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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The first big application is to use the DNA program <strong>to arrange the sequence of biosynthetic reaction enzymes</strong> and therefore guide the biosynthetic flow towards the desired products. We decided to test this idea on a previously characterized biosynthetic pathway, demonstrating the advantages of DNA programming. One important advantage is to increase the reaction rate of the overall biosynthetic pathway but it can also guide the biosynthetic flow towards one or other product and prevent side reactions. We have demonstrated both effects on the biosynthesis of violacein, a five step reaction, which can, by the addition of enzymes, yield three different products. This approach offers several potential advantages in comparison to protein-based scaffolds.</li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The first big application is to use the DNA program <strong>to arrange the sequence of biosynthetic reaction enzymes</strong> and therefore guide the biosynthetic flow towards the desired products. We decided to test this idea on a previously characterized biosynthetic pathway, demonstrating the advantages of DNA programming. One important advantage is to increase the reaction rate of the overall biosynthetic pathway but it can also guide the biosynthetic flow towards one or other product and prevent side reactions. We have demonstrated both effects on the biosynthesis of violacein, a five step reaction, which can, by the addition of enzymes, yield three different products. This approach offers several potential advantages in comparison to protein-based scaffolds.</li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Slo shema proof.png|center|frame|'''Figure 2:''' Enhancing and directing biosynthetic flow using DNA program]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Slo shema proof.png|center|frame|'''Figure 2:''' Enhancing and directing biosynthetic flow using DNA program<ins class="diffchange diffchange-inline">.</ins>]]</div></td></tr>
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</table>Tinailchttp://2010.igem.org/wiki/index.php?title=Team:Slovenia/PROJECT/introduction&diff=200952&oldid=prevRoookie at 23:42, 27 October 20102010-10-27T23:42:04Z<p></p>
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</table>Roookiehttp://2010.igem.org/wiki/index.php?title=Team:Slovenia/PROJECT/introduction&diff=200853&oldid=prevTinailc at 23:38, 27 October 20102010-10-27T23:38:05Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As DNA molecule is so extensively characterized, being sort of a pop culture molecule, finding a completely novel way of using it presents quite a challenge. DNA is the basic linear carrier of information and we thought that it could represent an ideal scaffold for information processing. Instead of seeing DNA in a traditional way, where triplet codons guide the ribosome to incorporate a defined sequence of amino acids into a newly formed protein, we envisioned a completely new way of coding the information using DNA scaffold. Instead of triplets, binding sites for different DNA-binding proteins could be used as functional units. For example, we can select blocks of nine nucleotides that act as the sites for binding different DNA-binding proteins.<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As DNA molecule is so extensively characterized, being sort of a pop culture molecule, finding a completely novel way of using it presents quite a challenge. DNA is the basic linear carrier of information and we thought that it could represent an ideal scaffold for information processing. Instead of seeing DNA in a traditional way, where triplet codons guide the ribosome to incorporate a defined sequence of amino acids into a newly formed protein, we envisioned a completely new way of coding the information using DNA scaffold. Instead of triplets, binding sites for different DNA-binding proteins could be used as functional units. For example, we can select blocks of nine nucleotides that act as the sites for binding different DNA-binding proteins.<br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:SLO_dnaprogram_shematsko.png|thumb|300px|center|Schematic overview of the idea of DNA as a program.]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:SLO_dnaprogram_shematsko.png|thumb|300px|center|<ins class="diffchange diffchange-inline">'''Figure 1:''' </ins>Schematic overview of the idea of DNA as a program.]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Outline of the idea</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Outline of the idea</h2></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The first big application is to use the DNA program <strong>to arrange the sequence of biosynthetic reaction enzymes</strong> and therefore guide the biosynthetic flow towards the desired products. We decided to test this idea on a previously characterized biosynthetic pathway, demonstrating the advantages of DNA programming. One important advantage is to increase the reaction rate of the overall biosynthetic pathway but it can also guide the biosynthetic flow towards one or other product and prevent side reactions. We have demonstrated both effects on the biosynthesis of violacein, a five step reaction, which can, by the addition of enzymes, yield three different products. This approach offers several potential advantages in comparison to protein-based scaffolds.</li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The first big application is to use the DNA program <strong>to arrange the sequence of biosynthetic reaction enzymes</strong> and therefore guide the biosynthetic flow towards the desired products. We decided to test this idea on a previously characterized biosynthetic pathway, demonstrating the advantages of DNA programming. One important advantage is to increase the reaction rate of the overall biosynthetic pathway but it can also guide the biosynthetic flow towards one or other product and prevent side reactions. We have demonstrated both effects on the biosynthesis of violacein, a five step reaction, which can, by the addition of enzymes, yield three different products. This approach offers several potential advantages in comparison to protein-based scaffolds.</li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Slo shema proof.png|center|frame|Enhancing and directing biosynthetic flow using DNA program]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Slo shema proof.png|center|frame|<ins class="diffchange diffchange-inline">'''Figure 2:''' </ins>Enhancing and directing biosynthetic flow using DNA program]]</div></td></tr>
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</table>Tinailchttp://2010.igem.org/wiki/index.php?title=Team:Slovenia/PROJECT/introduction&diff=200392&oldid=prevRoookie at 23:19, 27 October 20102010-10-27T23:19:00Z<p></p>
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</table>Roookiehttp://2010.igem.org/wiki/index.php?title=Team:Slovenia/PROJECT/introduction&diff=200354&oldid=prevRoookie at 23:18, 27 October 20102010-10-27T23:18:14Z<p></p>
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</table>Roookiehttp://2010.igem.org/wiki/index.php?title=Team:Slovenia/PROJECT/introduction&diff=200287&oldid=prevRoookie at 23:16, 27 October 20102010-10-27T23:16:30Z<p></p>
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</table>Roookiehttp://2010.igem.org/wiki/index.php?title=Team:Slovenia/PROJECT/introduction&diff=200264&oldid=prevRoookie at 23:15, 27 October 20102010-10-27T23:15:49Z<p></p>
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</table>Roookiehttp://2010.igem.org/wiki/index.php?title=Team:Slovenia/PROJECT/introduction&diff=200150&oldid=prevTinaL at 23:12, 27 October 20102010-10-27T23:12:13Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>Another application of the same principle is to use DNA-binding factors to <strong>extend and simplify the construction of oscillators</strong>. Modeling two different types of oscillators indicates that the use of synthetic DNA-binding proteins can provide tools to prepare orthogonal oscillators for both prokaryotic and eukaryotic cells, add new features to increase the robustness and independence of stochastic initial conditions and increase the selection of their frequency. For this purpose the basic type of building block was demonstrated to function in mammalian cells.</li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>Another application of the same principle is to use DNA-binding factors to <strong>extend and simplify the construction of oscillators</strong>. Modeling two different types of oscillators indicates that the use of synthetic DNA-binding proteins can provide tools to prepare orthogonal oscillators for both prokaryotic and eukaryotic cells, add new features to increase the robustness and independence of stochastic initial conditions and increase the selection of their frequency. For this purpose the basic type of building block was demonstrated to function in mammalian cells.</li></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Conclusions</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>Conclusions</h2></div></td></tr>
</table>TinaLhttp://2010.igem.org/wiki/index.php?title=Team:Slovenia/PROJECT/introduction&diff=200073&oldid=prevTinaL at 23:09, 27 October 20102010-10-27T23:09:31Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>DNA as a program</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2>DNA as a program</h2></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>As DNA molecule is so extensively characterized, being sort of a pop culture molecule, finding a completely novel way of using it presents quite a challenge. DNA is the basic linear carrier of information and we thought that it could represent an ideal scaffold for information processing. Instead of seeing DNA in a traditional way, where triplet codons guide the ribosome to incorporate a defined sequence of amino acids into a newly formed protein, we envisioned a completely new way of coding the information using DNA scaffold. Instead of triplets, binding sites for different DNA-binding proteins could be used as functional units. For example, we can select blocks of nine nucleotides that act as the sites for binding different DNA-binding proteins.<del class="diffchange diffchange-inline"><br></del><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>As DNA molecule is so extensively characterized, being sort of a pop culture molecule, finding a completely novel way of using it presents quite a challenge. DNA is the basic linear carrier of information and we thought that it could represent an ideal scaffold for information processing. Instead of seeing DNA in a traditional way, where triplet codons guide the ribosome to incorporate a defined sequence of amino acids into a newly formed protein, we envisioned a completely new way of coding the information using DNA scaffold. Instead of triplets, binding sites for different DNA-binding proteins could be used as functional units. For example, we can select blocks of nine nucleotides that act as the sites for binding different DNA-binding proteins.<br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:SLO_dnaprogram_shematsko.png|thumb|300px|center|Schematic overview of the idea of DNA as a program.]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:SLO_dnaprogram_shematsko.png|thumb|300px|center|Schematic overview of the idea of DNA as a program.]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>What could be the specific implementations of this idea?<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>What could be the specific implementations of this idea?<br></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li>The first big application is to use the DNA program <strong>to arrange the sequence of biosynthetic reaction enzymes</strong> and therefore guide the biosynthetic flow towards the desired products. We decided to test this idea on a previously characterized biosynthetic pathway, demonstrating the advantages of DNA programming. One important advantage is to increase the reaction rate of the overall biosynthetic pathway but it can also guide the biosynthetic flow towards one or other product and prevent side reactions. We have demonstrated both effects on the biosynthesis of violacein, a five step reaction, which can, by the addition of enzymes, yield three different products. This approach offers several potential advantages in comparison to protein-based scaffolds.</li><del class="diffchange diffchange-inline"><br></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li>The first big application is to use the DNA program <strong>to arrange the sequence of biosynthetic reaction enzymes</strong> and therefore guide the biosynthetic flow towards the desired products. We decided to test this idea on a previously characterized biosynthetic pathway, demonstrating the advantages of DNA programming. One important advantage is to increase the reaction rate of the overall biosynthetic pathway but it can also guide the biosynthetic flow towards one or other product and prevent side reactions. We have demonstrated both effects on the biosynthesis of violacein, a five step reaction, which can, by the addition of enzymes, yield three different products. This approach offers several potential advantages in comparison to protein-based scaffolds.</li></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Slo shema proof.png|center|frame|Enhancing and directing biosynthetic flow using DNA program]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Slo shema proof.png|center|frame|Enhancing and directing biosynthetic flow using DNA program]]</div></td></tr>
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</table>TinaLhttp://2010.igem.org/wiki/index.php?title=Team:Slovenia/PROJECT/introduction&diff=199956&oldid=prevTinaL at 23:06, 27 October 20102010-10-27T23:06:29Z<p></p>
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