Team:SUSTC-Shenzhen-B/introduction

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                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Overview</a></li>
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Overview</a></li>
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Algorithm</a></li>
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                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/august">August</a></li>
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/august">August</a></li>
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/September">September</a></li>
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/September">September</a></li>
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                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/October">October</a></li>
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                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/high.school.visits">High School Visits</a></li>
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                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/October">October</a></li>
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<article>
<article>
                                 <h1>Introduction</h1>
                                 <h1>Introduction</h1>
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<h3 class="STYLE10">Transcription:</h3>
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<p>The transcription stage, the reading of genetic information from DNA, is composed of promoter binding and the activation of RNA polymerase, RNA transcript initiation and promoter escape, RNA transcript elongation, and transcript termination, and release. </p>
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<br>
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                 <h3 class="STYLE10">What is terminator?</h3>
                 <h3 class="STYLE10">What is terminator?</h3>
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<p>Terminators are genetic parts that usually occur at the end of a gene or operon and cause transcription to stop. In prokaryotes, terminators usually fall into two categories (1) rho-independent terminators and (2) rho-dependent terminators.</p>
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<img src="http://2012.igem.org/wiki/images/1/15/Second_structure.JPG " alt="" class="img_fl img_border alignright" />
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<p>Terminators are genetic parts that cause transcription to stop, which usually occur at the end of a gene or operon. In prokaryotes, terminators usually fall into two categories (1) rho-independent terminators and (2) rho-dependent terminators.</p>
<p>Rho-independent terminators are generally composed of palindromic sequence that forms a stem loop rich in G-C base pairs followed by several T bases. The conventional model of transcriptional termination is that the stem loop causes RNA polymerase to pause and transcription of the poly-A tail causes the RNA:DNA duplex to unwind and dissociate from RNA polymerase.
<p>Rho-independent terminators are generally composed of palindromic sequence that forms a stem loop rich in G-C base pairs followed by several T bases. The conventional model of transcriptional termination is that the stem loop causes RNA polymerase to pause and transcription of the poly-A tail causes the RNA:DNA duplex to unwind and dissociate from RNA polymerase.
</p>   
</p>   
<br>  
<br>  
               <h3 class="STYLE10">Terminator Efficiency:</h3>
               <h3 class="STYLE10">Terminator Efficiency:</h3>
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<p>Although terminators are positioned at the ends of genes, they also play irreplaceable roles. It is important that transcription is imperfectly terminated at some terminator so that the ratio of the amount of the mRNA transcribed from upstream and that from downstream of the terminator is controlled. This regulation is qualified by the termination efficiency.</p>
+
<p>In prokaryotes, many termination sites serve as targets for regulating gene expression. It is important that transcription is imperfectly terminated at some terminator so that the ratio of the amount of the mRNA transcribed from upstream and that from downstream of the terminator is controlled. This regulation is quantified by the termination efficiency (%T), which is determined by the terminator structure's ability to block the transcription by detaching the RNA polymerase from the DNA. In both in vivo and in vitro, the terminator efficiency of the terminator ranges from 2% to 95%.</p>
<br>  
<br>  
 +
              <h3 class="STYLE10">Software:</h3>
 +
<p> We also developed a <a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/Download">software</a> and a <a href="http://www.terminatorefficiency.com/"> web server</a> for people to calculate their terminators and built a
 +
<a href="http://www.terminatorefficiency.com/Database.html">database</a>
 +
of terminator efficiency which we believe is the largest database of such kind.</p>
 +
 +
 +
<br>
 +
              <h3 class="STYLE10">Algorithm:</h3>
 +
<p> Now, our <a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">algorithm</a> is mainly based on a algorithm put forward by d'Aubenton Carafa. Also, we had a look at other terminator-finding algorithms.</p>
 +
 +
 +
<br>
 +
              <h3 class="STYLE10">Tutorial:</h3>
 +
<p> Our software is easy to use. If you need any help, click <a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/Tutorial">here</a>.</p>
 +
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                <h2><p>Explanations</p></h2>
 
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                <img src="http://2012.igem.org/wiki/images/e/e9/Transcription.jpg" alt="" class="img_fl img_border" /> 
 
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<p>The process of transcription</p>
 
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<br>
 
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                <img src="http://2012.igem.org/wiki/images/1/15/Second_structure.JPG " alt="" class="img_fl img_border" />
 
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<p>the secondary structure of terminator</p>
 
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                        <h4>Design Ideas</h4>
 
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Latest revision as of 03:55, 27 October 2012

Title

Introduction

What is terminator?

Terminators are genetic parts that cause transcription to stop, which usually occur at the end of a gene or operon. In prokaryotes, terminators usually fall into two categories (1) rho-independent terminators and (2) rho-dependent terminators.

Rho-independent terminators are generally composed of palindromic sequence that forms a stem loop rich in G-C base pairs followed by several T bases. The conventional model of transcriptional termination is that the stem loop causes RNA polymerase to pause and transcription of the poly-A tail causes the RNA:DNA duplex to unwind and dissociate from RNA polymerase.


Terminator Efficiency:

In prokaryotes, many termination sites serve as targets for regulating gene expression. It is important that transcription is imperfectly terminated at some terminator so that the ratio of the amount of the mRNA transcribed from upstream and that from downstream of the terminator is controlled. This regulation is quantified by the termination efficiency (%T), which is determined by the terminator structure's ability to block the transcription by detaching the RNA polymerase from the DNA. In both in vivo and in vitro, the terminator efficiency of the terminator ranges from 2% to 95%.


Software:

We also developed a software and a web server for people to calculate their terminators and built a database of terminator efficiency which we believe is the largest database of such kind.


Algorithm:

Now, our algorithm is mainly based on a algorithm put forward by d'Aubenton Carafa. Also, we had a look at other terminator-finding algorithms.


Tutorial:

Our software is easy to use. If you need any help, click here.

South University of Science and Technology of China