Team:Freiburg software

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<h1>Team Freiburg Software</h1>
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<h1 style="border-bottom: none;">Team Freiburg Bioware</h1>
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Introduction
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<br />
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<p>The first German team ever to participate in iGEM is back
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again and
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after last year's second place we're highly motivated &nbsp;to make
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some good piece of synthetic biology in 2009. In this year we want to
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create an universal restriction enzyme to facilitate labwork
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and enable new techniques. <br />
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<br />
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We're looking forward to meeting you on this year's jamboree!<br />
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<h2 class="art-PostHeaderIcon-wrapper"> &nbsp;Project
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Universal Endonuclease &ndash; Cutting Edge Technology</b>
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<p>Synthetic Biology aims at constructing whole new genomes. Such
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<p>Gene technology is driven by the use of restriction
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an
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endonucleases.
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effort is pushed forward by many users and relies on modular
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Yet, constraints of limited sequence length and variation recognized by
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combination of genetic elements. The genetic elements represent an
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available restriction enzymes pose a major roadblock for synthetic
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increasing complexity by assembling parts to devices and then systems.
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biology. We developed the basis for universal restriction enzymes,
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The construction process needs to be transparent and even at final
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primarily for routine cloning but also with potential for in vivo
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stages control at the basepair level is required. We propose to build a
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applications. We use a nucleotide cleavage domain fused to a binding
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user environment able to analyze and construct genetic parts and
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domain, which recognizes a programmable adapter that mediates binding
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ultimately genomes.
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to DNA and thus cleavage. As adapter we use readily available modified
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</p>
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oligonucleotides, as binding domain anticalins and as cleavage domain
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<p>We will build the software suite on the Google-Wave format,
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FokI moieties engineered for heterodimerization and activity. For
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which is currently in beta testing, and add molecular biology tools
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cloning, this universal enzyme has merely to be mixed with the sequence
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mainly from the BioJava library. The first goal is to provide basic
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specific oligonucleotide and the target DNA. Binding and release are
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molecular biology cloning functionality which appeals to the wet bench
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addressed with thermocycling. Additionally, we provide concepts for in
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scientist. On top of that, we would like to add specific synthetic
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vivo applications by external adapter delivery, activity regulation by
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biology functionality such as biobrick database access and part
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photo-switching, as well as for modifying an argonaute protein towards
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annotation. The software for the Jamboree will not be feature complete,
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a DNA endonuclease.
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but demonstrate the principle use, with some molecular biology standard
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tasks, as well as the power of the wave approach for a distributed
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collaborative synthetic biology effort. Many wave-robots with a
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manageable set of capabilities will divide and conquer the complex task
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of creating a genome in silico.
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</p>
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<p>The first developments of 'SynBioWave' will lay the ground for
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a useful grouping of functionality for wave-robots, how the calling of
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robots and their functions is managed, how robots act on DNA or protein
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sequences, how intermediate results are stored, etc... The process
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should be open and clear so that users can add and share robots useful
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for synthetic biology.
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<p><a href="https://2009.igem.org/Team:Freiburg_bioware/Team"><span
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<p><b>The Team</b><br />
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This year our team consists of 18 undergraduate students and 4 advisors.<br />
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<b>The Team</b><br />
 +
In 2009 our team consists of &nbsp;14 undergraduates and 4 advisors.<br />
<a href="https://2009.igem.org/Team:Freiburg_bioware/Team">Read
<a href="https://2009.igem.org/Team:Freiburg_bioware/Team">Read
more...</a></p>
more...</a></p>
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<p></p>
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<p><span style="font-weight: bold;"><a
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<span style="text-decoration: underline;"><img
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<p><b>Bioss</b><br />
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  src="https://static.igem.org/mediawiki/2009/3/34/Freiburg09_Bioss_portlet.jpg" /></a><br />
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We want to thank our main sponsors from the Center for Biological
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Bioss</span><br />
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Signalling Studies, Bioss.<br />
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We want to thank our main sponsor Bioss for supporting our project.<br />
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<a target="_blank" href="http://www.bioss.uni-freiburg.de">Read
+
<a href="http://www.bioss.uni-freiburg.de">Read more...</a></p>
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more...</a></p>
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Revision as of 15:57, 12 October 2009

FREiGEM 2009

Welcome

an image

Team Freiburg Bioware


The first German team ever to participate in iGEM is back again and after last year's second place we're highly motivated  to make some good piece of synthetic biology in 2009. In this year we want to create an universal restriction enzyme to facilitate labwork and enable new techniques.

We're looking forward to meeting you on this year's jamboree!


Project Summary


Universal Endonuclease – Cutting Edge Technology

Gene technology is driven by the use of restriction endonucleases. Yet, constraints of limited sequence length and variation recognized by available restriction enzymes pose a major roadblock for synthetic biology. We developed the basis for universal restriction enzymes, primarily for routine cloning but also with potential for in vivo applications. We use a nucleotide cleavage domain fused to a binding domain, which recognizes a programmable adapter that mediates binding to DNA and thus cleavage. As adapter we use readily available modified oligonucleotides, as binding domain anticalins and as cleavage domain FokI moieties engineered for heterodimerization and activity. For cloning, this universal enzyme has merely to be mixed with the sequence specific oligonucleotide and the target DNA. Binding and release are addressed with thermocycling. Additionally, we provide concepts for in vivo applications by external adapter delivery, activity regulation by photo-switching, as well as for modifying an argonaute protein towards a DNA endonuclease.

FREiGEM 2009

Team
The Team
In 2009 our team consists of  14 undergraduates and 4 advisors.
Read more...

bioss
Bioss
We want to thank our main sponsor Bioss for supporting our project.
Read more...

Visitors

 freigem09@googlemail.com

Retrieved from "http://2009.igem.org/Team:Freiburg_software"