 -webkit-transition-property: height, width;
    -moz-transition-property: height, width;
     -ms-transition-property: height, width;
      -o-transition-property: height, width;
         transition-property: height, width;

}
.isotope .isotope-item {

 -webkit-transition-property: -webkit-transform, opacity;
    -moz-transition-property:    -moz-transform, opacity;
     -ms-transition-property:     -ms-transform, opacity;
      -o-transition-property:      -o-transform, opacity;
         transition-property:         transform, opacity;

}
.rs-wrap:after,
.rs-slider:after,
.rs-thumb-wrap:after,
.rs-arrows:after,
.rs-caption:after {

   content: ".";
   display: block;
   height: 0;
   clear: both;
   line-height: 0;
   visibility: hidden;

}
/* ===[ Slider ]=== */
.rs-wrap {

   position: relative;
   max-width: 100%;

}
.rs-slide-bg { *zoom: 1 }
.rs-slider > li > a { display: block }
.rs-slider > li {

   list-style: none;
   filter: alpha(opacity=0);
   opacity: 0;
   width: 100%;
   height: 100%;
   margin: 0 -100% 0 0;
   padding: 0;
   float: left;
   position: relative;

   .rs-slider > li > a {
       padding: 0;
       background: none;
       -webkit-border-radius: 0;
       -moz-border-radius: 0;
       border-radius: 0;
   }

   .rs-slider > li img {
       display: block;
       max-width: 100%;
       max-height: 100%;
       -ms-interpolation-mode: bicubic;
   }

/* ===[ Thumbnails ]=== */
.rs-thumb-wrap { *zoom: 1 }

   .rs-thumb-wrap > a {
       display: block;
       float: left;
       position: relative;
       -moz-box-sizing: border-box;
       -webkit-box-sizing: border-box;
       box-sizing: border-box;
       -webkit-backface-visibility: hidden; /* Hardware accelerate to prevent jumps on transition */
   }

       .rs-thumb-wrap > a > img {
           max-width: 100%;
           max-height: 100%;
           display: block;
           -ms-interpolation-mode: bicubic;
       }

.rs-thumb-wrap > a:first-child { margin-left: 0!important }
/* ===[ Arrows ]=== */
.rs-arrows .rs-next,
.rs-arrows .rs-prev { z-index: 1; background-image: url("fancybox_sprite.png");}
.rs-arrows .rs-next,
.rs-arrows .rs-prev { z-index: 1; background-image: url("fancybox_sprite.png");}
.rs-arrows:hover .rs-next,
.rs-arrows:hover .rs-prev { z-index: 2; }
/* ===[ Captions ]=== */
.rs-caption {

   position: absolute;
   max-height: 100%;
   overflow: auto;
   -moz-box-sizing: border-box;
   -webkit-box-sizing: border-box;
   box-sizing: border-box;
   bottom: 0;
   left: 0;

}
.rs-caption.rs-top-left {

   top: 0;
   bottom: auto;

}
.rs-caption.rs-top-right {

   top: 0;
   right: 0;
   left: auto;
   bottom: auto;

}
.rs-caption.rs-bottom-left {

   bottom: 0;
   left: 0;

}
.rs-caption.rs-bottom-right {

   right: 0;
   left: auto;
   border-bottom: none;
   border-right: none;

}
.rs-caption.rs-top {

   top: 0;
   bottom: auto;
   width: 100%!important;

}
.rs-caption.rs-bottom { width: 100%!important }
.rs-caption.rs-left {

   top: 0;
   height: 100%;

}
.rs-caption.rs-right {

   top: 0;
   left: auto;
   right: 0;
   height: 100%;

}
/* ===[ Grid ]=== */
.rs-grid {

   position: absolute;
   overflow: hidden;
   width: 100%;
   height: 100%;
   display: none;

}
.rs-gridlet {

   position: absolute;
   opacity: 1;

}
/* Optional - remove captions at smaller screen widths
@media screen and (max-width: 480px) {
	.rs-caption { opacity: 0!important; }
}

/

.project_box > img {

   margin-left: 90px;

protocols, #polymers_protocols, #origami_protocols, #reaction_protocols, #nanocontainer_protocols, #imaging_protocols {

   font-size: 20px;
   font-weight: 300;
   margin-bottom: 30px;
   margin-left: 50px;

protocols > h2, #polymers_protocols > h2, #origami_protocols > h2, #reaction_protocols > h2, #nanocontainer_protocols > h2, #imaging_protocols > h2 {

   margin-bottom: 20px;
   margin-top: 20px;

protocols .interlude, #polymers_protocols .interlude, #origami_protocols .interlude, #reaction_protocols .interlude, #nanocontainer_protocols .interlude, #imaging_protocols .interlude {

   margin-left: -50px !important;

protocols > ul {

   margin-bottom: 30px;
   margin-left: 30px;
   margin-top: 20px;

}
li > ul {

   margin-left: 10px;

}	
/*achievement*/
.achievement_box{
	background: none repeat scroll 0 0 #FFFFFF;

   color: #000000;
   display: block;
   float: left;
   font-size: 18px;
   font-weight: 300;
   line-height: 1.6;
   margin-left: 180px;
   margin-right: auto;
   overflow: hidden;
   padding: 10px;
   width: 50%;

subnav-sticky-wrapper {

   height: 5px !important;

}
table {

   border-collapse: collapse;
   margin: auto auto 40px;
   width: 635px;;

}
th {

   background-color: #5F5F5F;
   border: 1px solid #999999;
   color: #FFFFFF;

}
tr td {

   border: 1px solid #999999;
   text-align: center;

}
tr.odd td {

   background-color: #EEEEEE;
   color: #000000;

}
.ref li {

   font-size: 14px;
   font-weight: 300;

}
</style>
<link href="http://openwetware.org/images/2/29/Nano_icon.png" rel="shortcut icon"> 

	
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<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Project Design</span></p>

                      <hr>

<p style = "color: #000000; font-size: 14px;">The overall design of this project is the construction of DNA antibodies that both simulate and outperform protein antibodies regarding structural and functional properties. We divided the aim of this project into two components: structure and function. </p>
<p style = "color: #000000; font-size: 14px;">Traditional antibodies are comprised of several immunoglobulin domains. There are both light chains (green and yellow) and heavy chains (red and blue). In total, there are 7 constant domains and 9 variable domains within the light and heavy chains. Essentially, it is the variable domain that gives the antibody special properties to bind to foreign antigens.</p>
<img src = "http://openwetware.org/images/f/f4/Screen_Shot_2014-10-23_at_12.17.38_AM.png">  
<p style = "color: #000000; font-size: 14px;">Furthermore, protein antibodies undergo VDJ recombination in which Variable, Diverse, and Joining gene segments coding the antibody can recombine in order to create diversity among the antibody structure and target specificity regarding receptors and foreign pathogens.</p>
<p style = "color: #000000; font-size: 14px;">Even though Antibodies are structurally and functionally sound, their overall potential is quite rigid with respect to structural DNA nanotechnology. Protein antibodies are quite difficult to incorporate into DNA structures because for one, they are protein based structures and two, the have structural limitations based on their overall shape and size limitations. DNA antibodies are composed of a base unit, which in this case is a DNA tile (shown in grey) and a characterizable portion which are the aptamers (shown in red, yellow, green, and blue). The tile can accommodate a variety of aptamers and orientations as shown below:
</p>
<img src = "http://openwetware.org/images/5/54/Screen_Shot_2014-10-23_at_12.24.13_AM.png">
<p style = "color: #000000; font-size: 14px;">Using the DNA tile and aptamers, we hope to mimic the antibody-antigen model. </p>
<img src = "http://openwetware.org/images/1/1b/Screen_Shot_2014-10-23_at_12.32.48_AM.png"><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">DNA Must Solve Three Things</span></p>
<hr>
<p style = "color: #000000; font-size: 14px;">1)The aptamer secondary structures must be characterized to the target site to induce binding.</p>
<p style = "color: #000000; font-size: 14px;">2)The combination/orientation of the aptamers relative to each other and the target site must be situated properly for optimal binding.</p>
<p style = "color: #000000; font-size: 14px;">3)The number of aptamers used to bind the target site may have negative effects. .</p><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Integrating Variability and Evolution</span></p>
<hr>
<p style = "color: #000000; font-size: 14px;text-decoration:underline;"><b>We construct Aptamer variety by setting the following:</b></p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1)Varying length</p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2)Random Body Sequence</p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3)Secondary Structures (Based on aptamer folding)</p>
<p style = "color: #000000; font-size: 14px;text-decoration:underline;"><b>Aptamer Evolution:</b></p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1)We use systematic evolution of ligands by exponential enrichment (SELEX) to characterize the aptamers to the target site. </p>
<p style = "color: #000000; font-size: 14px;text-decoration:underline;"><b>Base Structure (DNA Tile) variety:</b></p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1)Shape</p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2)Size</p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3)Aptamer Insert Orientation</p>
<p style = "color: #000000; font-size: 14px;text-decoration:underline;"><b>Base Structure (DNA Tile) evolution:</b></p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1)We evolve the optimal aptamer orientation to induce maximum binding.</p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2)We evolve the the optimal number of aptamers for maximum binding of our structures.</p>
<p style = "color: #000000; font-size: 14px;"><b>By applying these concepts, we are able to overcome the three factors that DNA antibodies need in order to support complementary (specific) binding with the target site. 
</b></p>
<br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">DNA Tile Antibody Creation</span></p>

                      <hr>
<a class="fancybox.iframe yt" href="//www.youtube.com/embed/6olQTUOQjCk?list=UUwmG88y6SZpJSxGwicxZEdw"><img src="http://openwetware.org/images/thumb/4/4e/Simulation_vid.jpg/800px-Simulation_vid.jpg"></a>

<p style = "color: #000000; font-size: 14px;">The orientation of the aptamer insert on the tile offers positional exchangeability as well as positional optimization of the aptamers. These different dynamics allow for optimized characterization of the target in mind as well as the opportunity to retrofit the DNA antibody to specific targeting sites.</p>
<p style = "color: #000000; font-size: 14px;">Creating a structurally and functionally specific DNA antibody that is specific to the target site can prove quite challenging. These are some factors that must be overcome. </p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1)The aptamer secondary structures must be characterized to the target site to induce binding</p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2)The combination/orientation of the aptamers relative to each other and the target site must be situated properly for optimal &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;binding.</p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3)The number of aptamers used to bind the target site may have negative effects. </p>	
<p style = "color: #000000; font-size: 14px;text-decoration: underline">Solving factor 1:</p>
<p style = "color: #000000; font-size: 14px;">In order to assure that the DNA aptamers used are capable of binding the target site, the secondary structure best suited for the binding site must be acquired. This is done by analyzing the aptamer total length and and random body length required for the target site. Based on the size of the target site, the DNA aptamer length is determined. To characterize binding, systematic evolution of ligands by exponential enrichment (SELEX) is performed to characterize the aptamers.</p>
<p style = "color: #000000; font-size: 14px;text-decoration: underline">Solving factor 2:</p>
<p style = "color: #000000; font-size: 14px;">Depending on whether or not the target site of interest has been characterized in advance and that the binding regions of interest on the target are known, the orientation of the aptamers are accustomed. If the specific binding regions of interest on the target site are known relative to their position, the orientation of the aptamers are positioned in space so that maximal binding can occur.If the binding regions on the target site are not known but the aptamers have been characterized, a process is conducted to characterize maximal orientation of the aptamers relative to the target site and each other:</p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The process is that the DNA aptamers are positioned on the tile in all possible arrangements to one another.</p>
<p style = "color: #000000; font-size: 14px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The most optimal binding arrangement found is then defined as the optimal binding orientation, or in short the “characterized orientation.”</p>


<p style = "color: #000000; font-size: 14px;text-decoration: underline">Solving factor 3:</p>
<p style = "color: #000000; font-size: 14px;">In order to see how many aptamers should be used, the number of binding sites on the target site must be characterized. If the goal is to bind multiple regions on the target site, then the number of aptamers must be adjusted accordingly. If the target site is not characterized for this feature, then “aptamer number specificity” must be determined. The process to determining aptamer number specificity is done similar to orientation specificity such that the aptamers used to bind are used in all possible combinations. That is the number of aptamers used to bind the target site is alternated relative to its orientation. Which ever combination of aptamer number works best is adopted. </p> <br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Conclusion</span></p>

                      <hr>

<p style = "color: #000000; font-size: 14px;">As shown above, our project design not only characterizes the DNA antibody structure, but also its binding properties relative to the target site. In our experiment, we exercise these concepts pertaining to the protein alpha-thrombin (A commonly used protein for aptamer testing). </p>
<img src = "http://openwetware.org/images/5/54/Screen_Shot_2014-10-23_at_12.24.13_AM.png">
<p style = "color: #000000; font-size: 14px;">The image above shows the DNA dile. Next, the aptamers are bound to the tile using known sequences. However, the exposed end of the aptamers are variable. The final step illustrates the target protein bound to the aptamer-tile complex. </p><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">References</span></p>
<p style = "color: #000000; font-size: 14px;">Barclay A (2003). "Membrane proteins with immunoglobulin-like domains – a master superfamily of interaction molecules". Semin Immunol 15 (4): 215–223</p>

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Biomod/2014/ASU/Design: Difference between revisions

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