Team:DTU Denmark/project

From 2009.igem.org

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<p align="left"><i>“Synthetic Biology is an art of engineering new biological systems that don’t exist in nature.”</i><br></p>
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<strong>Achievements</strong><br>
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<p align="right"><i>-Paras Chopra & Akhil Kamma</i><br><br></p>
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<strong>Redox sensing device</strong><br>
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<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>
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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.<br>
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<strong>Biobricks</strong><br>
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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>
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We have demonstrated that our USER fusion biobrick works as expected and documented it (silver medal)<br>
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<strong>USER fusion Assembly standard</strong><br>
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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>
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<br>
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<strong>USER-fusion primer design software</strong><br>
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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.
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Revision as of 19:59, 20 October 2009

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The project

Home The Team The Project Parts submitted Modelling Notebook

The redoxilator

 - Introduction
- Results
- Applications and perspectives
- Safety considerations
The USERTM assembly standard

 - USERTM fusion
USERTM fusion primer design software

 - Abstract
- Instructions
- Output format
The project


 Project abstract

The Redoxilator

By in silico design and computer modelling followed by gene synthesis, we have constructed a molecular NAD/NADH ratio sensing system in Saccharomyces cerevisiae. The sensor works as an inducible transcription factor being active only at certain levels of the NAD/NADH ratios. By the coupling of a yeast optimized fast degradable GFP, the system can be used for in vivo monitoring of NAD/NADH redox poise. A future novel application of the system is heterologous redox coupled protein production in yeast.

The redox coupled system

The USER fusion standard

Another part of our project is the proposal of a new parts-assembly standard for Biobricks based on USERTM cloning. With this technique, not based on restriction enzymes, all parts independent of function can be assembled without leaving any scars from the restriction enzyme digestions.


Biobricks designed and submitted

We have constructed and submitted 4 novel biobricks, specifically designed to be useful for construction of devices in the future:
1) A GFP variant optimized for expression in yeast
2) A protein destabilization sequence, which allows rapid protein turnover when appended to any protein
3) A device made from 1+2 as a proof of concept and very useful biobrick in itself: A fast degradable GFP that has a halflife of 30 min. compared to 7 hours without destabilization.
4) A USERTM cassette that will allow insertion of PCR fragments using the novel USERTM biobrick assembly standard.
More details about our biobricks under "parts submitted"

Synthetic Biology

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.

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.

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