Difference between revisions of "Team:SJTU-BioX-Shanghai/Basic Part"

(Prototype team page)
 
Line 1: Line 1:
−
{{SJTU-BioX-Shanghai}}
+
<html lang="en">
−
<html>
+
  
−
<div class="column full_size judges-will-not-evaluate">
+
<head>
−
<h3>★  ALERT! </h3>
+
    <meta charset="utf-8">
−
<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
+
    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
−
<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
+
    <meta http-equiv="x-ua-compatible" content="ie=edge">
−
</div>
+
    <link href="https://2017.igem.org/Template:SJTU-BioX-Shanghai/CSS/bootstrap?action=raw&ctype=text/css" rel="stylesheet">
−
<div class="clear"></div>
+
    <link href="https://2017.igem.org/Template:SJTU-BioX-Shanghai/CSS/ripple?action=raw&ctype=text/css" rel="stylesheet">
 +
    <link href="https://2017.igem.org/Template:SJTU-BioX-Shanghai/CSS/font-awesome?action=raw&ctype=text/css" rel="stylesheet">
 +
    <link href="https://2017.igem.org/Template:SJTU-BioX-Shanghai/CSS/style?action=raw&ctype=text/css" rel="stylesheet">
 +
    <!--[if lt IE 10]>
 +
            <center>您使用的是过时的浏览器，浏览本网页可能会有异常。</center>
 +
            <center>You are using an outdated browser and this page may not display properly.</center>
 +
        <![endif]-->
 +
    <style>
 +
        .full-bg.full-bg-0 {
 +
            background-image: url("https://static.igem.org/mediawiki/2017/e/ed/T--SJTU-BioX-Shanghai--17003.jpeg");
 +
        }
 +
       
 +
        @media only screen and (min-width: 768px) {
 +
            .full-bg.full-bg-0 {
 +
                background-image: url("https://static.igem.org/mediawiki/2017/e/e0/T--SJTU-BioX-Shanghai--17003-hi.jpeg");
 +
            }
 +
        }
 +
       
 +
        .my-title {
 +
            text-align: center;
 +
            padding-bottom:1rem
 +
        }
 +
       
 +
        .nav2-brand {
 +
            width: 8em;
 +
        }
 +
       
 +
        .maintext p {
 +
            text-align: justify;
 +
        }
 +
    </style>
 +
</head>
  
−
<div class="column full_width">
+
<body>
 +
    <div class="fluid-bg full-bg-body">
 +
        <div class="full-bg mainbox depth-1-half full-bg-0">
 +
            <nav class="navbar navbar1 navbar-expand-lg navbar-dark">
 +
                <div class="container">
 +
                    <a class="navbar-brand" href="https://2017.igem.org/Team:SJTU-BioX-Shanghai"><img src="https://static.igem.org/mediawiki/2017/b/be/T--SJTU-BioX-Shanghai--logo.png" height="55" /></a>
 +
                    <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarNav1" aria-controls="navbarNav1" aria-expanded="false" aria-label="Toggle navigation">
 +
                            <div class="hamburger" id="ham1">
 +
                                <span class="line"></span>
 +
                                <span class="line"></span>
 +
                                <span class="line"></span>
 +
                            </div>
 +
                        </button>
 +
                    <div class="collapse navbar-collapse" id="navbarNav1">
 +
                        <ul class="navbar-nav mr-auto">
 +
                            <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Description" class="nav-link">Project</a></li>
 +
                            <li class="nav-item active"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Notebook" class="nav-link">Wet Lab</a></li>
 +
                            <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Loader" class="nav-link">Device</a></li>
 +
                            <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Model" class="nav-link">Model</a></li>
 +
                            <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/HP" class="nav-link">Human Practice</a></li>
  
 +
                            <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Team" class="nav-link">Team</a></li>
 +
                        </ul>
 +
                        <ul class="navbar-nav ml-auto">
 +
                            <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Basic_Parts-cn" class="nav-link jtzw">简体中文</a></li>
 +
                        </ul>
 +
                    </div>
 +
                </div>
 +
            </nav>
 +
            <div class="navbox">
 +
                <nav class="navbar navbar3 navbar-dark">
 +
                    <div class="container">
 +
                        <a class="navbar-brand" href="#">Wet Lab</a>
 +
                    </div>
 +
                </nav>
 +
                <nav class="navbar navbar2 navbar-expand-lg navbar-dark">
 +
                    <div class="container">
 +
                        <div class="nav2-brand hide-nav2-brand">
 +
                            <a class="navbar-brand" href="#">Wet Lab</a>
 +
                        </div>
 +
                        <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarNav2" aria-controls="navbarNav2" aria-expanded="false" aria-label="Toggle navigation">
 +
                                <div class="hamburger" id="ham2">
 +
                                        <span class="line"></span>
 +
                                        <span class="line"></span>
 +
                                        <span class="line"></span>
 +
                                </div>
 +
                            </button>
 +
                        <div class="collapse navbar-collapse " id="navbarNav2">
 +
                            <ul class="navbar-nav mr-auto">
 +
                                <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Notebook" class="nav-link">Notebook</a></li>
 +
                                <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Protocol" class="nav-link">Protocol</a></li>
 +
                                <li class="nav-item active"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Basic_Parts" class="nav-link">Basic Parts</a></li>
 +
                                <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Composite_Parts" class="nav-link">Composite Parts</a></li>
 +
                                <li class="nav-item"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Part_Collection" class="nav-link">Part Collection</a></li>
 +
                            </ul>
 +
                        </div>
 +
                    </div>
 +
                </nav>
  
−
<h1>Basic Parts</h1>
+
            </div>
  
−
<p>
+
        </div>
−
A <b>basic part</b> is a functional unit of DNA that cannot be subdivided into smaller component parts. <a href="http://parts.igem.org/wiki/index.php/Part:BBa_R0051">BBa_R0051</a> is an example of a basic part, a promoter regulated by lambda cl.
+
        <div class="big-head h1-my-responsive"> <img src="https://static.igem.org/mediawiki/2017/5/52/T--SJTU-BioX-Shanghai--quan.png" class="img-fluid">Basic Parts</div>
−
</p>
+
        <div class="container maink">
 +
            <div class="container maintext">
 +
                <div class="row">
 +
                    <div class="col-lg-1">
 +
                    </div>
 +
                    <div class="col-12 col-lg-10">
 +
                        <div class="my-title h5-my-responsive">Introduction</div>
 +
                        <p>This year, our team will choose to present STAR 3, another modified STAR (Small Transcriptional-Activating RNA) for the award of the basic part (<a target="_blank" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2285020">BBa_K2285020</a>).
 +
                            Our project was based on iGEM16_Imperial STAR system (to distinguish it from our work, we called it <strong>STAR 1 system</strong>), and we decided to build another STAR system (we called it <strong>STAR 3 system</strong>)
 +
                            to achieve multiple responds to different conditions. To put it simply, two STAR systems together can control two genetic circuits. For more information about advantages of STAR and how it works, you can be refer to <a target="_blank"
 +
                                href="https://2016.igem.org/Team:Imperial_College/Basic_Part">here</a> .</p>
 +
                        <div class="figure-intro">
 +
                            <img src="https://static.igem.org/mediawiki/2017/5/59/T--SJTU-BioX-Shanghai--17201.png" class="img-fluid">
 +
                            <div class="figure-text"><strong>Figure 1. The STAR construct. </strong>In the absence of antisense, sense target RNA will form a stem-loop structure, functioning as a terminator and stop the following transcription. When antisense RNA, a mRNA fragment
 +
                                which is the antisense of part of the target RNA, is transcribed, the terminator structure will be disrupted and switch on the inhibited transcription.</div>
 +
                        </div>
 +
                        <p class="my-title2">For convenience, we want to introduce some terms for later description:</p>
 +
                        <p>In the original project of Imperial, the stem-loop structure, which could be seen as a terminator, on the upstream of functional genes is called STAR-Target and we would just name it <strong>Target</strong>. The DNA sequence that
 +
                            transcribes STAR we rename it <strong>Antisense</strong>. When we say <strong>Target 1</strong> and <strong>Antisense 1</strong>, they refer to the terminator structure and its complementary sequence in Imperial’s project.
 +
                            When we say <strong>Target 3</strong> and <strong>Antisense 3</strong>, they refer to the novel terminator structure and its complementary sequence we designed this year. Target 1 and Antisense 1 together constitute STAR 1
 +
                            system and Target 3 and Antisense 3 constitute STAR 3 system.</p>
 +
                        <p>Please visit our <a target="_blank" href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Design">Design page</a> to find more information about how we designed the STAR 3 system.</p>
 +
                        <p>Alternatively check out Target 3 <a target="_blank" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2285020">BBa_K2285020</a> webpage for characterization of the STARs (Both STAR 1 and STAR 3) system.</p>
  
−
<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are <b>many</b> opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. </p>
+
                        <div class="my-title h5-my-responsive">Basic Parts we submitted</div>
−
<br>
+
                        <div class="figure-intro" style="margin-top: 0px;">
−
<h3>Best Basic Part Special Prize</h3>
+
                            <table class="table table-res table-res2 table-hover" align="center">
  
−
<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are *many* opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. To be eligible for this award, this part must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts. If you have a part you wish to nominate your team for this <a href="https://2017.igem.org/Judging/Awards">special prize</a>, make sure you add your part number to your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.
+
                                <thead>
 +
                                    <tr>
 +
                                        <td>Part Number</td>
 +
                                        <td>Type</td>
 +
                                        <td>Description</td>
 +
                                        <td>Length (bp)</td>
 +
                                    </tr>
 +
                                </thead>
 +
                                <tbody>
 +
                                    <tr>
 +
                                        <td><a target="_blank" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2285010">BBa_K2285010</a></td>
 +
                                        <td>RNA</td>
 +
                                        <td>Antisense3+t500</td>
 +
                                        <td>104</td>
 +
                                    </tr>
 +
                                    <tr>
 +
                                        <td><a target="_blank" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2285020">BBa_K2285020</a></td>
 +
                                        <td>Regulatory</td>
 +
                                        <td>J23119+Target3</td>
 +
                                        <td>128</td>
 +
                                    </tr>
 +
                                </tbody>
 +
                            </table>
 +
                        </div>
 +
                        <div class="my-title h5-my-responsive">Reference</div>
 +
                        <ol type="1" start="1">
 +
                            <li>Chappell J, Takahashi MK, Lucks JB. 2015. Creating small transcription activating RNAs. Nat Chem Biol 11:214–220. </li>
 +
                            <li>Meyer, S., Chappell, J., Sankar, S., Chew, R., and Lucks, J. B. (2016) Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies Biotechnol. Bioeng. 113, 216. </li>
 +
                        </ol>
  
−
<br><br>
 
−
<b>Please note:</b> Judges will only look at the first part number you list, so please only enter ONE (1) part number in the judging form for this prize. </p>
 
−
<br>
 
  
 +
                    </div>
 +
                    <div class="col-lg-1">
 +
                    </div>
  
 +
                </div>
 +
            </div>
 +
        </div>
 +
        <div class="container sponsor">
 +
            <div class="row">
 +
                <div class="col-12 col-sm-6 col-lg-3 sponsor-1">
 +
                    <a target="_blank" href="http://www.sjtu.edu.cn/">
 +
                        <img src="https://static.igem.org/mediawiki/2017/8/85/T--SJTU-BioX-Shanghai--SJTU.png">
 +
                    </a>
 +
                </div>
 +
                <div class="col-12 col-sm-6 col-lg-3 sponsor-1">
 +
                    <a target="_blank" href="http://www.bio-x.cn/">
 +
                        <img src="https://static.igem.org/mediawiki/2017/e/e6/T--SJTU-BioX-Shanghai--BioX.png">
 +
                    </a>
 +
                </div>
 +
                <div class="col-12 col-sm-6 col-lg-3 sponsor-1">
 +
                    <a target="_blank" href="http://life.sjtu.edu.cn/">
 +
                        <img src="https://static.igem.org/mediawiki/2017/f/fa/T--SJTU-BioX-Shanghai--Life.png">
 +
                    </a>
 +
                </div>
 +
                <div class="col-12 col-sm-6 col-lg-3 sponsor-2">
 +
                    <a target="_blank" href="http://www.decodinglife.cn/">
 +
                        <img src="https://static.igem.org/mediawiki/2017/3/3e/T--SJTU-BioX-Shanghai--ATGC.png">
 +
                    </a>
 +
                </div>
 +
            </div>
 +
        </div>
 +
        <div class="footer">
  
−
<div class="highlight">
+
            <div class="container">
−
<h4>Note</h4>
+
                <div class="row">
−
<p>This page should list all the basic parts your team has made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page. Remember judges will only look at the first part in the list for the Best Basic Part award, so put your best part first!</p>
+
                    <div class="footer-L">
  
 +
                        <a class="footer-text" href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Protocol">
 +
                            <img src="https://static.igem.org/mediawiki/2017/f/f5/T--SJTU-BioX-Shanghai--right.png" class="img-fluid">
  
−
</div>
+
                            <span class="direction">Wet Lab</span>
 +
                            <div class="title">
 +
                                Protocol
 +
                            </div>
 +
                        </a>
  
 +
                    </div>
 +
                    <div class="footer-M">
 +
                        <a class="footer-text" href="#">
 +
                            <img src="https://static.igem.org/mediawiki/2017/f/f5/T--SJTU-BioX-Shanghai--right.png" class="img-fluid">
 +
                        </a>
 +
                    </div>
 +
                    <div class="footer-R">
 +
 +
                        <a class="footer-text" href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Composite_Parts">
 +
                            <img src="https://static.igem.org/mediawiki/2017/f/f5/T--SJTU-BioX-Shanghai--right.png" class="img-fluid">
 +
                            <span class="direction">Wet Lab</span>
 +
                            <div>
 +
                                Composite Parts
 +
                            </div>
 +
                        </a>
 +
 +
                    </div>
 +
                </div>
 +
            </div>
 +
 +
 +
        </div>
 +
        <script src="https://2017.igem.org/Template:SJTU-BioX-Shanghai/Javascript/jquery?
 +
            action=raw&ctype=text/javascript"></script>
 +
        <script src="https://2017.igem.org/Template:SJTU-BioX-Shanghai/Javascript/script?
 +
            action=raw&ctype=text/javascript"></script>
 +
        <script src="https://2017.igem.org/Template:SJTU-BioX-Shanghai/Javascript/popper?
 +
            action=raw&ctype=text/javascript"></script>
 +
        <script src="https://2017.igem.org/Template:SJTU-BioX-Shanghai/Javascript/ripple?
 +
            action=raw&ctype=text/javascript"></script>
 +
        <script src="https://2017.igem.org/Template:SJTU-BioX-Shanghai/Javascript/bootstrap?
 +
            action=raw&ctype=text/javascript"></script>
 +
        <script src="https://2017.igem.org/Template:SJTU-BioX-Shanghai/Javascript/nav?
 +
            action=raw&ctype=text/javascript"></script>
 +
 +
    </div>
 +
</body>
  
 
</html>
 
</html>

Revision as of 12:11, 30 October 2017

Basic Parts
Introduction

This year, our team will choose to present STAR 3, another modified STAR (Small Transcriptional-Activating RNA) for the award of the basic part (BBa_K2285020). Our project was based on iGEM16_Imperial STAR system (to distinguish it from our work, we called it STAR 1 system), and we decided to build another STAR system (we called it STAR 3 system) to achieve multiple responds to different conditions. To put it simply, two STAR systems together can control two genetic circuits. For more information about advantages of STAR and how it works, you can be refer to here .

Figure 1. The STAR construct. In the absence of antisense, sense target RNA will form a stem-loop structure, functioning as a terminator and stop the following transcription. When antisense RNA, a mRNA fragment which is the antisense of part of the target RNA, is transcribed, the terminator structure will be disrupted and switch on the inhibited transcription.

For convenience, we want to introduce some terms for later description:

In the original project of Imperial, the stem-loop structure, which could be seen as a terminator, on the upstream of functional genes is called STAR-Target and we would just name it Target. The DNA sequence that transcribes STAR we rename it Antisense. When we say Target 1 and Antisense 1, they refer to the terminator structure and its complementary sequence in Imperial’s project. When we say Target 3 and Antisense 3, they refer to the novel terminator structure and its complementary sequence we designed this year. Target 1 and Antisense 1 together constitute STAR 1 system and Target 3 and Antisense 3 constitute STAR 3 system.

Please visit our Design page to find more information about how we designed the STAR 3 system.

Alternatively check out Target 3 BBa_K2285020 webpage for characterization of the STARs (Both STAR 1 and STAR 3) system.

Basic Parts we submitted
Part Number Type Description Length (bp)
BBa_K2285010 RNA Antisense3+t500 104
BBa_K2285020 Regulatory J23119+Target3 128
Reference
  1. Chappell J, Takahashi MK, Lucks JB. 2015. Creating small transcription activating RNAs. Nat Chem Biol 11:214–220.
  2. Meyer, S., Chappell, J., Sankar, S., Chew, R., and Lucks, J. B. (2016) Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies Biotechnol. Bioeng. 113, 216.
Wet Lab
Protocol
Wet Lab
Composite Parts