Biomod/2014/ASU/Design: Difference between revisions
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<div id="bodyContent"> | <div id="bodyContent"> | ||
<h3 id="siteSub">From OpenWetWare</h3> | <h3 id="siteSub">From OpenWetWare</h3> | ||
<div id="contentSub"><span class="subpages">< <a href="/wiki/Biomod" title="Biomod">Biomod</a> | <a href="/wiki/Biomod/ | <div id="contentSub"><span class="subpages">< <a href="/wiki/Biomod" title="Biomod">Biomod</a> | <a href="/wiki/Biomod/2014" title="Biomod/2014">2014</a></span></div> | ||
<div id="jump-to-nav">Jump to: <a href="#column-one">navigation</a>, <a href="#searchInput">search</a></div> <!-- start content --> | <div id="jump-to-nav">Jump to: <a href="#column-one">navigation</a>, <a href="#searchInput">search</a></div> <!-- start content --> | ||
<p> | <p> | ||
| Line 100: | Line 100: | ||
padding: 0; | padding: 0; | ||
background: #fff; | background: #fff; | ||
border: | border: none; | ||
} | } | ||
| Line 117: | Line 117: | ||
border: 0; | border: 0; | ||
font: inherit; | font: inherit; | ||
} | } | ||
| Line 145: | Line 145: | ||
h1, h2, #super-list, .box, .tagline, #index-list { | h1, h2, #super-list, .box, .tagline, #index-list { | ||
font-family: | font-family: Times New Roman; | ||
font-size: 18px; | |||
} | } | ||
| Line 181: | Line 182: | ||
a img { border: none; } | a img { border: none; } | ||
a.anchor{display: block; position: relative | a.anchor{display: block; position: relative; visibility: hidden;} | ||
p{ | p{ | ||
| Line 197: | Line 198: | ||
} | } | ||
nav { | nav { | ||
| Line 211: | Line 205: | ||
top: 0px; | top: 0px; | ||
left: 0px; | left: 0px; | ||
bottom: 0px; | |||
right: 0px; | right: 0px; | ||
z-index: 100; | z-index: 100; | ||
| Line 217: | Line 212: | ||
nav ul { | nav ul { | ||
width: 100%; | width: 100%; | ||
margin: 0px auto; | margin: 0px auto; | ||
padding: 0px; | padding: 0px; | ||
| Line 226: | Line 222: | ||
} | } | ||
nav ul li.selected { | nav ul li.selected { | ||
border-bottom: 10px | border-bottom: solid 10px #580000; | ||
} | } | ||
nav ul li.home { | nav ul li.home { | ||
padding: | padding: 0px; | ||
} | } | ||
nav ul a { | nav ul a { | ||
float: left; | float: left; | ||
| Line 244: | Line 236: | ||
font-size: 20px; | font-size: 20px; | ||
font-weight: 300; | font-weight: 300; | ||
padding: | padding: 0px 20px 0; | ||
} | } | ||
#content { | #content { | ||
| Line 269: | Line 246: | ||
#filters > li{ | #filters > li{ | ||
margin: | margin: 0px; | ||
display: inline-block; | display: inline-block; | ||
} | } | ||
| Line 317: | Line 294: | ||
.box.b1x2{ | .box.b1x2{ | ||
width: 930px; | width: 930px; | ||
height: | height: 4830px; | ||
} | } | ||
| Line 727: | Line 704: | ||
position: fixed; | position: fixed; | ||
background: #fff; | background: #fff; | ||
color: # | color: #000000; | ||
display: table-cell; | display: table-cell; | ||
text-align: center; | text-align: center; | ||
| Line 745: | Line 722: | ||
.box figcaption { | .box figcaption { | ||
background: none repeat scroll 0 0 | background: none repeat scroll 0 0 #fff; | ||
bottom: 0; | bottom: 0; | ||
font-size: | color:#000000; | ||
font-size: 16px; | |||
font-weight: 300; | font-weight: 300; | ||
padding-left: 5px; | padding-left: 5px; | ||
text-align: | text-align: left; | ||
width: 100%; | width: 100%; | ||
z-index: 4; | z-index: 4; | ||
| Line 997: | Line 975: | ||
li > ul { | li > ul { | ||
margin-left: | margin-left: 10px; | ||
} | } | ||
| Line 1,016: | Line 994: | ||
width: 50%; | 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"> | |||
/ | |||
. | <script src="https://biomod2013.googlecode.com/svn/trunk/js/jquery.isotope.min.js"></script> | ||
<script src="https://biomod2013.googlecode.com/svn/trunk/js/jquery.refineslide.min.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/fb/jquery.fancybox.pack.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/fb/helpers/jquery.fancybox-buttons.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/fb/helpers/jquery.fancybox-media.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/fb/helpers/jquery.fancybox-thumbs.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.easing.min.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.scrollUp.min.js"></script> | |||
text | |||
/ | |||
. | |||
/ | |||
. | |||
text | |||
/ | |||
/ | <script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.stellar.min.js"></script> | ||
. | <script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.sticky.js"></script> | ||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.scrollTo.min.js"></script> | |||
. | <script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.localscroll.min.js"></script> | ||
<script> | |||
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ | |||
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), | |||
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) | |||
})(window,document,'script','//www.google-analytics.com/analytics.js','ga'); | |||
text | |||
/ | |||
ga('create', 'UA-45176973-1', 'openwetware.org'); | |||
ga('send', 'pageview'); | |||
/ | </script> | ||
/ | <style type="text/css"> | ||
/*! fancyBox v2.1.5 fancyapps.com | fancyapps.com/fancybox/#license */ | |||
.fancybox-wrap, | |||
.fancybox-skin, | |||
.fancybox-outer, | |||
.fancybox-inner, | |||
.fancybox-image, | |||
.fancybox-wrap iframe, | |||
.fancybox-wrap object, | |||
.fancybox-nav, | |||
.fancybox-nav span, | |||
.fancybox-tmp | |||
{ | |||
padding: 0; | |||
margin: 0; | |||
border: 0; | |||
outline: none; | |||
vertical-align: top; | |||
/ | |||
. | |||
. | |||
} | } | ||
. | .fancybox-wrap { | ||
position: absolute; | |||
top: 0; | |||
left: 0; | |||
z-index: 8020; | |||
} | } | ||
.fancybox-skin { | |||
position: relative; | |||
background: #f9f9f9; | |||
color: #444; | |||
text-shadow: none; | |||
-webkit-border-radius: 4px; | |||
-moz-border-radius: 4px; | |||
border-radius: 4px; | |||
} | } | ||
.fancybox-opened { | |||
z-index: 8030; | |||
} | } | ||
.fancybox-opened .fancybox-skin { | |||
-webkit-box-shadow: 0 10px 25px rgba(0, 0, 0, 0.5); | |||
-moz-box-shadow: 0 10px 25px rgba(0, 0, 0, 0.5); | |||
box-shadow: 0 10px 25px rgba(0, 0, 0, 0.5); | |||
} | } | ||
.fancybox-outer, .fancybox-inner { | |||
position: relative; | |||
} | } | ||
.fancybox-inner { | |||
overflow: hidden; | |||
} | } | ||
.fancybox-type-iframe .fancybox-inner { | |||
-webkit-overflow-scrolling: touch; | |||
} | } | ||
.fancybox-error { | |||
. | color: #444; | ||
font: 14px/20px "Helvetica Neue",Helvetica,Arial,sans-serif; | |||
margin: 0; | |||
padding: 15px; | |||
white-space: nowrap; | |||
/ | |||
} | } | ||
.fancybox-image, .fancybox-iframe { | |||
display: block; | |||
width: 100%; | |||
height: 100%; | |||
. | |||
} | } | ||
.fancybox-image { | |||
max-width: 100%; | |||
max-height: 100%; | |||
} | } | ||
#fancybox-loading, .fancybox-close, .fancybox-prev span, .fancybox-next span { | |||
. | background-image: url('http://openwetware.org/images/5/55/Fancybox_sprite.png'); | ||
} | } | ||
#fancybox-loading { | |||
position: fixed; | |||
top: 50%; | |||
left: 50%; | |||
margin-top: -22px; | |||
margin-left: -22px; | |||
background-position: 0 -108px; | |||
opacity: 0.8; | |||
cursor: pointer; | |||
z-index: 8060; | |||
} | } | ||
/ | #fancybox-loading div { | ||
width: 44px; | |||
height: 44px; | |||
background: url('http://openwetware.org/images/d/d0/Fancybox_loading.gif') center center no-repeat; | |||
} | } | ||
.fancybox-close { | |||
position: absolute; | |||
top: -18px; | |||
right: -18px; | |||
width: 36px; | |||
height: 36px; | |||
cursor: pointer; | |||
z-index: 8040; | |||
} | } | ||
.fancybox-nav { | |||
position: absolute; | |||
top: 0; | |||
width: 40%; | |||
height: 100%; | |||
cursor: pointer; | |||
text-decoration: none; | |||
background: transparent url('http://openwetware.org/images/c/c0/Blank.gif'); /* helps IE */ | |||
-webkit-tap-highlight-color: rgba(0,0,0,0); | |||
z-index: 8040; | |||
/ | |||
} | } | ||
.fancybox-prev { | |||
left: 0; | |||
} | } | ||
. | .fancybox-next { | ||
right: 0; | |||
} | } | ||
. | .fancybox-nav span { | ||
position: absolute; | |||
top: 50%; | |||
width: 36px; | |||
height: 34px; | |||
margin-top: -18px; | |||
cursor: pointer; | |||
z-index: 8040; | |||
visibility: hidden; | |||
} | } | ||
. | .fancybox-prev span { | ||
left: 10px; | |||
background-position: 0 -36px; | |||
} | } | ||
. | .fancybox-next span { | ||
right: 10px; | |||
background-position: 0 -72px; | |||
} | } | ||
. | .fancybox-nav:hover span { | ||
visibility: visible; | |||
} | } | ||
. | .fancybox-tmp { | ||
position: absolute; | |||
top: -99999px; | |||
left: -99999px; | |||
visibility: hidden; | |||
max-width: 99999px; | |||
max-height: 99999px; | |||
overflow: visible !important; | |||
} | } | ||
/* Overlay helper */ | |||
.fancybox-lock { | |||
overflow: hidden !important; | |||
width: auto; | |||
/* | |||
} | } | ||
. | .fancybox-lock body { | ||
overflow: hidden !important; | |||
} | } | ||
.fancybox-lock-test { | |||
overflow-y: hidden !important; | |||
} | } | ||
.fancybox-overlay { | |||
position: absolute; | |||
top: 0; | |||
left: 0; | |||
overflow: hidden; | |||
display: none; | |||
z-index: 8010; | |||
background: url('http://openwetware.org/images/e/e0/Fancybox_overlay.png'); | |||
} | } | ||
.fancybox-overlay-fixed { | |||
position: fixed; | |||
bottom: 0; | |||
right: 0; | |||
} | } | ||
.fancybox-lock .fancybox-overlay { | |||
overflow: auto; | |||
overflow-y: scroll; | |||
} | } | ||
/* Title helper */ | |||
.fancybox-title { | |||
visibility: hidden; | |||
font: normal 13px/20px "Helvetica Neue",Helvetica,Arial,sans-serif; | |||
position: relative; | |||
text-shadow: none; | |||
z-index: 8050; | |||
} | |||
.fancybox-opened .fancybox-title { | |||
visibility: visible; | |||
} | |||
.fancybox-title-float-wrap { | |||
position: absolute; | |||
bottom: 0; | |||
right: 50%; | |||
margin-bottom: -35px; | |||
z-index: 8050; | |||
text-align: center; | |||
} | |||
.fancybox-title-float-wrap .child { | |||
display: inline-block; | |||
margin-right: -100%; | |||
padding: 2px 20px; | |||
background: transparent; /* Fallback for web browsers that doesn't support RGBa */ | |||
background: rgba(0, 0, 0, 0.8); | |||
-webkit-border-radius: 15px; | |||
-moz-border-radius: 15px; | |||
border-radius: 15px; | |||
text-shadow: 0 1px 2px #222; | |||
color: #FFF; | |||
font-weight: bold; | |||
line-height: 24px; | |||
white-space: nowrap; | |||
} | |||
.fancybox-title-outside-wrap { | |||
position: relative; | |||
margin-top: 10px; | |||
color: #fff; | |||
} | |||
.fancybox-title-inside-wrap { | |||
padding-top: 10px; | |||
.fancybox- | |||
{ | |||
padding | |||
} | } | ||
.fancybox-wrap { | .fancybox-title-over-wrap { | ||
position: absolute; | position: absolute; | ||
bottom: 0; | |||
left: 0; | left: 0; | ||
color: #fff; | |||
padding: 10px; | |||
background: #000; | |||
background: rgba(0, 0, 0, .8); | |||
} | } | ||
/*Retina graphics!*/ | |||
@media only screen and (-webkit-min-device-pixel-ratio: 1.5), | |||
only screen and (min--moz-device-pixel-ratio: 1.5), | |||
only screen and (min-device-pixel-ratio: 1.5){ | |||
-moz- | |||
.fancybox- | #fancybox-loading, .fancybox-close, .fancybox-prev span, .fancybox-next span { | ||
background-image: url('http://openwetware.org/images/b/b8/Fancybox_sprite%402x.png'); | |||
} | background-size: 44px 152px; /*The size of the normal image, half the size of the hi-res image*/ | ||
} | |||
#fancybox-loading div { | |||
background-image: url('http://openwetware.org/images/0/01/Fancybox_loading%402x.gif'); | |||
background-size: 24px 24px; /*The size of the normal image, half the size of the hi-res image*/ | |||
} | |||
} | } | ||
#fancybox-buttons { | |||
position: | position: fixed; | ||
left: 0; | |||
width: 100%; | |||
z-index: 8050; | |||
} | } | ||
#fancybox-buttons.top { | |||
top: 10px; | |||
} | } | ||
#fancybox-buttons.bottom { | |||
bottom: 10px; | |||
} | } | ||
#fancybox-buttons ul { | |||
color: | display: block; | ||
width: 166px; | |||
height: 30px; | |||
margin: 0 auto; | |||
padding: 0; | |||
list-style: none; | |||
border: 1px solid #111; | |||
border-radius: 3px; | |||
-webkit-box-shadow: inset 0 0 0 1px rgba(255,255,255,.05); | |||
-moz-box-shadow: inset 0 0 0 1px rgba(255,255,255,.05); | |||
box-shadow: inset 0 0 0 1px rgba(255,255,255,.05); | |||
background: rgb(50,50,50); | |||
background: -moz-linear-gradient(top, rgb(68,68,68) 0%, rgb(52,52,52) 50%, rgb(41,41,41) 50%, rgb(51,51,51) 100%); | |||
background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,rgb(68,68,68)), color-stop(50%,rgb(52,52,52)), color-stop(50%,rgb(41,41,41)), color-stop(100%,rgb(51,51,51))); | |||
background: -webkit-linear-gradient(top, rgb(68,68,68) 0%,rgb(52,52,52) 50%,rgb(41,41,41) 50%,rgb(51,51,51) 100%); | |||
background: -o-linear-gradient(top, rgb(68,68,68) 0%,rgb(52,52,52) 50%,rgb(41,41,41) 50%,rgb(51,51,51) 100%); | |||
background: -ms-linear-gradient(top, rgb(68,68,68) 0%,rgb(52,52,52) 50%,rgb(41,41,41) 50%,rgb(51,51,51) 100%); | |||
background: linear-gradient(top, rgb(68,68,68) 0%,rgb(52,52,52) 50%,rgb(41,41,41) 50%,rgb(51,51,51) 100%); | |||
filter: progid:DXImageTransform.Microsoft.gradient( startColorstr='#444444', endColorstr='#222222',GradientType=0 ); | |||
} | |||
#fancybox-buttons ul li { | |||
float: left; | |||
margin: 0; | margin: 0; | ||
padding: | padding: 0; | ||
} | } | ||
#fancybox-buttons a { | |||
display: block; | display: block; | ||
width: | width: 30px; | ||
height: | height: 30px; | ||
text-indent: -9999px; | |||
background-color: transparent; | |||
background-image: url('fancybox_buttons.png'); | |||
background-repeat: no-repeat; | |||
outline: none; | |||
opacity: 0.8; | |||
} | } | ||
#fancybox-buttons a:hover { | |||
opacity: 1; | |||
} | } | ||
#fancybox- | #fancybox-buttons a.btnPrev { | ||
background- | background-position: 5px 0; | ||
} | } | ||
#fancybox- | #fancybox-buttons a.btnNext { | ||
background-position: -33px 0; | |||
border-right: 1px solid #3e3e3e; | |||
} | |||
background-position: | |||
} | |||
#fancybox- | #fancybox-buttons a.btnPlay { | ||
background-position: 0 -30px; | |||
background: | |||
} | } | ||
#fancybox-buttons a.btnPlayOn { | |||
position | background-position: -30px -30px; | ||
} | } | ||
#fancybox-buttons a.btnToggle { | |||
position: | background-position: 3px -60px; | ||
border-left: 1px solid #111; | |||
border-right: 1px solid #3e3e3e; | |||
width: 35px | |||
- | |||
} | } | ||
#fancybox-buttons a.btnToggleOn { | |||
background-position: -27px -60px; | |||
} | } | ||
#fancybox-buttons a.btnClose { | |||
border-left: 1px solid #111; | |||
width: 35px; | |||
background-position: -56px 0px; | |||
} | } | ||
#fancybox-buttons a.btnDisabled { | |||
opacity : 0.4; | |||
cursor: default; | |||
cursor: | |||
} | } | ||
#fancybox-thumbs { | |||
left: | position: fixed; | ||
left: 0; | |||
width: 100%; | |||
overflow: hidden; | |||
z-index: 8050; | |||
} | } | ||
#fancybox-thumbs.bottom { | |||
bottom: 2px; | |||
} | } | ||
#fancybox-thumbs.top { | |||
top: 2px; | |||
} | } | ||
#fancybox-thumbs ul { | |||
position: | position: relative; | ||
list-style: none; | |||
margin: 0; | |||
padding: 0; | |||
} | } | ||
#fancybox-thumbs ul li { | |||
float: left; | |||
padding: 1px; | |||
opacity: 0.5; | |||
} | } | ||
#fancybox-thumbs ul li.active { | |||
opacity: 0.75; | |||
padding: 0; | |||
border: 1px solid #fff; | |||
} | } | ||
#fancybox-thumbs ul li:hover { | |||
opacity: 1; | |||
} | } | ||
#fancybox-thumbs ul li a { | |||
display: block; | |||
position: relative; | |||
overflow: hidden; | overflow: hidden; | ||
border: 1px solid #222; | |||
background: #111; | |||
outline: none; | |||
} | } | ||
#fancybox-thumbs ul li img { | |||
position: | display: block; | ||
position: relative; | |||
border: 0; | |||
padding: 0; | |||
max-width: none; | |||
} | } | ||
p.serif { | |||
. | font-family: "Times New Roman", Times, serif; | ||
} | |||
.box.b1x3{ | |||
width: 853px; | |||
height: 465px; | |||
} | } | ||
#b2x2 | |||
{ | |||
position:fixed; | |||
} | } | ||
#main-nav { | |||
width: 100%; | |||
height: 67px; | |||
background: #f2f2f2; | |||
} | } | ||
#main-nav .subnav { | |||
. | display: none; | ||
position: absolute; | |||
top: 67px; | |||
left: 0px; | |||
right:0px; | |||
width: 100%; | |||
list-style-type: none; | |||
background: #f2f2f2; | |||
margin: 0; | |||
border:solid 1px #eeeeee; | |||
z-index:5; | |||
padding:0; | |||
} | } | ||
#main-nav .subnav li { | |||
display: block; | |||
border-bottom: solid 1px #580000; | |||
margin:0; | |||
} | |||
#main-nav .subnav li a { | |||
color: #333; | |||
height:18px; | |||
font-size:20px; | |||
} | } | ||
#main-nav .subnav li a:hover { | |||
background:#f9f9f9; | |||
} | |||
#nav-primary { | |||
list-style-type: none; | |||
margin: 0; | |||
float: left; | |||
padding:0; | |||
} | |||
#nav-primary li { | |||
float: left; | |||
position: relative; | |||
} | |||
#nav-primary li a { | |||
float: left; | |||
color: #000; | |||
text-align: center; | |||
font-size: 20px; | |||
height: 40px; | |||
padding-top: 35px; | |||
line-height: 13px; | |||
width:120px; | |||
text-decoration:none; | |||
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<section id="content"> | |||
<nav id = "main-nav"> | |||
<ul id="nav-primary" > | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU"><i class="menu-icon icon-team"></i><span>Main</span></a></li> | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Project"><i class="menu-icon icon-team"></i><span>Project</span></a></li> | |||
<li class = "selected"><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Design"><i class="menu-icon icon-studio"></i><span>Design</span></a></li> | |||
<li><a href="#"><i class="menu-icon icon-studio"></i><span>Experiment</span></a> | |||
<ul class = "subnav"> | |||
<li><a href = "http://openwetware.org/wiki/Biomod/2014/ASU/Materials"><span>Materials</span></a></li> | |||
<li><a href = "http://openwetware.org/wiki/Biomod/2014/ASU/Protocols"><span>Protocols</span></a></li> | |||
</ul></li> | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Results"><i class="menu-icon icon-studio"></i><span>Results</span></a></li> | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Discussion"><i class="menu-icon icon-studio"></i><span>Discussion</span></a></li> | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Team"><i class="menu-icon icon-studio"></i><span>Team</span></a></li> | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Acknowledgement"><i class="menu-icon icon-studio"></i><span>Acknowledgements</span></a></li> | |||
</ul> | |||
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<div id="container" class="clearfix"> | |||
<div id = "b2x2"> | |||
<div class="box b2x2 tease" data-symbol="intro" data-category="student"> | |||
<img src = "http://openwetware.org/images/1/1b/Rsz_ascube.png"> | |||
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</div> | |||
<div class="box b1x2" data-symbol="description" data-category="student"> | |||
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Overall Design</span></p> | |||
<hr> | |||
<p style = "color: #000000; font-size: 18px;">The goal of this project was to develop a method to make a DNA structure with the same capabilities for protein binding as a protein antibody. We aimed to design a DNA structure with the ability to specifically bind to a target by exploiting the 3 dimensional surface of the protein. </p> | |||
# | |||
</ | |||
<p style = "color: #000000; font-size: 18px;">Traditional antibodies are comprised of several domains comprising light chains and heavy chains (Figure D1). The antibody consists of a variable domain and a constant domain (Figure D2) in which the variable domain allows the antibody to bind to foreign antigens.</p><br> | |||
<img src = "http://openwetware.org/images/2/22/Screen_Shot_2014-10-25_at_8.32.26_PM.png"><br> | |||
<p style = "color: #000000; font-size: 18px;">One of the key design strategies for our project was to create a wide variety of DNA ‘antibodies’ by adding random sequences into oligonucleotides which are then incorporated into a DNA tile. These oligonucleotides will then form into a diverse range of secondary structures. The aim is that tiles with a correct combination of oligonucleotides will coordinate among themselves to bind a target protein. | |||
Using these DNA tiles and oligonucleotides, we hope to mimic the antibody-antigen model as depicted in Figure D3:</p><br> | |||
<img src = "http://openwetware.org/images/3/35/Screen_Shot_2014-10-25_at_9.03.08_PM.png"><br> | |||
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">DNA Tile Design</span></p> | |||
<hr> | |||
<p style = "color: #000000; font-size: 18px;">Previous studies have shown that multiple aptamers for alpha-thrombin on the edge of a DNA tile could bind a protein multivalently at specific distances from one another<sup style = "font-size: 12px;">2</sup>. However, we have focused on multivalency to the geometric face of a DNA nanostructure, rather than the edge, because (1) this limits the number of possible conformations that a set of strands can take, simplifying the selective process, (2) it allows for two-dimensional rather than solely one-dimensional spacing of aptamer elements, and (3) planar spaces on larger origami structures generally have a large amount of functionalizable space, while edges are frequently nonexistent or busy.</p> | |||
<p style = "color: #000000; font-size: 18px;">The DNA tile structure was designed to be 28 nm x 9 nm. The tile consisted of 4 DNA bundles (helices) consisting of a total of 84 base pairs. The 4 oligonucleotides are incorporated in the 2nd and 3rd bundles as shown below in Figure D4: </p><br> | |||
<img src = "http://openwetware.org/images/1/11/Screen_Shot_2014-10-25_at_9.05.40_PM.png"><br> | |||
<p style = "color: #000000; font-size: 18px;">Alpha-thrombin was chosen as the target protein for this project as it was well characterized and had been used previously in studies investigating aptamer binding. The size of the DNA tile was chosen so that oligonucleotides could be inserted at a spacing relative to the dimensions of alpha-thrombin shown below. </p><br> | |||
<img src = "http://openwetware.org/images/8/81/Screen_Shot_2014-10-25_at_9.07.16_PM.png"><br> | |||
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Oligonucleotide Design</span></p> | |||
<hr> | |||
<p style = "color: #000000; font-size: 18px;">We had to consider several factors in the design of the oligonucleotide strands to maximize the chances for the binding of the DNA antibody to alpha-thrombin. In order to achieve this we created 46 base pair oligonucleotides containing a 20 base pair random DNA sequence in the middle of the strand. Two known DNA sequences flank the random oligonucleotide sequence: a conserved 15 base pair region at the 5’ end of each sequence allows for amplification by PCR, and another 11 base pair region at the 3’ end is responsible for correct insertion into the DNA tile and also acts as a primer during PCR.</p><br> | |||
<img src = "http://openwetware.org/images/8/8f/Screen_Shot_2014-10-25_at_9.09.28_PM.png"><br> | |||
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Selection Process</span></p> | |||
<hr> | |||
<p style = "color: #000000; font-size: 18px;">One of the key challenges in this process is the characterization of binding between proteins and DNA antibodies. A pool of DNA antibodies were created using random sequences which result in many thousands of different oligonucleotide combinations and sequences on each DNA tile. Each of these combinations of random oligonucleotides will create unique and diverse secondary and quaternary structures on the DNA tile as the oligonucleotides interact with themselves and one another. The protein will selectively bind DNA antibodies with a complementary structure. This will allow for selection of single DNA antibodies from a pool of many thousands of variations. Electrophoretic mobility shift assay (EMSA) and affinity chromatography was used to characterize this process and to identify the DNA antibodies that have bound to the target protein. Randomized oligonucleotides which compose the selected antibodies can then be amplified by PCR and then reutilised in a new generation of tiles composed of oligonucleotides from the enriched pool. This process of selection can then be repeated in a similar method to systematic evolution of ligands by exponential enrichment (SELEX). Multiple cycles of this procedure can be performed to narrow the pool and enhance specific binding.</p><br> | |||
<img src = "http://openwetware.org/images/f/fe/Screen_Shot_2014-10-25_at_9.11.35_PM.png"><br> | |||
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">DNA Antibody Potential Applications</span></p> | |||
<hr> | |||
<p style = "color: #000000; font-size: 18px;">DNA antibodies due to their versatility in structure and function can be used for a variety of applications such as:</p> | |||
<p style = "color: #000000; font-size: 18px;"> 1) Immunology and drug targeting/delivery.</p> | |||
<p style = "color: #000000; font-size: 18px;"> 2) Low cost high stability antibody substitute</p> | |||
<p style = "color: #000000; font-size: 18px;"> 3) Enhanced programmable antibodies</p> | |||
<p style = "color: #000000; font-size: 18px;"> 4) Precipitation/tagging of proteins</p> | |||
<p style = "color: #000000; font-size: 18px;"> 5) Incorporation into larger DNA nanostructures </p> | |||
<br> | |||
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Conclusion of Project Design</span></p> | |||
<hr> | |||
<p style = "color: #000000; font-size: 18px;">As shown above, our project design not only characterizes the DNA antibody structure, but also the binding properties relative to the target protein. In our experiment, we utilize several conformations of oligonucleotides at the insertion site of the DNA tile in order to explore different pathways of constructing DNA antibodies.</p><br> | |||
<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> | |||
<br> | |||
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">References:</span></p> | |||
<hr> | |||
<p style = "color: #000000; font-size: 18px;"> 1. Barclay A (2003). "Membrane proteins with immunoglobulin-like domains – a master superfamily of interaction </p> | |||
<p style = "color: #000000; font-size: 18px;"> molecules". Semin Immunol 15 (4): 215–223</p> | |||
<p style = "color: #000000; font-size: 18px;"> 2. Rinker, S., Ke, Y., Liu, Y. Chhabra, R., Yan, H. Self-assembled DNA nanostructures for distance-dependent</p> | |||
<p style = "color: #000000; font-size: 18px;"> multivalent ligand-protein binding. Nature Nanotechnology 3, 418-422 (2008).</p> | |||
<p style = "color: #000000; font-size: 18px;"> 3. https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/1/t7009pis.pdf</p> | |||
</div> | </div> | ||
Latest revision as of 23:36, 25 October 2014
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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%;
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text-align: center;
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z-index: 99;
background-image: url("http://openwetware.org/images/5/55/Fancybox_sprite.png");
width: 36px;
height: 36px;
top: 200px;
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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;
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position: fixed;
background: #fff;
color: #000000;
display: table-cell;
text-align: center;
vertical-align: middle;
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figure.box > *{
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text-align: left;
width: 100%;
z-index: 4;
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/* Start: Recommended Isotope styles */
/**** Isotope Filtering ****/
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- /
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margin-bottom: 30px;
margin-left: 50px;
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li > ul {
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font-weight: 300;
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font-size: 14px;
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</p><p>
<section id="content">
<nav id = "main-nav">
<ul id="nav-primary" >
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU"><i class="menu-icon icon-team"></i><span>Main</span></a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Project"><i class="menu-icon icon-team"></i><span>Project</span></a></li>
<li class = "selected"><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Design"><i class="menu-icon icon-studio"></i><span>Design</span></a></li>
<li><a href="#"><i class="menu-icon icon-studio"></i><span>Experiment</span></a>
<ul class = "subnav">
<li><a href = "http://openwetware.org/wiki/Biomod/2014/ASU/Materials"><span>Materials</span></a></li>
<li><a href = "http://openwetware.org/wiki/Biomod/2014/ASU/Protocols"><span>Protocols</span></a></li>
</ul></li>
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Results"><i class="menu-icon icon-studio"></i><span>Results</span></a></li>
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<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Overall Design</span></p>
<hr>
<p style = "color: #000000; font-size: 18px;">The goal of this project was to develop a method to make a DNA structure with the same capabilities for protein binding as a protein antibody. We aimed to design a DNA structure with the ability to specifically bind to a target by exploiting the 3 dimensional surface of the protein. </p>
<p style = "color: #000000; font-size: 18px;">Traditional antibodies are comprised of several domains comprising light chains and heavy chains (Figure D1). The antibody consists of a variable domain and a constant domain (Figure D2) in which the variable domain allows the antibody to bind to foreign antigens.</p><br>
<img src = "http://openwetware.org/images/2/22/Screen_Shot_2014-10-25_at_8.32.26_PM.png"><br>
<p style = "color: #000000; font-size: 18px;">One of the key design strategies for our project was to create a wide variety of DNA ‘antibodies’ by adding random sequences into oligonucleotides which are then incorporated into a DNA tile. These oligonucleotides will then form into a diverse range of secondary structures. The aim is that tiles with a correct combination of oligonucleotides will coordinate among themselves to bind a target protein.
Using these DNA tiles and oligonucleotides, we hope to mimic the antibody-antigen model as depicted in Figure D3:</p><br>
<img src = "http://openwetware.org/images/3/35/Screen_Shot_2014-10-25_at_9.03.08_PM.png"><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">DNA Tile Design</span></p>
<hr>
<p style = "color: #000000; font-size: 18px;">Previous studies have shown that multiple aptamers for alpha-thrombin on the edge of a DNA tile could bind a protein multivalently at specific distances from one another<sup style = "font-size: 12px;">2</sup>. However, we have focused on multivalency to the geometric face of a DNA nanostructure, rather than the edge, because (1) this limits the number of possible conformations that a set of strands can take, simplifying the selective process, (2) it allows for two-dimensional rather than solely one-dimensional spacing of aptamer elements, and (3) planar spaces on larger origami structures generally have a large amount of functionalizable space, while edges are frequently nonexistent or busy.</p>
<p style = "color: #000000; font-size: 18px;">The DNA tile structure was designed to be 28 nm x 9 nm. The tile consisted of 4 DNA bundles (helices) consisting of a total of 84 base pairs. The 4 oligonucleotides are incorporated in the 2nd and 3rd bundles as shown below in Figure D4: </p><br>
<img src = "http://openwetware.org/images/1/11/Screen_Shot_2014-10-25_at_9.05.40_PM.png"><br>
<p style = "color: #000000; font-size: 18px;">Alpha-thrombin was chosen as the target protein for this project as it was well characterized and had been used previously in studies investigating aptamer binding. The size of the DNA tile was chosen so that oligonucleotides could be inserted at a spacing relative to the dimensions of alpha-thrombin shown below. </p><br>
<img src = "http://openwetware.org/images/8/81/Screen_Shot_2014-10-25_at_9.07.16_PM.png"><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Oligonucleotide Design</span></p>
<hr>
<p style = "color: #000000; font-size: 18px;">We had to consider several factors in the design of the oligonucleotide strands to maximize the chances for the binding of the DNA antibody to alpha-thrombin. In order to achieve this we created 46 base pair oligonucleotides containing a 20 base pair random DNA sequence in the middle of the strand. Two known DNA sequences flank the random oligonucleotide sequence: a conserved 15 base pair region at the 5’ end of each sequence allows for amplification by PCR, and another 11 base pair region at the 3’ end is responsible for correct insertion into the DNA tile and also acts as a primer during PCR.</p><br>
<img src = "http://openwetware.org/images/8/8f/Screen_Shot_2014-10-25_at_9.09.28_PM.png"><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Selection Process</span></p>
<hr>
<p style = "color: #000000; font-size: 18px;">One of the key challenges in this process is the characterization of binding between proteins and DNA antibodies. A pool of DNA antibodies were created using random sequences which result in many thousands of different oligonucleotide combinations and sequences on each DNA tile. Each of these combinations of random oligonucleotides will create unique and diverse secondary and quaternary structures on the DNA tile as the oligonucleotides interact with themselves and one another. The protein will selectively bind DNA antibodies with a complementary structure. This will allow for selection of single DNA antibodies from a pool of many thousands of variations. Electrophoretic mobility shift assay (EMSA) and affinity chromatography was used to characterize this process and to identify the DNA antibodies that have bound to the target protein. Randomized oligonucleotides which compose the selected antibodies can then be amplified by PCR and then reutilised in a new generation of tiles composed of oligonucleotides from the enriched pool. This process of selection can then be repeated in a similar method to systematic evolution of ligands by exponential enrichment (SELEX). Multiple cycles of this procedure can be performed to narrow the pool and enhance specific binding.</p><br>
<img src = "http://openwetware.org/images/f/fe/Screen_Shot_2014-10-25_at_9.11.35_PM.png"><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">DNA Antibody Potential Applications</span></p>
<hr>
<p style = "color: #000000; font-size: 18px;">DNA antibodies due to their versatility in structure and function can be used for a variety of applications such as:</p>
<p style = "color: #000000; font-size: 18px;"> 1) Immunology and drug targeting/delivery.</p>
<p style = "color: #000000; font-size: 18px;"> 2) Low cost high stability antibody substitute</p>
<p style = "color: #000000; font-size: 18px;"> 3) Enhanced programmable antibodies</p>
<p style = "color: #000000; font-size: 18px;"> 4) Precipitation/tagging of proteins</p>
<p style = "color: #000000; font-size: 18px;"> 5) Incorporation into larger DNA nanostructures </p>
<br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Conclusion of Project Design</span></p>
<hr>
<p style = "color: #000000; font-size: 18px;">As shown above, our project design not only characterizes the DNA antibody structure, but also the binding properties relative to the target protein. In our experiment, we utilize several conformations of oligonucleotides at the insertion site of the DNA tile in order to explore different pathways of constructing DNA antibodies.</p><br>
<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>
<br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">References:</span></p>
<hr>
<p style = "color: #000000; font-size: 18px;"> 1. Barclay A (2003). "Membrane proteins with immunoglobulin-like domains – a master superfamily of interaction </p>
<p style = "color: #000000; font-size: 18px;"> molecules". Semin Immunol 15 (4): 215–223</p>
<p style = "color: #000000; font-size: 18px;"> 2. Rinker, S., Ke, Y., Liu, Y. Chhabra, R., Yan, H. Self-assembled DNA nanostructures for distance-dependent</p>
<p style = "color: #000000; font-size: 18px;"> multivalent ligand-protein binding. Nature Nanotechnology 3, 418-422 (2008).</p>
<p style = "color: #000000; font-size: 18px;"> 3. https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/1/t7009pis.pdf</p>
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