Team:DTU Denmark/USERprogram

When designing constructs with more than two biobricks using USER fusion, it is essential to avoid identical fusion tails to ensure correct order of the biobricks. Furthermore, the DNA denaturation temperature (T_M) of the primer fragments must be pairwise within 2 ^oC degrees of each other, for successful PCR amplication of the biobricks. Selection of optimal fusion tails is achieved by employing a simple, but powerful sorting algorithm utilizing the fact that the relative penalty for increasing the length of, and shifting the center of fusion regions, is the same, i.e. one base added/removed from final primers. Adjusting the T_M of primer pairs is done by sampling the various allowed lengths of the primers (18-24 bases), thus changing the CG ration and affecting T_M until an acceptable solution is achieved. The suggested primers are presented in a clear and intuitive fashion, diplaying both list view and a graphical overview of fusion regions and related primers. PHUSER is tested to handle primer design for constructs with between 2 and 9 biobricks at the time, but in theory, if enough unique fusion tails exist, many more biobricks can be fused in the same reaction.

Questions or comments? Please Email us

Design your primers with PHUSER here

Achievements

Redox sensing device
Two novel genes have been designed and synthesized each comprised of 5 genetic elements. Together they function as a device termed the Redoxilator that can sense the internal redox state of a yeast cell, and output a reporter signal. Extensive mathematical modelling was performed to simulate how the construct would operate in vivo.

Biobricks
DNA of several new biobricks have been designed and submitted including a yeast optimized GFP reporter protein, a protein degradation sequence and a fast degradable yeast GFP. (Bronze medal)

We have demonstrated that our USER fusion biobrick works as expected and documented it (silver medal)

USER fusion Assembly standard
A new biobrick assembly standard that allows the rapid construction of multi-part devices have been developed and documented. The assembly standard offers many benefits: All restriction sites are allowed, multiple biobricks can be joined in one step, the result is scar-free making it ideal for protein fusions and more. (Gold medal)

USER-fusion primer design software
A novel and very useful software tool have been developed that can automatically design the optimal primers for USER fusion assembly of 2-9 biobricks, taking several parameters into account.

Comments or questions to the team? Please Email us -- Comments of questions to webmaster? Please Email us

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-   <font color="#990000" face="arial" size="3">
+<p>
+ <font color="#990000" face="arial" size="3">
     <br>
-    The redoxilator<br><br>
+    The redoxilator<br>
     </font>
+</p>
     <font color="" face="arial" size="2">
-     <a href="https://2009.igem.org/Team:DTU_Denmark/theory" CLASS=leftbar>- Introduction</a><br>
+     <a href="https://2009.igem.org/Team:DTU_Denmark/genetic_design" CLASS=leftbar>- Genetic design</a><br>
-     <a href="https://2009.igem.org/Team:DTU_Denmark/yeast" CLASS=leftbar>- Results</a><br>
+     <a href="https://2009.igem.org/Team:DTU_Denmark/applications" CLASS=leftbar>- Applications and perspectives</a><br>
-     <a href="https://2009.igem.org/Team:DTU_Denmark/practicalapproach" CLASS=leftbar>- Applications and perspectives</a><br><br>
+     <a href="https://2009.igem.org/Team:DTU_Denmark/safety" CLASS=leftbar>- Safety considerations</a><br>
     </font>
+<p>
     <font color="#990000" face="arial" size="3">
-     <br>The USER<sup>TM</sup> assembly standard<br><br>
+     <br>The USER assembly standard<br>
     </font>
+</p>
     <font face="arial" size="2">
-     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprinciple" CLASS=leftbar>- Principle</a><br>
+     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprinciple" CLASS=leftbar>- USER fusion of biobricks</a><br>
-    <a href="https://2009.igem.org/Team:DTU_Denmark/USERconcept" CLASS=leftbar>- Proof of concept</a><br>
-    <a href="https://2009.igem.org/Team:DTU_Denmark/USERmanual" CLASS=leftbar>- Manual</a><br><br>
     </font>
+<p>
     <font color="#990000" face="arial" size="3">
-     <br>USER<sup>TM</sup> fusion primer design software<br><br>
+     <br>USER fusion primer design software<br>
     </font>
+</p>
     <font face="arial" size="2">
      <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogram" CLASS=leftbar>- Abstract</a><br>
      <a href="https://2009.igem.org/Team:DTU_Denmark/USERprograminstructions" CLASS=leftbar>- Instructions</a><br>
      <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogramoutputformat" CLASS=leftbar>- Output format</a><br>
+   </font>
+<p>
+   <font color="#990000" face="arial" size="3">
+    <br>Experimental results<br>
+   </font>
+</p>
+   <font face="arial" size="2">
+    <a href="https://2009.igem.org/Team:DTU_Denmark/results" CLASS=leftbar>- Results and discussion</a><br>
     </font>
    </td>
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    <font color="#990000" face="arial" size="5">
    <br>
-    <b>The project</b><br><br><br>
+    <b>The project</b><br><br>
    </font>
    <font color="#333333" face="arial" size="2.5">
@@ Line 202: / Line 214: @@
-<font size="4"><b>USER fusion primer design software</b></font><br><br>
+<font size="4"><b>The USER fusion primer design software: PHUSER<br>(<u>P</u>rimer <u>H</u>elp for <u>USER</u>)</b></font><br><br>
 <font size="3"><b>Abstract</b></font><br>
-<p align="justify">When designing constructs with more than two biobricks using USER(TM) fusion, it is essential to avoid identical fusion tails to ensure correct order of the biobricks. Furthermore, the DNA denaturation temperature (T<sub>M</sub>) of the primer fragments must be pairwise within 2<sup>o</sup>C degrees, for PCR amplication of the biobricks. Selection of optimal fusion tails is achieved by employing a simple, but powerful sorting algorithm utilizing the fact that the relative penalty for increasing length of, and shifting center of fusion regions, is the same, i.e. one base added/removed from final primers. Adjusting the T<sub>M</sub> of primer pairs is done by randomly sampling the various allowed lengths of the primers (18-24 bases), thus changing the CG ration and affecting T<sub>M</sub>, until an acceptable solution is achieved. The suggested primers are presented in a clear and intuitive fashion, diplaying both list view and a graphical overview of fusion regions and related primers. The program is tested to handle primer design for constructs with between 2 and 9 biobricks at the time, but in theory, if enough unique fusion tails exists, many more biobricks can be fused in the same reaction.</p><br>
+<p align="justify">When designing constructs with more than two biobricks using USER fusion, it is essential to avoid identical fusion tails to ensure correct order of the biobricks. Furthermore, the DNA denaturation temperature (T<sub>M</sub>) of the primer fragments must be pairwise within 2 <sup>o</sup>C degrees of each other, for successful PCR amplication of the biobricks. Selection of optimal fusion tails is achieved by employing a simple, but powerful sorting algorithm utilizing the fact that the relative penalty for increasing the length of, and shifting the center of fusion regions, is the same, i.e. one base added/removed from final primers. Adjusting the T<sub>M</sub> of primer pairs is done by sampling the various allowed lengths of the primers (18-24 bases), thus changing the CG ration and affecting T<sub>M</sub> until an acceptable solution is achieved. The suggested primers are presented in a clear and intuitive fashion, diplaying both list view and a graphical overview of fusion regions and related primers. PHUSER is tested to handle primer design for constructs with between 2 and 9 biobricks at the time, but in theory, if enough unique fusion tails exist, many more biobricks can be fused in the same reaction.</p><br>
-<a href="https://2009.igem.org/Team:DTU_Denmark/USERprogram" CLASS=leftbar>Design your primers here</a><br><br>
+<!-- <p align="justify"><i>Article submitted October 2009 - publication pending</i></p> -->
+<p>Questions or comments? Please <a href="mailto:lronn@bio.dtu.dk" CLASS=email>Email us</a></p><br>
-<p>Corresponding author: Lars Rønn Olsen. Questions or comments?<a href="mailto:lronn@bio.dtu.dk" CLASS=email>Email corresponding author</a></p><br>
+<b>Design your primers with PHUSER <a href="http://igem.grafiki.org/" CLASS=leftbar target="blank">here</a></b><br><br>
-<p align="justify"><i>Article submitted October 2009 - publication pending</i></p>
@@ Line 220: / Line 231: @@
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    <font face="arial" size="2">
-  <b>Synthetic Biology</b><br><br>
@@ Line 226: / Line 236: @@
-<p align="left"><i>“Synthetic Biology is an art of engineering new biological systems that don’t exist in nature.”</i><br></p>
+<p>
+<strong>Achievements</strong><br>
-<p align="right"><i>-Paras Chopra & Akhil Kamma</i><br><br></p>
+<br>
+<strong>Redox sensing device</strong><br>
+Two novel genes have been designed and synthesized each comprised of 5 genetic elements. Together they function as a device termed the Redoxilator that can sense the internal redox state of a yeast cell, and output a reporter signal. Extensive mathematical modelling was performed to simulate how the construct would operate <i>in vivo</i>.<br>
+<br>
+<strong>Biobricks</strong><br>
+DNA of several new biobricks have been designed and submitted including a yeast optimized GFP reporter protein, a protein degradation sequence and a fast degradable yeast GFP. (Bronze medal)<br>
+<br>
+We have demonstrated that our USER fusion biobrick works as expected and documented it (silver medal)<br>
+<br>
+<strong>USER fusion Assembly standard</strong><br>
+A new biobrick assembly standard that allows the rapid construction of multi-part devices have been developed and documented. The assembly standard offers many benefits: All restriction sites are allowed, multiple biobricks can be joined in one step, the result is scar-free making it ideal for protein fusions and more. (Gold medal)<br>
+<br>
+<strong>USER-fusion primer design software</strong><br>
+A novel and very useful software tool have been developed that can automatically design the optimal primers for USER fusion assembly of 2-9 biobricks, taking several parameters into account.
+</p>
-<p>In nature, biological molecules work together in complex systems to serve purposes of the cell. In synthetic biology these molecules are used as individual functional units that are combined to form tailored systems exhibiting complex dynamical behaviour. From ‘design specifications’ generated from computational modelling, engineering-based approaches enables the construction of such new specified gene-regulatory networks. The ultimate goal of synthetic biology is to construct systems that gain new functions, and the perspectives of the technology are enormous. It has already been used in several medical projects2 and is predicted to play a major role in biotech-production and environmental aspects.</p>
    </font>