Team:Harvard/Test Page

From 2011.igem.org

(Difference between revisions)
(Created page with "<html> <style type="text/css"> #p-logo>a>img { position: relative !important; left: -1px !important; } #top-section { width: 962px !important; overflow: ...")
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<html>
<html>
-
<style type="text/css">
+
<head>
-
#p-logo>a>img {
+
<script type = "text/javascript">
-
      position: relative !important;
+
  function chuck_norris(){
-
      left: -1px !important;
+
-
}
+
-
#top-section {
+
var rand= Math.floor(Math.random()*18);
-
      width: 962px !important;
+
var facts=new Array();
-
      overflow: hidden;
+
-
}
+
-
#globalWrapper {
 
-
      padding-bottom: 0px;
 
-
}
 
-
#footer-box {
+
facts[0]='"Keep your zinc fingers away from Chuck Norris, because he can replace zinc in their structure."';
-
      width: 952px;
+
facts[1]='"When Chuck Norris transfects cells, he just takes the plasmid and orders the cell: "Eat, b****."';
-
}
+
facts[2]='"Chuck Norris sonicates with his own voice."';
 +
facts[3]='"Chuck Norris gets HEK293 cells by scratching his kidney."';
 +
facts[4]='"Chuck Norris runs western blot by putting SDS gel into a copying machine."';
 +
facts[5]='"Chuck Norris can separate biosynthetic products with a knife."';
 +
facts[6]='"When split fluorescent protein meets Chuck Norris, there is no possibility to fail the fret effect."';
 +
facts[7]='"Chuck Norris can excite fluorescent proteins with energy that is lower than the energy emitted."';
 +
facts[8]='"Chuck Norris\' oscillator oscillates faster than light."';
 +
facts[9]='"Chuck Norris can model the behaviour of an oscillator without any parameters."';
 +
facts[10]='"T7 RNA polymerase always asks Chuck Norris before it binds to promoter."';
 +
facts[11]='"Chuck Norris\" carotenoids are hydrophillic and cells excrete them into the culture broth."';
 +
facts[12]='"Chuck Norris doesn\"t need primary metabolism in order to produce carotene."';
 +
facts[13]='"Chuck Norris performs double digest with only one enzyme."';
 +
facts[14]='"Chuck Norris can PCR eukaryotic gene without introns."';
 +
facts[15]='"Chuck Norris is not afraid of the wiki freeze"';
 +
facts[16]='"There are G, C, T, A and the Chuck Norris nucleotide. It is self complementary and forms four hydrogen bonds."';
 +
facts[17]='"Chuck Norris can do PCR without a template nucleic acid. "';
 +
facts[18]='"Chuck Norris\" DNA is positively charged and has three grooves: minor, major and another one undefinable by common laws of nature. "';
 +
 
 +
document.getElementById('chuck_bes').innerHTML=facts[rand];
-
#allcontent, #p-logo {
 
-
      width: 950px !important;
 
}
}
-
.firstHeading {
+
function goto(url) 
-
   display:none;
+
{
 +
  window.location.href = url; 
 +
} 
 +
</script>
 +
<SCRIPT language="JavaScript">
 +
<!--
 +
 
 +
//-->
 +
</SCRIPT>
 +
   <style type="text/css">
 +
html { min-height: 100%; margin-bottom: 1px; }
 +
#thumbsi{
 +
margin-top:77px;
}
}
 +
html { overflow: -moz-scrollbars-vertical !important; }
 +
#toc{
 +
background-color:#ececec;
 +
margin-top:9px;
 +
}
 +
#toc li a{
 +
color:black;
 +
}
 +
#toc li a .toctext{
 +
text-decoration:underline;
 +
}
 +
#small_text{
 +
font-size:12px;
 +
}
body {
body {
-
+
    background-color: black;
-
background-image:none;
+
background-image:url("https://static.igem.org/mediawiki/2010/9/93/SLOBackground.jpg");
-
background-position: center;
+
background-position: left top;  
-
background-repeat: no-repeat;
+
background-repeat: repeat-x repeat-y;  
-
background-attachment: fixed;      
+
background-attachment: fixed;
-
margin-left: auto;
+
  }
-
        margin-right: auto;
+
pre {
-
font-family: Helvetica, Arial, sans-serif;
+
background-color:transparent;
-
width: 900px;
+
border:0px;
-
}
+
}
-
table {
+
div.thumb{
-
        color: #254117;
+
border-color:transparent;
-
font-family: Helvetica, Arial, sans-serif;
+
-
        }
+
-
#content {
+
}
-
        color: #254117;
+
a:hover{
-
font-family: Helvetica, Arial, sans-serif;
+
text-decoration:none;
-
width: 950px;
+
}
-
        line-height: 1.2em;
+
 +
#contentSub {
 +
display:none;
}
}
-
a {
+
#siteSub {
-
  text-decoration: none;
+
display:none;
-
  color: #7F5217;
+
}
-
  }
+
-
 
+
-
a:visited{
+
-
      color:#660000;
+
-
      text-decoration: none;
+
-
      }
+
-
a:hover {
+
#search-controls {
-
color: #A0C544;
+
display:none;
-
        text-decoration: none;
+
}
-
}
+
-
+
.firstHeading {
-
h1, h2, h3, h4, h5, h6 {
+
display:none;
-
        color: #254117;
+
}
}
-
#headerlinks{
+
 
-
      margin-left: -20px;
+
#search-controls {
 +
margin-top:30px;
}
}
-
#nav, #nav ul {
+
#footer-box {
-
padding: 0;
+
display:none;
-
list-style: none;
+
}
-
}
+
-
.abstractext{
+
#top-section {
-
float:right;
+
height: 5px;
-
width="400px"
+
border-left: none;
 +
border-right: none;
}
}
-
#nav a {
+
.left-menu {
-
display: block;
+
margin-top:-15px;
-
width: 149px;
+
}
}
-
#nav li {
+
.left-menu ul {
-
float: left;
+
border: none;
-
width: 149px;
+
-
margin-right: 41px;
+
}
}
-
#nav li ul {
+
#menubar li a {
-
position: absolute;
+
color: white;
-
width: 149px;
+
-
left: -999em;
+
}
}
-
#nav li:hover ul {
+
#menubar{
-
left: auto;
+
color: white;
-
      text-decoration: none;
+
}
-
      color: white !important;
+
 +
#menubar.right-menu {
 +
margin-top:-20px;
}
}
-
#nav li:hover ul, #nav li.sfhover ul {
+
.right-menu ul {
-
left: auto;
+
border: none;
-
      text-decoration: none;
+
-
      color: white !important;
+
}
}
-
sfHover = function() {
+
#menubar{
-
var sfEls = document.getElementById("nav").getElementsByTagName("LI");
+
top:15px;
-
for (var i=0; i<sfEls.length; i++) {
+
z-index:25;
-
sfEls[i].onmouseover=function() {
+
 
-
this.className+=" sfhover";
+
}
-
}
+
img[src*="/wiki/skins/common/images/wiki.png"]{
-
sfEls[i].onmouseout=function() {
+
    width:0;
-
this.className=this.className.replace(new RegExp(" sfhover\\b"), "");
+
    height:60px;
-
}
+
    padding-right:975px;
-
}
+
    background:transparent;
 +
}
 +
#p-logo a{
 +
color:#C9C9C9;
 +
}
 +
#content{
 +
background-color: transparent;
 +
border-left: none;
 +
border-right: none;
 +
width:975px;
 +
font-family:"Accidental Presidency","Times New Roman",Georgia,Serif;
 +
font-smooth:always;
}
}
-
if (window.attachEvent) window.attachEvent("onload", sfHover);
 
-
 
-
.bannerimage {
 
-
 
-
}
 
-
a.bannerlinks {
 
-
  color: white !important;
 
-
  text-decoration: none;
 
-
  }
 
 +
#globalWrapper{
 +
background-color: black;
 +
background-image:url("https://static.igem.org/mediawiki/2010/9/93/SLOBackground.jpg");
 +
background-position: left top;
 +
background-repeat: repeat-x repeat-y;
 +
background-attachment: fixed;
 +
}
-
a.bannertoplinks {
+
#banner{
-
  color: white !important;
+
background-image:url("https://static.igem.org/mediawiki/2010/a/a2/SLOBanner.png");
-
  text-decoration: none;  
+
background-position: center;
 +
background-repeat: no-repeat;
 +
width:931;
 +
height:127px;
 +
font-family:Arial;
 +
font-size:12px;
 +
padding-left:268px;
}
}
-
a.bannerlinks:hover, a.bannertoplinks:hover {
+
a{
-
  background-color: #A0C544;
+
outline: 0 none;
-
  color: white;
+
}
-
  }
+
-
a.labnotebook{
+
#vsebina{
-
  color: #254117;
+
background: transparent;
-
  text-decoration: none;
+
float: right;
-
    }
+
width: 735px;
 +
margin-top:10px;
 +
-webkit-border-radius: 5px;
 +
-moz-border-radius: 5px;
 +
border-radius: 5px;
 +
font-size:15px;
 +
font-weight:normal;
 +
font-smooth:always;
 +
letter-spacing:0.5px;
 +
font-smooth: 1em;
 +
}
 +
 
 +
#meni{
 +
background: transparent;
 +
float: left;
 +
width: 209px;
 +
padding-top:15px;
 +
margin-top:10px;
 +
}
-
a.labnotebook:hover{
+
#meni a{
-
color: #254117;
+
color:white;
-
  text-decoration: none;
+
}
}
-
a.labnotebook:visited{
+
#meni a:visited{
-
color: #254117;
+
color:white;
-
  text-decoration: none;
+
}
}
-
 
-
.bannerlinks {
 
-
background-color: #7F5217;
 
-
border-style: solid;
 
-
border-color: white;
 
-
border-width: 1px;
 
-
color: white;
 
-
padding: 3px 20px 3px 20px;
 
-
        margin-left: -19px;
 
-
}
 
-
.bannertoplinks {
+
#gumb1{
-
background-color: #827B60;
+
margin-left:0px;
-
border-style: solid;
+
margin-top:-1px;
-
border-color: white;
+
width:135px;
-
border-width: 1px;
+
float:left;
-
color: white;
+
color:white;
-
        margin-bottom: -2px;
+
text-align:center;
-
padding: 3px 20px 3px 20px;
+
font-style:italic;
-
}
+
display:block;
-
.bannertoplinkslast{
+
-
      background-color: #827B60;
+
-
border-style: solid;
+
-
border-color: white;
+
-
border-width: 1px;
+
-
color: white;
+
-
        margin-bottom: -2px;
+
-
padding: 3px 20px 3px 20px;
+
}
}
-
#twitter_div {
+
#gumb1:hover{
-
font-size: 0.8em;
+
background-image:url("https://static.igem.org/mediawiki/2010/a/a2/SLOstopnja1over.png");
-
        margin-right: 0px;
+
background-position: center;  
-
}
+
background-repeat: no-repeat;
-
#twitter_div ul {
+
}
-
line-height: 1.3em;
+
-
        list-style-type: none;
+
-
}
+
-
#twitter_div img {
+
#gumb2{
-
        float: left;
+
background-image:url("https://static.igem.org/mediawiki/2010/7/76/Sloprojectstopnja1.png");
-
        margin-top:.5em;
+
margin-left:0px;
-
        margin-right:.5em;
+
margin-top:-2px;
-
        }
+
width:143px;
 +
float:left;
 +
color:white;
 +
text-align:center;
 +
font-style:italic;
 +
height:30px;
 +
display:block;
-
#twitter_update_list {
+
}
-
        margin-left: 0px;
+
#gumb2:hover{
-
        }
+
background-image:url("https://static.igem.org/mediawiki/2010/b/b0/Sloprojectstopnja1over.png");
 +
margin-left:0px;
 +
margin-top:-2px;
 +
width:143px;
 +
float:left;
 +
height:30px;
 +
color:white;
 +
text-align:center;
 +
font-style:italic;
 +
height:26px;
 +
}
-
#twitter_head {
+
#gumb3{
-
        margin-bottom: .6em;
+
background-image:url("https://static.igem.org/mediawiki/2010/3/3f/Slomethodsstopnja1.png");
-
        border-bottom: 1px solid #AAA;
+
margin-left:0px;
-
        font-size: 150%;
+
margin-top:-2px;
-
        }
+
width:175px;
 +
float:left;
 +
color:white;
 +
text-align:center;
 +
font-style:italic;
 +
height:30px;
 +
display:block;
 +
}
 +
#gumb3:hover{
 +
background-image:url("https://static.igem.org/mediawiki/2010/8/81/SLOmethodsstopnja1over.png");
 +
margin-left:0px;
 +
margin-top:-2px;
 +
width:175px;
 +
float:left;
 +
color:white;
 +
text-align:center;
 +
font-style:italic;
 +
height:26px;
-
#twitter_head  p {layout:block; margin-bottom:2px;}
+
}
-
#twitter_head  a {float:right; layout:block;}
+
-
#sidebar {
+
#gumb4{
-
        right:5px;
+
background-image:url("https://static.igem.org/mediawiki/2010/c/cf/SLOteamstopnja1.png");
-
width: 300px;
+
margin-left:0px;
-
float: right;
+
margin-top:-2px;
-
margin-right: 0px;
+
width:143px;
-
border: none;
+
float:left;
-
padding: 0px;
+
color:white;
-
        padding-top:5px;
+
text-align:center;
-
}
+
font-style:italic;
 +
height:30px;
 +
display:block;
 +
}
-
#abstract {
+
#gumb4:hover{
-
width: 600px;
+
background-image:url("https://static.igem.org/mediawiki/2010/9/94/SLOteamstopnja1over.png");
-
border-style: solid;
+
margin-left:0px;
-
border-color: white;
+
margin-top:-2px;
-
border-width: 1px;
+
width:143px;
-
padding: 10px;
+
float:left;
-
line-height: 1.2em;
+
color:white;
-
        font-size: 14px;
+
text-align:center;
-
}
+
font-style:italic;
-
+
height:30px;
-
+
-
#rightgroup {
+
-
float: right;
+
-
width: 300px;
+
-
padding: 10px;
+
-
}
+
-
+
-
#leftgroup {
+
-
width: 300px;
+
-
padding: 10px;
+
-
        margin-right: 20px;
+
-
}
+
-
+
-
#maincontent {
+
-
width: 610px;
+
-
}
+
-
#headerlinks > #nav > li {
 
-
        border-bottom: 4px solid white;
 
}
}
 +
#gumb5{
 +
background-image:url("https://static.igem.org/mediawiki/2010/1/1c/SLOhumanstopnja1.png");
-
#sidebar a{
+
margin-left:0px;
-
      text-decoration: none;
+
margin-top:-2px;
-
      color: #7F5217;
+
width:170px;
 +
float:left;
 +
color:white;
 +
text-align:center;
 +
font-style:italic;
 +
height:26px;
 +
display:block;
}
}
-
#sidebar a:hover{
+
#gumb5:hover{
-
    color: #A0C544;
+
background-image:url("https://static.igem.org/mediawiki/2010/a/a2/SLOstopnja1over.png");
-
    text-decoration: none;
+
background-position: center;
 +
background-repeat: no-repeat;
 +
 
 +
}
 +
#gumbi1{
 +
color:white;
 +
font-style:italic;
 +
margin-left:114px;
 +
padding-top:54px;
 +
text-align:center;
}
}
-
a.sidebarlinks {
+
a #gumbi1{
-
display: block;
+
color:white;
-
width: 300px;
+
-
font-size: 1.2em;
+
-
text-align: center;
+
-
background-color: #827B60;
+
-
color: white !important;
+
-
padding: 10px 0px 10px 0px;
+
-
margin-bottom: 5px
+
-
}
+
-
a.sidebarlinks:hover {
+
}
-
background-color: #A0C544;
+
#gumbi1 a{
-
        color: white !important;
+
color:white;
-
}
+
-
a.timelinelinks {
 
-
      color: #7F5217 !important;
 
}
}
-
a.timelinelinks:hover {
+
#lgumbi{
-
      color: #A0C544 !important;
+
color:white;
 +
font-size:22px;
 +
padding-left:0px;
 +
}
 +
#lgumbi a{
 +
color:white;
 +
}
 +
#lgumbi a:visited{
 +
color:white;
 +
}
 +
#chuck{
 +
width:201px;
 +
height:254px;
 +
background-image:url("https://static.igem.org/mediawiki/2010/4/4a/SLOchuck.png");
 +
margin-top:60px;
 +
color:white;
 +
}
 +
#chuck_nas{
 +
font-family:Calibri;
 +
font-size:16px;
 +
font-weight:bold;
 +
padding-top:1px;
 +
margin-left:6px;
 +
}
 +
#chuck_bes{
 +
font-family:Calibri;
 +
font-size:18px;
 +
font-style:italic;
 +
margin-left:22px;
 +
padding-right:23px;
}
}
-
#content {
+
#vsebina_top{
-
      padding: 6px;
+
background-image:url("https://static.igem.org/mediawiki/2010/3/3a/SLOUpborder.png");
-
      padding-top: 1px;
+
background-position:top;
 +
height:9px;
 +
margin-left:-23px;
}
}
 +
#vsebina_mid{
 +
background-color:transparent;
 +
height:500px;
 +
}
 +
#vsebina_mid_left{
 +
background-image:url("https://static.igem.org/mediawiki/2010/9/99/SLOleftborder.png");
 +
background-repeat:repeat-y;
 +
float:left;
 +
height:100%;
 +
margin-left:-23px;
 +
width:11px;
 +
}
 +
#vsebina_mid_right{
 +
background-image:url("https://static.igem.org/mediawiki/2010/b/bd/SLORightborder.png");
 +
background-repeat:repeat-y;
 +
float:left;
 +
height:100%;
 +
width:7px;
 +
}
 +
#vsebina_mid_center{
 +
background-color:#ECECEC;
 +
float:left;
 +
font-family:Arial;
 +
font-size:14px;
 +
margin-left:-12px;
 +
height:100%;
 +
width:740px;
 +
}
 +
#vsebina_foot{
 +
background-image:url("https://static.igem.org/mediawiki/2010/1/17/SLODownborder.png");
 +
background-position:left center;
 +
height:9px;
 +
margin-left:-23px;
 +
}
 +
#naslov {
 +
background-color:#CECDCD;
 +
color:#B22020;
 +
float:left;
 +
font-family:"Candara","Arial";
 +
font-size:30px;
 +
height:30px;
 +
margin-left:-10px;
 +
margin-top:9px;
 +
padding-left:12px;
 +
padding-top:4px;
 +
width:55%;
 +
}
 +
#stopnja3{
 +
background-image:url(https://static.igem.org/mediawiki/2010/3/38/SLOstopnja3.png);
 +
color:white;
 +
display:block;
 +
float:left;
 +
font-family:"Calibri","Arial";
 +
font-size:19px;
 +
height:21px;
 +
margin-left:43.6px;
 +
margin-right:-10px;
 +
margin-top:-9px;
 +
padding-top:3px;
 +
text-align:center;
 +
width:140px;
 +
}
 +
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<a href="#naslov"><span id="stopnja3a">summary</span></a><a href="/Team:Slovenia/scheme"><span id="stopnja3">scheme</span></a><a href="#achieve"><span id="stopnja3">achievements</span></a>
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Information encoded by triplet nucleotides of DNA determines the order of incorporation of amino acids into proteins. We envisioned an alternative use of DNA as the scaffold for encoding information. We used DNA sequence as a program consisting of series of blocks of nine or more nucleotides. If we add desired functional proteins fused with DNA-binding domains that bind to those DNA blocks, the functional proteins spontaneously arrange along the DNA in a defined order, depending only on the program DNA sequence. This DNA-guided assembly platform provides particularly powerful tool for engineering biosynthetic pathways. We selected six different zinc fingers and determined their binding to their corresponding DNA target sequences using surface plasmon resonance, mobility shift analysis and &beta;-galactosidase reporter assay. FRET effect was used to demonstrate simultaneous binding of four different zinc fingers with split fluorescent proteins to the program DNA in mammalian cells. The real world application of the DNA-guided biosynthesis was demonstrated on a violacein biosynthetic pathway consisting of five enzymes. In addition to violacein the native biosynthetic pathway produces large amount of a green side product deoxychromoviridans. In our designed biosynthetic pathway, however, this side product was absent. Furthermore, the yield of violacein production was 6-fold higher in the presence of DNA program coding for the linear order of enzymes in comparison to the scrambled DNA program. These results demonstrate that the correct order of enzymes in the biosynthetic assembly is important rather than just enzyme clustering. Artificial DNA-binding domains also have great potential for information processing and our modeling demonstrates the potentials for expanding repertoire and features of genetic oscillators.
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<div id="abstract">
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<h1>this is just a test - zinc finger madness is on ze vay<iframe src="http://www.facebook.com/plugins/like.php?href=&layout=standard&show-faces=true&width=50&height=25&action=like&colorscheme=light" scrolling="no" frameborder="0" allowTransparency="true" style="border:none; overflow:hidden; width:50px; height:25px;margin:10px 0 0 0;"></iframe></h1>
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<p>The Harvard iGarden is a venture into plant engineering. Our aim is to create a toolkit for the cultivation of a personalized garden containing features introduced through synthetic biology. In addition to a "genetic fence" designed to prevent the spread of introduced genetic material, we have developed three independent features to be included in this toolkit - inclusion of novel flavors, knockdown of plant allergens, and modification of petal color.</p>
 
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<p>All parts are BioBrick compatible and introduced into plants through agrobacterium-mediated transformation, using existing plant vectors modified with the BioBrick multiple cloning site.</p>
+
In conclusion, our project demonstrates novel application of DNA as the carrier of information in synthetic biology. With over 700 available characterized zinc fingers almost limitless number of combinations is on hand, providing a strong support for maturation of synthetic biology from craft towards the engineering science. <html>
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<p>The Harvard iGarden, beyond being an application of the BioBrick system to plant engineering, is an effort to raise public awareness of synthetic biology, production of food, and how the two can intertwine. We envision the iGarden as a medium through which the non-scientist can see the power and potential of synthetic biology and apply it to everyday life. </p>
 
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<div id="naslov"  >achievements</div>
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<li>We designed a new platform of DNA-guided scaffold to      arrange various functional protein domains in a defined linear order &nbsp;</li>
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<li>We prepared biobricks and characterized binding of six      distinct zinc finger proteins to their target DNA binding sites by various      methods both in vitro (SPR, EMSA, sequence-enabled reassembly of split      fluorescent proteins) and in vivo by &beta;-galactosidase repression assay</li>
 +
<li>We proved simultaneous binding of 4 zinc finger      proteins to adjacent sites on program DNA by FRET</li>
 +
<li>We designed chimeric violacein biosynthetic enzymes with      added zinc finger&nbsp;DNA binding domains. In the presence of&nbsp;correct      DNA program the yield of violacein production improves 6 fold. </li>
 +
<li>We suppressed formation of side reaction product      deoxychromoviridans in the violacein biosynthetic pathway in the presence      of DNA program</li>
 +
<li>We performed both deterministic and stochastic      simulations of Smolen oscillator and repressilator&nbsp;comprising zinc      finger based repressors using realistic kinetic parameters      and Poisson-distributed time delay. In these models we demonstrated that this system      exhibits oscillations only in topologies comprising odd number of repressor elements while the increased number increases the stability and extends      the time constant of oscillator. </li>
 +
<li>We demonstrated the functionality of designed DNA      binding domains as building blocks of the genetic oscillator</li>
 +
<li>We submitted 151&nbsp;parts to the registry, which can      be used for application of our DNA-guided platform for biosynthesis,      building oscillators, characterizing DNA binding domains etc.</li>
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Revision as of 20:04, 6 July 2011

Team Slovenia project scheme link
summary
Information encoded by triplet nucleotides of DNA determines the order of incorporation of amino acids into proteins. We envisioned an alternative use of DNA as the scaffold for encoding information. We used DNA sequence as a program consisting of series of blocks of nine or more nucleotides. If we add desired functional proteins fused with DNA-binding domains that bind to those DNA blocks, the functional proteins spontaneously arrange along the DNA in a defined order, depending only on the program DNA sequence. This DNA-guided assembly platform provides particularly powerful tool for engineering biosynthetic pathways. We selected six different zinc fingers and determined their binding to their corresponding DNA target sequences using surface plasmon resonance, mobility shift analysis and β-galactosidase reporter assay. FRET effect was used to demonstrate simultaneous binding of four different zinc fingers with split fluorescent proteins to the program DNA in mammalian cells. The real world application of the DNA-guided biosynthesis was demonstrated on a violacein biosynthetic pathway consisting of five enzymes. In addition to violacein the native biosynthetic pathway produces large amount of a green side product deoxychromoviridans. In our designed biosynthetic pathway, however, this side product was absent. Furthermore, the yield of violacein production was 6-fold higher in the presence of DNA program coding for the linear order of enzymes in comparison to the scrambled DNA program. These results demonstrate that the correct order of enzymes in the biosynthetic assembly is important rather than just enzyme clustering. Artificial DNA-binding domains also have great potential for information processing and our modeling demonstrates the potentials for expanding repertoire and features of genetic oscillators. In conclusion, our project demonstrates novel application of DNA as the carrier of information in synthetic biology. With over 700 available characterized zinc fingers almost limitless number of combinations is on hand, providing a strong support for maturation of synthetic biology from craft towards the engineering science.
achievements

  • We designed a new platform of DNA-guided scaffold to arrange various functional protein domains in a defined linear order  
  • We prepared biobricks and characterized binding of six distinct zinc finger proteins to their target DNA binding sites by various methods both in vitro (SPR, EMSA, sequence-enabled reassembly of split fluorescent proteins) and in vivo by β-galactosidase repression assay
  • We proved simultaneous binding of 4 zinc finger proteins to adjacent sites on program DNA by FRET
  • We designed chimeric violacein biosynthetic enzymes with added zinc finger DNA binding domains. In the presence of correct DNA program the yield of violacein production improves 6 fold.
  • We suppressed formation of side reaction product deoxychromoviridans in the violacein biosynthetic pathway in the presence of DNA program
  • We performed both deterministic and stochastic simulations of Smolen oscillator and repressilator comprising zinc finger based repressors using realistic kinetic parameters and Poisson-distributed time delay. In these models we demonstrated that this system exhibits oscillations only in topologies comprising odd number of repressor elements while the increased number increases the stability and extends the time constant of oscillator.
  • We demonstrated the functionality of designed DNA binding domains as building blocks of the genetic oscillator
  • We submitted 151 parts to the registry, which can be used for application of our DNA-guided platform for biosynthesis, building oscillators, characterizing DNA binding domains etc.

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