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Team:DTU Denmark/USERprogram
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<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(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"><i>Article submitted October 2009 - publication pending</i></p> | ||
<p>Corresponding author: Lars Rønn Olsen. Questions or comments? <a href="mailto:lronn@bio.dtu.dk" CLASS=email></a></p><br> | <p>Corresponding author: Lars Rønn Olsen. Questions or comments? <a href="mailto:lronn@bio.dtu.dk" CLASS=email></a></p><br> | ||
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<a href="https://2009.igem.org/Team:DTU_Denmark/USERprogram" CLASS=leftbar>Design your primers here</a><br> | <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogram" CLASS=leftbar>Design your primers here</a><br> | ||
Revision as of 14:01, 18 October 2009
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The redoxilator - Introduction - Results - Applications and perspectives The USERTM assembly standard - Principle - Proof of concept - Manual USERTM fusion primer design software - Abstract - Instructions - Output format |
The project USER fusion primer design software Abstract 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 (TM) of the primer fragments must be pairwise within 2oC 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 TM 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 TM, 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. Article submitted October 2009 - publication pending Corresponding author: Lars Rønn Olsen. Questions or comments? Design your primers here |
Synthetic Biology “Synthetic Biology is an art of engineering new biological systems that don’t exist in nature.” -Paras Chopra & Akhil Kamma 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. |
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