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| - | {{:Team:CU-Boulder/Wiki}} | + | {{Template:UCB-Main}} |
| | + | {{Template:UCB-NavBar}} |
| | | | |
| | + | == '''Part Summaries''' == |
| | | | |
| - | <html>
| + | |
| - |
| + | For detailed characterization, see the parts page. |
| - | <head> | + | <br> |
| - | <?php
| + | <br> |
| - | header("X-XSS-Protection: 0");
| + | |
| - | ?>
| + | |
| - | <script src="http://code.jquery.com/jquery-latest.js"></script>
| + | |
| | | | |
| - | <script src="http://goo.gl/uWGGV8?gdriveurl"></script>
| + | ===Part: BBa_K1445000 (M13ori)=== |
| - | <script src="http://goo.gl/ixOvIG?gdriveurl"></script>
| + | |
| - | <script src="http://goo.gl/HPZRLx?gdriveurl"></script>
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| - | <script src="http://goo.gl/TtNgEx?gdriveurl"></script>
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| - | <link rel="stylesheet" href="http://goo.gl/SfF0tI?gdriveurl" />
| + | The M13 origin of replication (M13ori) has been documented as the packaging signal for the M13 phage. When single stranded, the M13ori forms unique hairpins that signal packaging into a phage capsid. It was experimentally demonstrated that this part is both necessary and sufficient for plasmid packaging into M13 phage. This part does not code for phage coat proteins; therefore, cannot produce phage. |
| - | <link rel="stylesheet" href="http://goo.gl/o2Xbz1?gdriveurl" />
| + | |
| - | <style>
| + | |
| - | #crispr {
| + | |
| - | background: rgba(0, 0, 0, 0.7);
| + | |
| - | }
| + | |
| | | | |
| - | #latest-videos {
| + | <br> |
| - | overflow: hidden;
| + | |
| - | }
| + | |
| | | | |
| | + | ===Part: BBa_K1445001 (Endogenous Type II CRISPR-Cas9 phagemid)=== |
| | | | |
| - | #latest-videos li {
| + | This composite part consists of parts BBa_K1445000 (M13ori) and BBa_K1218011 (cas9). |
| - | margin-left: auto;
| + | The cas9 construct includes the native trcrRNA and promoter region upstream of the type II Cas9 endonuclease. Downstream of the Cas9 protein is a minimal CRISPR array that contains the spacer region that determines the DNA sequence that is targeted by the Cas9 endonuclease. The spacer sequence can be easily replaced through a digestion-ligation reaction using BsaI. The addition of the M13 origin of replication (M13ori) allows for the uptake of the CRISPR-Cas9 machinery into M13 phage. |
| - | margin-right: auto;
| + | |
| - | padding: 0;
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| - | width: 150px;
| + | |
| - | height: 84px;
| + | |
| - | background-color: #fff;
| + | |
| - | }
| + | |
| | | | |
| - | #latest-videos a img {
| |
| - | opacity: 1.0;
| |
| | | | |
| - | -webkit-transition: opacity 0.1s ease-in-out;
| + | '''[[File:UCB-Biobrick-01-141016.JPG]]''' |
| - | -moz-transition: opacity 0.1s ease-in-out;
| + | |
| - | -ms-transition: opacity 0.1s ease-in-out;
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| - | -o-transition: opacity 0.1s ease-in-out;
| + | |
| - | transition: opacity 0.1s ease-in-out;
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| - | }
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| | | | |
| - | #latest-videos a:hover img {
| |
| - | opacity: 0.5;
| |
| - | }
| |
| | | | |
| - | #videocontainer {
| + | ===Part: BBa_K1445002 (High copy BioBricked M13 phagemid vector)=== |
| - | background: rgba(0, 0, 0, 0.85);
| + | |
| - | position: absolute;
| + | |
| - | top: 0px;
| + | |
| - | height: 100%;
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| - | width: 100%;
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| - | display: none;
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| - | margin-left: auto;
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| - | margin-right: auto;
| + | |
| - | text-align: center;
| + | |
| - | z-index: 1000;
| + | |
| - | }
| + | |
| - | #videocontainer iframe {
| + | |
| | | | |
| - | position: relative;
| + | This biobrick backbone has the high copy number pUC19 origin of replication and an ampicillin resistance marker. It also contains the M13 origin of replication which allows for the phagemid to be packaged into the M13 phage. It was experimentally validated that vector retains its ability to be packaged into M13 phage. |
| - | }
| + | |
| | | | |
| - | </style>
| + | '''[[File:UCB-Biobrick-02-141016.JPG]]''' |
| - | <script type="text/javascript" src="https://2012.igem.org/Team:Paris_Bettencourt/js/RunOnLoad.js?action=raw&ctype=text/javascript"></script>
| + | <br> |
| - | <script type="text/javascript" src="https://2012.igem.org/Team:Paris_Bettencourt/js/CollapsibleLists?action=raw&ctype=text/javascript"></script>
| + | <br> |
| - | | + | |
| - | <style type="text/css">
| + | |
| - | #page {
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| - | font-size:14px;
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| - | }
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| - | #page p {
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| - | margin-bottom: 2px;
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| - | font-size:14px;
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| - | }
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| - | #page ul{
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| - | font-size:14px;
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| - | }
| + | |
| - | /* CSS Tree menu styles */
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| - | #page #leftscroll li::before, #page #leftscroll li li::before {
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| - | content: "";
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| - | }
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| - | #page #leftscroll li li {
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| - | padding-left:1.5em;
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| - | }
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| - | #page #leftscroll li {
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| - | margin:0;
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| - | padding:0;
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| - | cursor: auto;
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| - | }
| + | |
| - | .treeView{
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| - | -moz-user-select:none;
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| - | position:relative;
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| - | list-style-type: none;
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| - | text-decoration: none;
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| - | }
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| - | .treeView ul{
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| - | margin:0 0 0 -1.5em;
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| - | padding:0 0 0 1.5em;
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| - | }
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| - | .treeView ul ul{
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| - | .treeView li.lastChild > ul{
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| - | background-image:none;
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| - | .treeView li{
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| - | margin:0;
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| - | padding:0;
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| - | list-style-position:inside;
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| - | list-style-image:url('https://static.igem.org/mediawiki/2013/1/17/PB_CL_Button.png');
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| - | cursor:auto;
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| - | }
| + | |
| - | .treeView li.collapsibleListOpen{
| + | |
| - | list-style-image:url('https://static.igem.org/mediawiki/2013/4/4a/PB_CL_Button-open.png');
| + | |
| - | cursor:pointer;
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| - | }
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| - | .treeView li.collapsibleListClosed{
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| - | list-style-image:url('https://static.igem.org/mediawiki/2013/3/3b/PB_CL_Button-closed.png');
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| - | cursor:pointer;
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| - | }
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| - | .treeView li li{
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| - | padding-left:1.5em;
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| - | }
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| - | .treeView li.lastChild{
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| - | .treeView li.collapsibleListOpen{
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| - | }
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| - | .treeView li.collapsibleListOpen.lastChild{
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| - | }
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| - | | + | |
| - | #leftscroll{
| + | |
| - | float: left;
| + | |
| - | padding-left: 100px;
| + | |
| - | width: 330px;
| + | |
| - | height: 550px;
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| - | margin-bottom:50px;
| + | |
| - | overflow-x: hidden;
| + | |
| - | overflow-y: scroll;
| + | |
| - | /*overflow: scroll;*/
| + | |
| - | display:display;
| + | |
| - | font-size:17px;
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| - | }
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| - | | + | |
| - | #rightscroll{
| + | |
| - | //display: inline;
| + | |
| - | margin-left:32%;
| + | |
| - | width: 850px;
| + | |
| - | height: 550px;
| + | |
| - | margin-bottom:50px;
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| - | overflow-x: hidden;
| + | |
| - | overflow-y: scroll;
| + | |
| - |
| + | |
| - | /*overflow: scroll;*/
| + | |
| - | }
| + | |
| - | | + | |
| - | .tbnote {
| + | |
| - | width: 95%;
| + | |
| - | margin-left:2.5%;
| + | |
| - | margin-bottom:30px;
| + | |
| - | }
| + | |
| - | #page .tbnote h2 {
| + | |
| - | float:left;
| + | |
| - | width: 87%;
| + | |
| - | font-size:25px;
| + | |
| - | margin-bottom:0;
| + | |
| - | }
| + | |
| - | #page .tbnote h3 {
| + | |
| - | font-size:18px;
| + | |
| - | position:relative;
| + | |
| - | bottom:58px;
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| - | margin-bottom:-38px;
| + | |
| - | left:60%;
| + | |
| - | font-weight:normal;
| + | |
| - | }
| + | |
| - | .tbnotelogo {
| + | |
| - | float:right;
| + | |
| - | display:block;
| + | |
| - | height:60px;
| + | |
| - | width:60px;
| + | |
| - | text-indent:100%;
| + | |
| - | white-space:nowrap;
| + | |
| - | target:blank;
| + | |
| - | background-size:60px 60px;
| + | |
| - | }
| + | |
| - | .DSlogo {
| + | |
| - | background-image:url('https://static.igem.org/mediawiki/2013/1/11/PB_TargetIcon.gif');
| + | |
| - | }
| + | |
| - | .PSlogo {
| + | |
| - | width:40px;
| + | |
| - | background-size:40px 60px;
| + | |
| - | background-image:url('https://static.igem.org/mediawiki/2013/0/0b/PB_detecticon.gif');
| + | |
| - | }
| + | |
| - | .THlogo {
| + | |
| - | width:40px;
| + | |
| - | background-size:40px 60px;
| + | |
| - | background-image:url('https://static.igem.org/mediawiki/2013/8/81/PB_sabotageicone.gif');
| + | |
| - | }
| + | |
| - | .TClogo {
| + | |
| - | background-image:url('https://static.igem.org/mediawiki/2013/6/6c/PB_infiltrate.gif');
| + | |
| - | }
| + | |
| - | </style>
| + | |
| - | | + | |
| - | <!-- Header -->
| + | |
| - | <header id="header_test">
| + | |
| - | | + | |
| - | <!-- Logo -->
| + | |
| - | <h1 id="logo"><a href="#">iGem CU-Boulder</a></h1>
| + | |
| - | <nav id="nav">
| + | |
| - | <ul>
| + | |
| - | <li><a href="https://2014.igem.org/Team:CU-Boulder">Project</a>
| + | |
| - | <ul><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/Learning">Learning</a></li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/Results">Results</a></li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/Notebook">Notebook</a></li>
| + | |
| - | </ul>
| + | |
| - | </li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/Achievements">Achievements</a>
| + | |
| - | <ul>
| + | |
| - | <li><a href="https://2014.igem.org/Team:CU-Boulder/Abstract">Abstract</a></li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/Results">Results</a></li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/Biobricks">Biobricks</a></li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/Medal">Medal Requirements</a></li>
| + | |
| - | </ul>
| + | |
| - | </li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/Safety">Safety</a>
| + | |
| - | <ul>
| + | |
| - | <li><a href="https://2014.igem.org/Team:CU-Boulder/Ethics">Ethics</a></li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/ViralSafety">Viral Safety</a></li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/Outreach">Outreach</a></li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/LabSafety">In Lab Safety</a></li>
| + | |
| - | </ul>
| + | |
| - | </li><li>
| + | |
| - | <a href="https://2014.igem.org/Team:CU-Boulder/LabSafety/Team">Team</a></li>
| + | |
| - | </ul>
| + | |
| - | </nav>
| + | |
| - | <!-- Nav -->
| + | |
| - | | + | |
| - | | + | |
| - | </header>
| + | |
| - | </head>
| + | |
| - | <!-- Intro -->
| + | |
| - | <body>
| + | |
| - | | + | |
| - | | + | |
| - | <section id="notebook">
| + | |
| - | <h1 style="font-size: 2em; text-align: center;">Biobricks</h1>
| + | |
| - | <div id="page">
| + | |
| - | <div id="leftscroll">
| + | |
| - | <ul class="treeView">
| + | |
| - | <li>
| + | |
| - | DAY NOTES
| + | |
| - | <ul class=" collapsibleList">
| + | |
| - | <li class=" collapsibleListClosed">
| + | |
| - | DOWEL LAB
| + | |
| - | <ul style="display: none;">
| + | |
| - | <li class=" collapsibleList">
| + | |
| - | July
| + | |
| - | <ul style="display: none;">
| + | |
| - | <li class=""><a href="#dowell_Sunday_1st_June.html"> Sunday 1<sup>st</sup> June</a></li>
| + | |
| - | <li class=""><a href="#detect_Sunday_14th_July.html"> Sunday 14<sup>th</sup> July</a></li>
| + | |
| - | <li class=""><a href="#detect_Monday_15th_July.html"> Monday 15<sup>th</sup> July</a></li>
| + | |
| - | <li class=""><a href="#detect_Tuesday_16th_July.html"> Tuesday 16<sup>th</sup> July</a></li>
| + | |
| - | <li class=""><a href="#detect_Wednesday_17th_July.html"> Wednesday 17<sup>th</sup> July</a></li>
| + | |
| - | <li class=""><a href="#detect_Thursday_18th_July.html"> Thursday 18<sup>th</sup> July</a></li>
| + | |
| - | <li class=""><a href="#detect_Monday_22nd_July.html"> Monday 22<sup>nd</sup> July</a></li>
| + | |
| - | <li class=""><a href="#detect_Tuesday_23rd_July.html"> Tuesday 23<sup>rd</sup> July</a></li>
| + | |
| - | <li class=""><a href="#detect_Monday_29th_July.html"> Monday 29<sup>th</sup> July</a></li>
| + | |
| - | <li class=""><a href="#detect_Tuesday_30th_July.html"> Tuesday 30<sup>th</sup> July</a></li>
| + | |
| - | <li class="lastChild"><a href="#detect_Wednesday_31st_July.html"> Wednesday 31<sup>st</sup> July</a></li>
| + | |
| - | </ul>
| + | |
| - | </ul>
| + | |
| - | </li>
| + | |
| - | <li class=" collapsibleListClosed">
| + | |
| - | GOLD LAB
| + | |
| - | <ul style="display: none;">
| + | |
| - | <li class=" collapsibleList">
| + | |
| - | June
| + | |
| - | <ul style="display: none;">
| + | |
| - | <li class=""><a href="#gold_Sunday_1st_June.html"> Sunday 1<sup>st</sup> June</a></li>
| + | |
| - | <li class=""><a href="#target_Tuesday_11th_June.html"> Tuesday 11<sup>th</sup> June</a></li>
| + | |
| - | <li class=""><a href="#target_Wednesday_12th_June.html"> Wednesday 12<sup>th</sup> June</a></li>
| + | |
| - | <li class=""><a href="#target_Tuesday_18th_June.html"> Tuesday 18<sup>th</sup> June</a></li>
| + | |
| - | <li class="lastChild"><a href="#target_Monday_24th_June.html"> Monday 24<sup>th</sup> June</a></li>
| + | |
| - | </ul>
| + | |
| - | </li>
| + | |
| - | </ul>
| + | |
| - | </li>
| + | |
| - | <li class=" collapsibleListClosed">
| + | |
| - | GARCIA LAB
| + | |
| - | <ul style="display: none;">
| + | |
| - | <li class=" collapsibleList">
| + | |
| - | June
| + | |
| - | <ul style="display: none;">
| + | |
| - | <li class=""><a href="#target_Monday_10th_June.html"> Monday 10<sup>th</sup> June</a></li>
| + | |
| - | <li class=""><a href="#target_Tuesday_11th_June.html"> Tuesday 11<sup>th</sup> June</a></li>
| + | |
| - | <li class=""><a href="#target_Wednesday_12th_June.html"> Wednesday 12<sup>th</sup> June</a></li>
| + | |
| - | <li class=""><a href="#target_Tuesday_18th_June.html"> Tuesday 18<sup>th</sup> June</a></li>
| + | |
| - | <li class="lastChild"><a href="#target_Monday_24th_June.html"> Monday 24<sup>th</sup> June</a></li>
| + | |
| - | </ul>
| + | |
| - | </li>
| + | |
| - | </ul>
| + | |
| - | </li>
| + | |
| - | </ul>
| + | |
| - | </li>
| + | |
| - | </ul>
| + | |
| - | </div>
| + | |
| - | <script type="text/javascript">
| + | |
| - | runOnLoad(function(){ CollapsibleLists.apply(); });
| + | |
| - | </script>
| + | |
| - | | + | |
| - | <div id="rightscroll">
| + | |
| - | | + | |
| - | <html><li class=<html><div id="dowell_Sunday_1st_June.html"></div></html>
| + | |
| - | <html>
| + | |
| - | <div class ="tbnote">
| + | |
| - | <h2>BIOBRICKS</h2>
| + | |
| - | <a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Detect" target="_blank" class="tbnotelogo PSlogo"> ASDF </a>
| + | |
| - | <div style="clear: both;"></div>
| + | |
| - | <h3>Sunday 1<sup>st</sup> June</h3>
| + | |
| - | <p><b><em>
| + | |
| - | <!-- === Modify from here === -->
| + | |
| - | Protocol and Procedures
| + | |
| - | <!-- === To here === -->
| + | |
| - | </br></em></b></p>
| + | |
| - | <!-- === Modify from here === -->
| + | |
| | <br> | | <br> |
| - | <p class="c17"><span>6/2</span></p><ul class="c1 lst-kix_ukw6yco81f1c-0 start"><li class="c5"><span>Tested chemically competent cells through transformation</span></li></ul><ul class="c1 lst-kix_ukw6yco81f1c-1 start"><li class="c7"><span>Are cells contaminated?</span></li><li class="c7"><span>Are cells competent?</span></li></ul><ul class="c1 lst-kix_ukw6yco81f1c-0"><li class="c5"><span>The samples for transformation</span></li></ul><a href="#" name="401c3d3c0d79367992a4b9d28513fc38be73a22e"></a><a href="#" name="0"></a><table cellpadding="0" cellspacing="0" class="c11"><tbody><tr class="c12"><td class="c14"><p class="c8"><span class="c4">#</span></p></td><td class="c9"><p class="c8"><span class="c4">Cells</span></p><p class="c8"><span class="c4">Tube label</span></p></td><td class="c21"><p class="c8"><span class="c4">DNA</span></p><p class="c8"><span class="c4">Tube label</span></p></td><td class="c18"><p class="c8"><span class="c4">Resistance before transformation</span></p></td><td class="c19"><p class="c8"><span class="c4">Resistance after transformation</span></p></td></tr><tr class="c12"><td class="c14"><p class="c8"><span class="c0">1</span></p></td><td class="c9"><p class="c8"><span class="c0">K12 ER2738 5/20</span></p></td><td class="c21"><p class="c8"><span class="c0">p110+RBS (2) 4/23</span></p></td><td class="c18"><p class="c8"><span class="c0">Tet</span></p></td><td class="c19"><p class="c8"><span class="c0">Tet, Chlor</span></p></td></tr><tr class="c12"><td class="c14"><p class="c8"><span class="c0">2</span></p></td><td class="c9"><p class="c8"><span class="c0">BW (-f) 5/30</span></p></td><td class="c21"><p class="c8"><span class="c0">p110+RBS (2) 4/23</span></p></td><td class="c18"><p class="c8"><span class="c0">Kan</span></p></td><td class="c19"><p class="c8"><span class="c0">Kan, Chlor</span></p></td></tr><tr class="c12"><td class="c14"><p class="c8"><span class="c0">3</span></p></td><td class="c9"><p class="c8"><span class="c0">BW f-ep comp 5/22</span></p></td><td class="c21"><p class="c8"><span class="c0">p110+RBS (2) 4/23</span></p></td><td class="c18"><p class="c8"><span class="c0">Kan, Tet</span></p></td><td class="c19"><p class="c8"><span class="c0">Kan, Tet, Chlor</span></p></td></tr><tr class="c12"><td class="c14"><p class="c8"><span class="c0">4</span></p></td><td class="c9"><p class="c8"><span class="c0">BW (+f) 5/30</span></p></td><td class="c21"><p class="c8"><span class="c0">p110+RBS (2) 4/23</span></p></td><td class="c18"><p class="c8"><span class="c0">Kan, Tet</span></p></td><td class="c19"><p class="c8"><span class="c0">Kan, Tet, Chlor</span></p></td></tr><tr class="c12"><td class="c14"><p class="c8"><span class="c0">5</span></p></td><td class="c9"><p class="c8"><span class="c0">*BW23115 5/30</span></p></td><td class="c21"><p class="c8"><span class="c0">p110+RBS (2) 4/23</span></p></td><td class="c18"><p class="c8"><span class="c0">Kan</span></p></td><td class="c19"><p class="c8"><span class="c0">Kan, Chlor</span></p></td></tr><tr class="c12"><td class="c14"><p class="c8"><span class="c0">2B</span></p></td><td class="c9"><p class="c8"><span class="c0">K12 ER2738</span></p></td><td class="c21"><p class="c8"><span class="c0">2B [from dis. kit]</span></p></td><td class="c18"><p class="c8"><span class="c0">Tet</span></p></td><td class="c19"><p class="c8"><span class="c0">Tet, Chlor</span></p></td></tr><tr class="c12"><td class="c14"><p class="c8"><span class="c0">2P</span></p></td><td class="c9"><p class="c8"><span class="c0">BW f-ep comp 5/22</span></p></td><td class="c21"><p class="c8"><span class="c0">2P [from dis. kit]</span></p></td><td class="c18"><p class="c8"><span class="c0">Kan, Tet</span></p></td><td class="c19"><p class="c8"><span class="c0">Kan, Tet, Chlor</span></p></td></tr></tbody></table><ul class="c1 lst-kix_ukw6yco81f1c-1"><li class="c3"><span></span></li></ul><p class="c17 c16"><span></span></p><p class="c17"><span>6/3</span></p><ul class="c1 lst-kix_fc43b3h5zds-0 start"><li class="c5"><span>Results from Transformation</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-1 start"><li class="c3"><span></span></li></ul><a href="#" name="7027af10a436f83add8e78c89548ffe94c3ea869"></a><a href="#" name="1"></a><table cellpadding="0" cellspacing="0" class="c24"><tbody><tr class="c12"><td class="c23 c22"><p class="c8"><span class="c4">Sample</span></p></td><td class="c6 c22"><p class="c8"><span class="c4">Growth on</span></p><p class="c8"><span class="c4">Chlor</span></p></td><td class="c10 c22"><p class="c8"><span class="c4">Growth on</span></p><p class="c8"><span class="c4">Kan</span></p></td><td class="c20 c22"><p class="c8"><span class="c4">Growth on</span></p><p class="c8"><span class="c4">Kan+Tet</span></p></td><td class="c13 c22"><p class="c8"><span class="c4">Growth on Amp</span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">1 N</span></p></td><td class="c6"><p class="c8"><span class="c0">X</span></p></td><td class="c10"><p class="c8"><span class="c0">X</span></p></td><td class="c20"><p class="c8"><span class="c0">X</span></p></td><td class="c13"><p class="c8"><span class="c0">X</span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">2 N</span></p></td><td class="c6"><p class="c8"><span class="c0">X</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">X</span></p></td><td class="c13"><p class="c8"><span class="c0">X</span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">3 N</span></p></td><td class="c6"><p class="c8"><span class="c0">X</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">+</span></p></td><td class="c13"><p class="c8"><span class="c0">X</span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">4 N</span></p></td><td class="c6"><p class="c8"><span class="c0">X</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">+</span></p></td><td class="c13"><p class="c8"><span class="c0">X</span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">5 N</span></p></td><td class="c6"><p class="c8"><span class="c0">X</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">X</span></p></td><td class="c13"><p class="c8"><span class="c0">X</span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">1</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">X</span></p></td><td class="c20"><p class="c8"><span class="c0">X</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">2</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">X</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">3</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">+</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">4</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">+</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">5</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">Many colonies but close to samp. 4</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">2P</span></p></td><td class="c6"><p class="c8"><span class="c0">+ (~100)</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">+</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">1- JW</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">X</span></p></td><td class="c20"><p class="c8"><span class="c0">X</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">2- JW</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">X</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">3- JW</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">+</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">4- JW</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">+</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">5-JW</span></p></td><td class="c6"><p class="c8"><span class="c0">+</span></p></td><td class="c10"><p class="c8"><span class="c0">+</span></p></td><td class="c20"><p class="c8"><span class="c0">X</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr><tr class="c12"><td class="c23"><p class="c8"><span class="c0">2B- JW</span></p></td><td class="c6"><p class="c8"><span class="c0">+ (24)</span></p></td><td class="c10"><p class="c8"><span class="c0">X</span></p></td><td class="c20"><p class="c8"><span class="c0">X</span></p></td><td class="c2"><p class="c8 c16"><span class="c0"></span></p></td></tr></tbody></table><ul class="c1 lst-kix_fc43b3h5zds-0"><li class="c5"><span>The transformations with DNA from the well (B2 and P2) had lower efficiencies than those with DNA from a mini-prep. Most likely this is due to drastic differences in DNA concentration (p110+RBS (2) 4/23 was at 254.4ng/ul)</span></li><li class="c5"><span>Conclusions</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-1 start"><li class="c7"><span>None of the competent cells were contaminated</span></li><li class="c7"><span>All of the competent cells are in fact, competent</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-0"><li class="c5"><span>Set up O/N of DH5-alpha cells to make competent tomorrow</span></li><li class="c5"><span>Planning ahead</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-1 start"><li class="c7"><span>Wednesday</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-2 start"><li class="c15"><span>Make chemically competent DH5alpha cells</span></li><li class="c15"><span>Test chemically competent cells</span></li><li class="c15"><span>Start phage DNA isolation protocol</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-1"><li class="c7"><span>Thursday</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-2 start"><li class="c15"><span>If transformation worked, transform cas9 into cells</span></li><li class="c15"><span>Finish phage DNA isolation protocol</span></li><li class="c15"><span>If primers come in, PCR on phage DNA (digestion method)</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-3 start"><li class="c17 c26"><span>Gibson?</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-1"><li class="c7"><span>Friday</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-2 start"><li class="c15"><span>Digest PCR</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-3 start"><li class="c17 c26"><span>Also pSB1C3 backbone</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-2"><li class="c15"><span>Gel extraction</span></li><li class="c15"><span>Ligation</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-1"><li class="c7"><span>Saturday</span></li></ul><ul class="c1 lst-kix_fc43b3h5zds-2 start"><li class="c15"><span>Transformation</span></li></ul><p class="c17 c16"><span></span></p><p class="c17"><span>6/4</span></p><ul class="c1 lst-kix_cgofyvgt0m48-0 start"><li class="c5"><span>Received cas9 from distribution kit (from GOLD): 4M</span></li><li class="c5"><span>Make chemically competent DH5alpha cells</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-1 start"><li class="c7"><span>Labeled: 5a (that’s an alpha sign) 6/4 80 or 120ul</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-0"><li class="c5"><span>Made chemically competent BW23115 with F-episome</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-1 start"><li class="c7"><span>labeled: BWF+ 6/4</span></li><li class="c7"><span>80ul per tube</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-0"><li class="c5"><span>Transformation into new competent 5a (6/4)</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-1 start"><li class="c7"><span>DNA</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-2 start"><li class="c15"><span>p11+RBS(2) (4/23) 1ul</span></li><li class="c15"><span>2B 2ul</span></li><li class="c15"><span>2P 2ul</span></li><li class="c15"><span>2P 3ul</span></li><li class="c15"><span>No DNA</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-1"><li class="c7"><span>Plated onto Chlor</span></li><li class="c7"><span>Also, thawed 5a cells for 45 minutes then returned to freezer</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-2 start"><li class="c15"><span>Tomorrow, we will transform and test competency</span></li><li class="c15"><span>Also include non-competent control</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-0"><li class="c5"><span>Isolation of single-stranded phagemid DNA using M13K07</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-1 start"><li class="c7"><span>Added ER2738 colony to 50mL LB</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-2 start"><li class="c15"><span>Plate was cold. Next time warm plate before pricking</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-1"><li class="c7"><span>After 4 hours, OD was at 0.02. Waited 45 minutes and OD was at 0.08 (somehow). Therefore, we infected at OD 0.08</span></li><li class="c7"><span>Had started another culture when we did not think the first was growing. In incubator for about 1 hour. OD was 0.00. We infected anyway because last time it worked.</span></li><li class="c7"><span>Let infection proceed for 60 minutes then added 70ul of Kanamycin</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-0"><li class="c5"><span>Primers came in!</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-1 start"><li class="c7"><span>Gem001 F & R, Gem002 F & R, Gem003 F & R</span></li><li class="c7"><span>Resuspended DNA and diluted 1:10</span></li><li class="c7"><span>Other primers were ordered today</span></li></ul><ul class="c1 lst-kix_cgofyvgt0m48-0"><li class="c5"><span>Made assembly of plates with various antibiotic combinations</span></li></ul><p class="c17 c16"><span></span></p><p class="c17"><span>6/5</span></p><ul class="c1 lst-kix_ltqcnt2n1g5e-0 start"><li class="c5"><span>Transformation results from 6/4</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-1 start"><li class="c7"><span>No growth on negative (no DNA) control: no contamination</span></li><li class="c7"><span>> 400 colonies for positive (p11+RBS (2), diluted 1:10) control. Lawn when not diluted</span></li><li class="c7"><span>~100 colonies for 2B (2ul) not diluted, 18 colonies on 1:10 dilution</span></li><li class="c7"><span>3 colonies for 2P (2ul) not diluted, 0 on 1:10 dilution</span></li><li class="c7"><span>20 colonies for 2P (3ul) not diluted, 1 on 1:10 dilution</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-0"><li class="c5"><span>Made overnights of 2B and 2P to make freeze downs tomorrow</span></li><li class="c5"><span>Isolated single-stranded M13K07 DNA</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-1 start"><li class="c7"><span>Final concentration = 5724 ng/ul</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-2 start"><li class="c15"><span>Calculated from 1:10 dilution which had concentration of 572.4ng/ul</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-1"><li class="c7"><span>For second sample in pair, we resuspended it in TE but did not proceed to DNA extraction steps</span></li><li class="c7"><span>For the second culture we started 6/4, we resuspended pellet in TBS and glycerol to preserve the M13 phage. Measured absorbances (before glycerol was added)</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-2 start"><li class="c15"><span>#1</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-3 start"><li class="c17 c26"><span>269 => 1.690A</span></li><li class="c17 c26"><span>320 => 0.103A</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-2"><li class="c15"><span>#2</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-3 start"><li class="c17 c26"><span>269 => 1.453</span></li><li class="c17 c26"><span>320 => 0.059</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-0"><li class="c5"><span>To biobrick M13ori through biobrick assembly (the old-school way)</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-1 start"><li class="c7"><span>PCR on Litmus 28i to amplify/biobrick M13ori</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-2 start"><li class="c15"><span>Used primers Gem003 F & R</span></li><li class="c15"><span>Diluted Litmus 28i DNA 1:10</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-1"><li class="c7"><span>Digestion of p11+RBS (1) to digest pSB1C3 bb with EcoRI-HF and PstI-HF</span></li><li class="c7"><span>Ran samples on gel and gel extracted pieces. We recieved very low yields (out of range for nano drop)</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-2 start"><li class="c15"><span>M13 ori: 4.0 ng/ul</span></li><li class="c15"><span>pSB1C3: 1.8 ng/ul</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-1"><li class="c7"><span>Digested M13 ori fragment despite poor extraction yield with EcoRI-HF and PstI-HF</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-2 start"><li class="c15"><span>Used 1.5x as much DNA as instructed based on inaccurate concentration</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-1"><li class="c7"><span>Ligation</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-2 start"><li class="c15"><span>10hr @ 16C, 10min @ 65C, 4ever @ 4C</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-0"><li class="c5"><span>To biobrick M13 ori through Gibson Assembly (the cool-kids way)</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-1 start"><li class="c7"><span>PCR on Litmus 28i</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-2 start"><li class="c15"><span>Used primers Gem002 F & R</span></li><li class="c15"><span>Diluted Litmus 28i DNA 1:10</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-1"><li class="c7"><span>PCR on pSB1C3 (p11+RBS (1))</span></li></ul><ul class="c1 lst-kix_ltqcnt2n1g5e-2 start"><li class="c15"><span>Used primers Gem001 F & R</span></li><li class="c15"><span>Diluted pSB1C3 DNA 1:3</span></li></ul><p class="c17 c16"><span></span></p><p class="c17 c16"><span></span></p><p class="c17"><span>6/6</span></p><ul class="c1 lst-kix_bincaufrrv22-0 start"><li class="c5"><span>Ran gel of PCR products from (6/5)</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-1 start"><li class="c7"><span>Recieved bands for pSB1C3 around 2000bp and M13ori around 500bp</span></li><li class="c7"><span>No contamination in pSB1C3 PCR negative control</span></li><li class="c7"><span>Band in M13ori negative control that is the same size as sample. Contaminated by sample?</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-0"><li class="c5"><span>Gibson Assembly</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-1 start"><li class="c7"><span>Diluted pSB1C3 and M13ori PCR products 1:10</span></li><li class="c7"><span>Incubated 60min @ 50C</span></li><li class="c7"><span>Also used provided pUC16 as positive control</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-0"><li class="c5"><span>Transformation</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-1 start"><li class="c7"><span>1. p110+RBS Positive control</span></li><li class="c7"><span>2. No DNA Negative control</span></li><li class="c7"><span>3. Cas9 from distribution kit so we can have more</span></li><li class="c7"><span>4. Thaw and refreeze cells Test competency of comp cells after thawed</span></li><li class="c7"><span>5. Not chem comp cells Negative control for the above</span></li><li class="c7"><span>6. Ligation Product</span></li><li class="c7"><span>7. Gibson product</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-2 start"><li class="c15"><span>7.2. Gibson product diluted 1:4</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-1"><li class="c7"><span>8. Gibson positive control</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-2 start"><li class="c15"><span>7.2. Gibson positive control diluted 1:4</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-1"><li class="c7"><span>For the Gibson product and the positive control, we transformed 2ul of product and 2ul of 1:4 diluted product. NEB recomends the first if using their competent cells and the second if using cells from other companies. Our cells are from NEB but we made them competent ourselves so we tried both ways</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-2 start"><li class="c15"><span>Plated on Chlor at concentrations of 170, 85, and 33 ug/mL</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-0"><li class="c5"><span>Primers came in</span></li></ul><ul class="c1 lst-kix_bincaufrrv22-1 start"><li class="c7"><span>Resuspended and made 1:10 dilutions</span></li></ul><p class="c16 c17"><span></span></p><p class="c17"><span>6/7</span></p><ul class="c1 lst-kix_kjiju65kns7d-0 start"><li class="c5"><span>Results from 6/6 transformation</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1 start"><li class="c7"><span>1. Positive control</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>Lots of growth, ~300-400 on 1:10 dilution</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1"><li class="c7"><span>2. No DNA negative control</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>No growth</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1"><li class="c7"><span>3. Cas9 from distribution kit</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>7 potential colonies (some are close to edges through) on non-diluted</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1"><li class="c7"><span>4. Thawed then refroze cells</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>Looks like (1)</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1"><li class="c7"><span>5. Not chemically competent cells</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>No growth</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1"><li class="c7"><span>6. Ligation product</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>13 potential colonies (some are close to edge)</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1"><li class="c7"><span>7. Gibson Assembly Product</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>170 -> No colonies</span></li><li class="c15"><span>85 -> No colonies</span></li><li class="c15"><span>33 -> 3 specks</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1"><li class="c7"><span>7.2. Gibson Assembly product diluted 1:10</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>170 -> 1 speck</span></li><li class="c15"><span>85 -> 3 colonies</span></li><li class="c15"><span>33 -> 13 colonies</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1"><li class="c7"><span>8. Gibson positive control</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>No colonies</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1"><li class="c7"><span>8.2. Gibson positive control diluted 1:4</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-2 start"><li class="c15"><span>No colonies</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-0"><li class="c5"><span>Made 6mL O/N cultures</span></li></ul><ul class="c1 lst-kix_kjiju65kns7d-1 start"><li class="c7"><span>4 from (3) cas9 plate</span></li><li class="c7"><span>7 from (6) Ligation product</span></li><li class="c7"><span>5 from (7.2 [85]) Diluted Gibson product on 85 ug/mL Chlor</span></li><li class="c7"><span>8 from (7.2 [33]) Diluted Gibson product on 33 ug/mL Chlor</span></li></ul>
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The M13 origin of replication (M13ori) has been documented as the packaging signal for the M13 phage. When single stranded, the M13ori forms unique hairpins that signal packaging into a phage capsid. It was experimentally demonstrated that this part is both necessary and sufficient for plasmid packaging into M13 phage. This part does not code for phage coat proteins; therefore, cannot produce phage.
This composite part consists of parts BBa_K1445000 (M13ori) and BBa_K1218011 (cas9).
The cas9 construct includes the native trcrRNA and promoter region upstream of the type II Cas9 endonuclease. Downstream of the Cas9 protein is a minimal CRISPR array that contains the spacer region that determines the DNA sequence that is targeted by the Cas9 endonuclease. The spacer sequence can be easily replaced through a digestion-ligation reaction using BsaI. The addition of the M13 origin of replication (M13ori) allows for the uptake of the CRISPR-Cas9 machinery into M13 phage.
This biobrick backbone has the high copy number pUC19 origin of replication and an ampicillin resistance marker. It also contains the M13 origin of replication which allows for the phagemid to be packaged into the M13 phage. It was experimentally validated that vector retains its ability to be packaged into M13 phage.
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