Biomod/2014/UCR/Breaking RNA/Results: Difference between revisions
No edit summary |
No edit summary |
||
Line 24: | Line 24: | ||
<br /> | <br /> | ||
<font size="4.5"> | <font size="4.5"> | ||
<h1>Aptamer- | <h1>Aptamer-Kleptamer Pairs</h1> | ||
</font> | </font> | ||
Revision as of 23:17, 19 October 2014
<html lang=""> <head>
<meta charset='utf-8'> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel="stylesheet" href="styles.css"> <script src="http://code.jquery.com/jquery-latest.min.js" type="text/javascript"></script> <script src="script.js"></script> <title>Breaking RNA</title>
<style>
- column-one,.toc {
display: none;
} body.mediawiki {
background: url(http://openwetware.org/images/8/8c/Breaking_RNA_Background.png); background-size: cover;
}
- globalWrapper{
width: 80%; margin-left: 10%; position: absolute;
}
- content{
margin: 0px;
<!-- background: #e6e6e6; -->
background: white;
}
h1,h2,h3,p,ul,li {
font-family: 'Open Sans', sans-serif; font-weight: 300; color: Black; text-align: justify;
} h1
{ text-align: center; }
h3
{ font-size: 20px; position: relative; text-align:center; }
p
{ font-size: 16px; line-height: 30px; padding: 10px 150px; }
- objectives
{ }
- objectives ul
{ padding: 0 0 0 30%; margin: 0 auto; }
- objectives li
{ font-size: 18px; list-style: none; line-height: 30px; }
- submenu
{ margin: 0px 40px 0px 22px; }
- submenu a
{ color: black; text-decoration: underline; }
- submenu a:hover
{ color: rgba(255,255,255,0.99); }
- submenu ul
{ text-align: center; padding: 8px 0px; border: 3px solid black; background: rgba(70,150,70,0.8);
<!--background: url(http://openwetware.org/images/8/8c/Breaking_RNA_Background.png);
background-size: cover;-->
}
- submenu li
{ font-size: 18px; color: black; padding: 0px 20px; display: inline-block; }
- supplemenu
{ margin: 0px 40px 0px 22px; }
- supplemenu a
{ color: black; text-decoration: underline; }
- supplemenu a:hover
{ color: rgba(255,255,255,0.99); }
- supplemenu ul
{ text-align: center; padding: 15px 0px; border: 3px solid black; background: rgba(70,150,70,0.8);
}
- supplemenu li
{ font-size: 18px; color: black; padding: 0px 10px; display: inline-block; }
- floatmenu
{ position: fixed; bottom: 0; width: 78%; font-size: 18px; color: black; padding: 0px 10px; background: rgba(70,150,70,1); border: 3px solid black; }
- floatmenu td
{ text-align: center; height: 36px; }
- floatmenu td:hover
{ background: white; }
- button
{ border-left: 3px solid black; }
- floatmenu a
{ text-decoration: none; color: black; }
@import url(http://fonts.googleapis.com/css?family=Open+Sans:700);
#cssmenu {
background: url(http://openwetware.org/images/8/8c/Breaking_RNA_Background.png); background-size: cover; width: auto; border: 3px solid rgba(0,0,0,0.8);
} #cssmenu ul { list-style: none; margin: 0; padding: 0; line-height: 1;
text-align:center;
display: block; zoom: 1; } #cssmenu ul:after { content: " "; display: block; font-size: 0; height: 0; clear: both; visibility: hidden; } #cssmenu ul li { display: inline-block; padding: 0; margin: 0;
line-height: 1;
} #cssmenu.align-right ul li { float: right; } #cssmenu.align-center ul { text-align: center; } #cssmenu ul li a { color: #ffffff; text-decoration: none; display: block; padding: 15px 25px; font-family: 'Open Sans', sans-serif; font-weight: 300; text-transform: uppercase; font-size: 14px; position: relative; -webkit-transition: color .25s; -moz-transition: color .25s; -ms-transition: color .25s; -o-transition: color .25s; transition: color .25s; } #cssmenu ul li a:hover { color: #f2ff00; } #cssmenu ul li a:hover:before { width: 100%; } #cssmenu ul li a:after { content: ""; display: block; position: absolute; right: -3px; top: 19px; height: 6px; width: 6px; background: #ffffff; opacity: .5; } #cssmenu ul li a:before { content: ""; display: block; position: absolute; left: 0; bottom: 0; height: 3px; width: 0; background: #f2ff00; -webkit-transition: width .25s; -moz-transition: width .25s; -ms-transition: width .25s; -o-transition: width .25s; transition: width .25s; } #cssmenu ul li.last > a:after, #cssmenu ul li:last-child > a:after { display: none; } #cssmenu ul li.active a { color: #f2ff00; } #cssmenu ul li.active a:before { width: 100%; } #cssmenu.align-right li.last > a:after, #cssmenu.align-right li:last-child > a:after { display: block; } #cssmenu.align-right li:first-child a:after { display: none; } @media screen and (max-width: 768px) {
#supplemenu ul li {
float: none; display: block; } #supplemenu ul li a { width: 100%; } #cssmenu ul li { float: none; display: block; } #cssmenu ul li a { width: 100%; -moz-box-sizing: border-box; -webkit-box-sizing: border-box; box-sizing: border-box; border-bottom: 1px solid #ffffff; } #cssmenu ul li.last > a, #cssmenu ul li:last-child > a { border: 0; } #cssmenu ul li a:after { display: none; } #cssmenu ul li a:before { display: none; } }
</style>
</head>
<body>
</body>
</html>
Contents
ODE Models
Aptamer-Kleptamer Pairs
The oligonucleotide sequences are specified in the Supplementary section. Once we designed the necessary genelets and strands for our RNA clocks and switches systems, it was important to characterize and verify that our DNA sequences were designed correctly.
Enzyme Inhibition with RNA Aptamers
The topologies of our RNA clocks and switches rely on the idea that inhibition of a module is possible, whether it is self-mediated or caused by another module. A fluorescent RNA aptamer genelets, Malachite Green and Spinach, are used to characterize and quantify our system. This reporting system will be our visual determining guide for whether the enzyme's transcriptional funciton is altered, specifically inhibition. A spectrofluorometer is used to characterize the inhibition of T7 RNA Polymerase and SP6 RNA Polymerase by measuring fluorescence in the system.
These experiments successfully demonstrated three important concepts that are necessary to achieve oscillations and bistablity behaviors for our systems:
1) The proper binding of specific enzymes to the inhibiting aptamer sequences.
2) The production of RNA aptamer strands through transcription of DNA to RNA.
3) Inhibitor aptamer RNA product successfully suppresses the transcriptional function of their specific target enzyme.
DNA Strands Binding to RNA Aptamers
Aptamer-Kleptamer Interaction
Assembling the Circuits
<html> <body> <div id='cssmenu'> <ul>
<li><a href='http://openwetware.org/wiki/Biomod/2014/UCR/Breaking_RNA'><span>Home</span></a></li> <li><a href='http://openwetware.org/wiki/Biomod/2014/UCR/Breaking_RNA/Project'><span>Motivation & Objectives</span></a></li> <li><a href='http://openwetware.org/wiki/Biomod/2014/UCR/Breaking_RNA/Methods'><span>Results</span></a></li> <li><a href='http://openwetware.org/wiki/Biomod/2014/UCR/Breaking_RNA/Results'><span>Methods</span></a></li> <li><a href='http://openwetware.org/wiki/Biomod/2014/UCR/Breaking_RNA/Members'><span>Supplement</span></a></li> <li><a href='http://openwetware.org/wiki/Biomod/2014/UCR/Breaking_RNA/Achievements'><span>Team</span></a></li>
</ul> </div> </body> </html>