Biomod/2012/Tianjin/Project/YDNA: Difference between revisions
No edit summary |
No edit summary |
||
| Line 9: | Line 9: | ||
float:left; | float:left; | ||
width:310px; | width:310px; | ||
} | |||
</style> | </style> | ||
<!-- Abstract in the page starts here --> | <!-- Abstract in the page starts here --> | ||
| Line 24: | Line 24: | ||
<div id="outborder" style="background: #FAFAFA url(http://biomod.net/sites/all/themes/biomod/images/stripe.png) repeat; height:360px; width:640px; padding:10px;"> | <div id="outborder" style="background: #FAFAFA url(http://biomod.net/sites/all/themes/biomod/images/stripe.png) repeat; height:360px; width:640px; padding:10px;"> | ||
<div id="inborder" style="background: #fff;height:340px;width:620px;padding:10px | <div id="inborder" style="background: #fff;height:340px;width:620px;padding:10px;"> | ||
<a href="http://openwetware.org/index.php?title=Biomod/2012/Tianjin/Project/YDNA&action=edit">this page edit</a> | <a href="http://openwetware.org/index.php?title=Biomod/2012/Tianjin/Project/YDNA&action=edit">this page edit</a> | ||
<div id="frametext"><br><br><span style="font-size:300%;">T</span>he Y-DNA was synthesized from three ssDNAs, each of which has partial complementary sequences to the other two ssDNAs. The Y-DNAs we produced only contains a blunt end, which makes it unable to polymerize. In order to polymerize, we need to create a sticky end in each branch, then use T4 ligase to link these ends.</div> | <div id="frametext"><br><br><span style="font-size:300%;">T</span>he Y-DNA was synthesized from three ssDNAs, each of which has partial complementary sequences to the other two ssDNAs. The Y-DNAs we produced only contains a blunt end, which makes it unable to polymerize. In order to polymerize, we need to create a sticky end in each branch, then use T4 ligase to link these ends.</div> | ||
Revision as of 11:11, 27 October 2012
<html> <style> /* Back to top css */ .back-to {
position: fixed; bottom: 35px; *bottom: 50px; _bottom: 35px; right: 10px; z-index: 999; width: 50px; zoom: 1 }
- html .back-to {
/* 不能用 _position 这种写法，因为它在IE7+也会执行expression。。。 */
position: expression(function(ele){ele.runtimeStyle.position='absolute';Expressions.style.position.fixed(ele);}(this))
}
.back-to {
float: right; display: block; width: 50px; height: 50px; background: url(http://a.xnimg.cn/imgpro/button/back-home.png) no-repeat 0 0; outline: 0 none; text-indent: -9999em;
}
.back-to:hover {
background-position: -50px 0 }
.back-to .back-top {
float: right; display: block; width: 50px; height: 50px; background: url(http://a.xnimg.cn/imgpro/button/back-top.png) no-repeat 0 0; margin-left: 10px; outline: 0 none; text-indent: -9999em }
.back-to .backtotop {
float: left; display: block; width: 50px; height: 50px; background: #666 url(http://a.xnimg.cn/imgpro/arrow/btt.png) 8px -57px no-repeat; margin-bottom: 15px; outline: 0 none; text-indent: -9999em; -moz-border-radius: 4px; -khtml-border-radius: 4px; -webkit-border-radius: 4px; border-radius: 4px; position: relative -moz-box-shadow: 0px 0px 15px #ccc; -webkit-box-shadow: 0px 0px 15px #ccc; box-shadow: 0px 0px 15px #ccc; }
.back-to .backtotop:hover {
background-color: #333; background-position: 8px 13px }
.back-to .backtotop .back-tip {
position: absolute; visibility: hidden; top: -31px; left: -10px }
.back-to .backtotop:hover .back-tip {
visibility: visible }
.back-to .back-top:hover {
background-position: -50px 0 }
/* changed default background */
.container{background-color: #ffffff; margin-top:0px}
- column-content {width: 0px; float: left; margin: 0 0 0 0;padding: 0;}
.firstHeading {display:none; width:0px;}
- column-one {display:none; width:0px;background-color: #ffffff;}
- globalWrapper{width: 970px; background-color: #ffffff; margin-left: auto; margin-right: auto;
-moz-box-shadow: 0px 0px 15px #ccc; -webkit-box-shadow: 0px 0px 15px #ccc; box-shadow: 0px 0px 15px #ccc;}
- content{ margin: 0 0 0 0; align: center; padding: 12px 12px 12px 12px; width: 940px;background-color: #ffffff; border: 0;}
- bodyContent{ width: 940px; align: center; background-color: #ffffff;}
- column-content{width: 970px;background-color: #ffffff;}
body { background: url(http://openwetware.org/images/1/13/TJU2012-Bg.gif) repeat-x #F9F9F7; }
/* basic link rules */
a:link {
color: #4F6DDC;
}
a:visited {
color: #4F6DDC;
}
a:hover {
color: #4F6DDC;
text-decoration: none;
}
/* -- navigator css -- */
- navDiv ul { margin: 0; padding: 0;}
- navDiv li { margin: 0; padding: 0;}
- navDiv a { margin: 0; padding: 0;}
- navDiv ul {list-style: none; z-index:999;}
- navDiv a {text-decoration: none;}
- navDiv
{ position: relative; height: 40px; width:970px; left: -12px; top: 0px; background-color: #111; background-repeat: repeat-x; box-shadow: 0px 5px 8px rgba(0,0,0,0.4); margin-bottom:20px; }
- navDiv > ul > li {
float: left; margin-left: 38px; position: relative;
}
- navDiv > ul > li > a {
color: #aaa; font-family: Verdana, 'Lucida Grande'; font-size: 15px; line-height: 40px; padding: 11px 20px;
-webkit-transition: color .15s;
-moz-transition: color .15s;
-o-transition: color .15s;
transition: color .15s;
}
- navDiv > ul > li > a:hover {color: #333333; background-color: #FFFFFF;}
- navDiv > ul > li > ul
{
opacity: 0; visibility: hidden; padding: 16px 0 20px 0; background-color: rgb(250,250,250); text-align: left; position: absolute; top: 30px; left: 50%; margin-left: -90px; width: 180px;
-webkit-transition: all .3s .1s;
-moz-transition: all .3s .1s;
-o-transition: all .3s .1s;
transition: all .3s .1s;
-webkit-border-radius: 5px;
-moz-border-radius: 5px;
border-radius: 5px;
-webkit-box-shadow: 0px 1px 3px rgba(0,0,0,.4);
-moz-box-shadow: 0px 1px 3px rgba(0,0,0,.4);
box-shadow: 0px 1px 3px rgba(0,0,0,.4);
}
- navDiv > ul > li:hover > ul
{
opacity: 1; top: 40px; visibility: visible;
}
- navDiv > ul > li > ul:before
{
content: ''; display: block; border-color: transparent transparent rgb(250,250,250) transparent; border-style: solid; border-width: 10px; position: absolute; top: -20px; left: 50%; margin-left: -10px;
}
- navDiv > ul ul > li { position: relative;}
- navDiv ul ul a
{
color: rgb(50,50,50); font-family: Verdana, 'Lucida Grande'; font-size: 13px; background-color: rgb(250,250,250); padding: 5px 8px 7px 16px; display: block;
-webkit-transition: background-color .1s;
-moz-transition: background-color .1s;
-o-transition: background-color .1s;
transition: background-color .1s;
}
- navDiv ul ul a:hover {background-color: rgb(240,240,240);}
- navDiv ul ul ul
{
visibility: hidden; opacity: 0; position: absolute; top: -16px; left: 206px; padding: 16px 0 20px 0; background-color: rgb(250,250,250); text-align: left; width: 160px;
-webkit-transition: all .3s;
-moz-transition: all .3s;
-o-transition: all .3s;
transition: all .3s;
-webkit-border-radius: 5px;
-moz-border-radius: 5px;
border-radius: 5px;
-webkit-box-shadow: 0px 1px 3px rgba(0,0,0,.4);
-moz-box-shadow: 0px 1px 3px rgba(0,0,0,.4);
box-shadow: 0px 1px 3px rgba(0,0,0,.4);
}
- navDiv ul ul > li:hover > ul { opacity: 1; left: 196px; visibility: visible;}
- navDiv ul ul a:hover
{
background-color: #777777; color: rgb(240,240,240);
}
/* Abstract in pages css */
- tianjin-right-content {
float: right; width: 280px; margin-left: 20px; font-family:"Calibri"; font-size:120%; }
- tianjin-right-content ul {
margin: 0; padding: 0 1em; }
- tianjin-right-content ul li {
list-style: none; margin: 0 0 1em 0; } .tianjin-description { font-size: small; color: #8A8A8A; }
/* Text content css*/
- text-content {
width:620px; font-family:"Calibri"; font-size:120%; padding: 10px 10px 10px 10px; }
/* footer in the middle */
- footer{position: center; width: 970px;}
</style>
<!--header starts here-->
<div id="header"> <div class="title" style="height: 180px;"> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin"><img src ="http://openwetware.org/images/7/79/TJU2012-Header.png"></a> <div style="float:right;"><img src="http://openwetware.org/images/c/cd/TJU2012-logo.png"></div> <div class="topsearch" style="position:absolute;top:175px;right:90px;"> <form method="GET" action="http://www.google.com/search"> <input type="hidden" name="hl" value="en"> <input type="hidden" name="sitesearch" value="openwetware.org"> <input type="hidden" name="domains" value="openwetware.org"> <input type="hidden" name="as_epq" value="Tianjin"> <input type="text" name="q" class="frm"><input type="submit" class="btn" value="Search"> </form> </div> </div> </div>
<!--navigator starts here-->
<div id="navDiv">
<ul>
<li class='active '><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin'><span>Home</span></a></li>
<li class='active '><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Team'><span>Team</span></a>
</li>
<li class='has-sub'><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Background'><span>Designs</span></a>
<ul>
<li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Background'><span>Background</span></a></li>
<li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/LogicGate'><span>The Logic Gate</span></a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/YDNA"><span>Y-DNA</span></a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Origami"><span>The Origami Amplifier</span></a></li>
</ul>
</li>
<li class='has-sub'><a href='#'><span>Experiments and Results</span></a>
<ul>
<li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/LogicGate'><span>The Logic Gate</span></a></li>
<li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/YDNA'><span>Y-DNA</span></a></li>
<li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/Origami'><span>The Origami Amplifier</span></a></li>
</ul>
</li> <li class='active'><a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Protocol"><span>Protocol</span></a>
</li>
<li class='active'><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Attributions'><span>Attributions</span></a></li>
</ul> </div>
<div id="toolBackTo" class="back-to" style="left: 1175px; "> <a stats="site_footer_back_to_top" class="backtotop" href="#top" onclick="if(Sizzle('#sidebar2 .ready-to-fix')[0]) Sizzle('#sidebar2 .ready-to-fix')[0].style.position = 'static';window.scrollTo(0,0);if(Sizzle('#sidebar2 .ready-to-fix')[0]) Sizzle('#sidebar2 .ready-to-fix')[0].style.position = '';return false;">Back to top <img stats="site_footer_back_to_top" src="http://openwetware.org/images/a/a7/TJU2012-Back-tip.png" class="back-tip"> </a> </div>
</html>
<html> <style>
- frametext {
font-family:Cambria,Calibri; font-size:140%; line-height:140%; float:left; width:310px; } </style> <!-- Abstract in the page starts here -->
<div id="tianjin-right-content"> <ul><li> <a href="#" title="#">Background</a> </li><li> <a href="#" title="#">The Logic Gate</a><div class="tianjin-description">1xxx</div> </li><li> <strong class="selflink">Y-DNA</strong><div class="tianjin-description">2xxx</div> </li><li> <a href="#" title="#">The Origami Amplifier</a><div class="tianjin-description">3xxx</div> </li></ul> </div>
<!-- main text frame starts here -->
<div id="outborder" style="background: #FAFAFA url(http://biomod.net/sites/all/themes/biomod/images/stripe.png) repeat; height:360px; width:640px; padding:10px;"> <div id="inborder" style="background: #fff;height:340px;width:620px;padding:10px;"> <a href="http://openwetware.org/index.php?title=Biomod/2012/Tianjin/Project/YDNA&action=edit">this page edit</a> <div id="frametext"><br><br><span style="font-size:300%;">T</span>he Y-DNA was synthesized from three ssDNAs, each of which has partial complementary sequences to the other two ssDNAs. The Y-DNAs we produced only contains a blunt end, which makes it unable to polymerize. In order to polymerize, we need to create a sticky end in each branch, then use T4 ligase to link these ends.</div> </div> </div>
<!-- text starts here --> <div id="text-content"> </html>
Y-DNA
The Y-DNA was synthesized from three ssDNAs, each of which has partial complementary sequences to the other two ssDNAs. From last part, we know that our logic gate have a high selectivity and is a precise logic gate. It occurred to us that we can utilize this logic gate to control the formation of Y-DNA by making the logic gate one of the ssDNAs. Without adding any ions, the logic gate remain in its original structure, which leave no sequence available to form Y-DNA with other two ssDNAs. If we add Cu2+, the Cuzyme will self-cleave and reveal a long sequence, making it feasible to form a Y-DNA. Moreover, we knew how many logic gate have self-cleave according to our research in the previous part, so we can control the cut logic gate generated. In this way, we can control when and how many Y-DNA be produced.
Because we want to use the logic gate to form Y-DNA, we need to specifically investigate its behavior in Y-DNA formation. Using NuPack (Figure X), we predicted that our original logic gate may fail. First, we simulated the scenario when there is only the logic gate and two ssDNAs in the solution. The result showed that the
