http://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&feed=atom&action=historyTeam:TUDelft/Temperature design2 - Revision history2024-03-28T17:27:07ZRevision history for this page on the wikiMediaWiki 1.16.5http://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=94237&oldid=prevBavandenberg: /* Secondary structure stability and switching temperature */2008-10-29T19:33:10Z<p><span class="autocomment">Secondary structure stability and switching temperature</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Secondary structure stability and switching temperature====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Secondary structure stability and switching temperature====</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:HairpinStability.png|thumb|200px|right|'''Figure 1:''' '''A.''' A lot of G-C base pairs make a very stable hairpin (having a very low free energy). <del class="diffchange diffchange-inline">'</del>'''B.''' The same hairpin structure with A-U base pairs is much less stable (having a higher free energy). '''C-E''' Bulge loops and internal loops destabilize the structure even further.]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:HairpinStability.png|thumb|200px|right|'''Figure 1:''' '''A.''' A lot of G-C base pairs make a very stable hairpin (having a very low free energy). '''B.''' The same hairpin structure with A-U base pairs is much less stable (having a higher free energy). '''C-E''' Bulge loops and internal loops destabilize the structure even further.]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The switching temperature of the RNA thermometer depends on the stability of the hairpin structure that surrounds the Shine Dalgarno region (see also [[Team:TUDelft/Temperature_analysis#Requirements_for_an_RNA_thermometer|Requirements for an RNA therometer]]). This secondary structure will melt when it is exposed to a certain amount of heat. The more stable the hairpin structure is, the more heat will be needed to melt it, and the less stable the hairpin structure is, the less heat will be needed to melt it. In case of the RNA thermometer, this melting is needed to expose the Shine Dalgarno sequence which will cause the initiation of translation.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The switching temperature of the RNA thermometer depends on the stability of the hairpin structure that surrounds the Shine Dalgarno region (see also [[Team:TUDelft/Temperature_analysis#Requirements_for_an_RNA_thermometer|Requirements for an RNA therometer]]). This secondary structure will melt when it is exposed to a certain amount of heat. The more stable the hairpin structure is, the more heat will be needed to melt it, and the less stable the hairpin structure is, the less heat will be needed to melt it. In case of the RNA thermometer, this melting is needed to expose the Shine Dalgarno sequence which will cause the initiation of translation.</div></td></tr>
</table>Bavandenberghttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=94229&oldid=prevBavandenberg: /* Secondary structure stability and switching temperature */2008-10-29T19:32:50Z<p><span class="autocomment">Secondary structure stability and switching temperature</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In other words, a less stable hairpin structure will melt at a lower temperature than a more stable hairpin and thus, for the less stable hairpin, the translation will initiate at a lower temperature than the more stable one. This way we could theoretically shift the switching temperature to a lower or higher temperature by making the hairpin structure surrounding the SD region less or more stable respectively.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In other words, a less stable hairpin structure will melt at a lower temperature than a more stable hairpin and thus, for the less stable hairpin, the translation will initiate at a lower temperature than the more stable one. This way we could theoretically shift the switching temperature to a lower or higher temperature by making the hairpin structure surrounding the SD region less or more stable respectively.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The stability of the hairpin structure depends on the base-pairing nucleotides within the secondary structure. For example, C-G base pairs are very strong, so a hairpin structure containing a lot of those base pairs will be very stable. A-U and U-G base pairs are less strong, so these can be used to destabilize the hairpin structure. The same can be achieved by incorporating bulge and internal loops within the hairpin structure ([https://2008.igem.org/Image:HairpinStability.png figure 1]).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The stability of the hairpin structure depends on the base-pairing nucleotides within the secondary structure. For example, C-G base pairs are very strong, so a hairpin structure containing a lot of those base pairs will be very stable. A-U and U-G base pairs are less strong, so these can be used to destabilize the hairpin structure. The same can be achieved by incorporating bulge <ins class="diffchange diffchange-inline">loops </ins>and internal loops within the hairpin structure ([https://2008.igem.org/Image:HairpinStability.png figure 1]).</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Constraints====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Constraints====</div></td></tr>
</table>Bavandenberghttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=86451&oldid=prevBavandenberg: /* Temperature sensitive hairpin parts */2008-10-29T08:04:10Z<p><span class="autocomment">Temperature sensitive hairpin parts</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The only sequence that has to be designed is the sequence of the temperature sensitive hairpin. The rest of the structure is kept intact to stay as close as possible to the secondary structure of the original RNA thermometer that is used as starting point. It has been shown by Chowdhury <span id="cite_ref_2">[[Team:TUDelft/Temperature_design2#cite_note_2|[2]]]</span> that a temperature sensitive hairpin on itself, so without the rest of the ROSE structure, also works as a temperature sensitive switch.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The only sequence that has to be designed is the sequence of the temperature sensitive hairpin. The rest of the structure is kept intact to stay as close as possible to the secondary structure of the original RNA thermometer that is used as starting point. It has been shown by Chowdhury <span id="cite_ref_2">[[Team:TUDelft/Temperature_design2#cite_note_2|[2]]]</span> that a temperature sensitive hairpin on itself, so without the rest of the ROSE structure, also works as a temperature sensitive switch.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Three temperature sensitive hairpins are added to the registry to test if these short sequences can also be used as temperature sensitive switch. These are the temperature sensitive hairpins of the ROSE RNA thermometer as designed in the first design phase (<code>BBa_K115001</code>), and the temperature sensitive hairpins of the 27°C and 32°C switch as designed in the second design phase (<code>BBa_K115016</code> and <code>BBa_K115017</code>). This are the parts <code>BBa_K115020</code>, <code>BBa_K115019</code>, and <code>BBa_K115018</code> respectively.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Three temperature sensitive hairpins are added to the registry to test if these short sequences can also be used as temperature sensitive switch. These are the temperature sensitive hairpins of the ROSE RNA thermometer as designed in the first design phase (<ins class="diffchange diffchange-inline">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K115001 </ins><code>BBa_K115001</code><ins class="diffchange diffchange-inline">]</ins>), and the temperature sensitive hairpins of the 27°C and 32°C switch as designed in the second design phase (<ins class="diffchange diffchange-inline">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K115016 </ins><code>BBa_K115016</code><ins class="diffchange diffchange-inline">] </ins>and <ins class="diffchange diffchange-inline">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K115017 </ins><code>BBa_K115017</code><ins class="diffchange diffchange-inline">]</ins>). This are the parts <ins class="diffchange diffchange-inline">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K115020 </ins><code>BBa_K115020</code><ins class="diffchange diffchange-inline">]</ins>, <ins class="diffchange diffchange-inline">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K115019 </ins><code>BBa_K115019</code><ins class="diffchange diffchange-inline">]</ins>, and <ins class="diffchange diffchange-inline">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K115018 </ins><code>BBa_K115018</code><ins class="diffchange diffchange-inline">] </ins>respectively.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>If these short hairpins happen to be enough to get a working RNA thermometer, this would be a nice starting point for a third design phase in which these small parts are further optimized. For us, there's not enough time left to do this, but it could be a good starting point for a next years iGEM project.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>If these short hairpins happen to be enough to get a working RNA thermometer, this would be a nice starting point for a third design phase in which these small parts are further optimized. For us, there's not enough time left to do this, but it could be a good starting point for a next years iGEM project.</div></td></tr>
</table>Bavandenberghttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=86438&oldid=prevBavandenberg: /* Design phase II: Changing the switching temperature of the RNA thermometer */2008-10-29T08:00:54Z<p><span class="autocomment">Design phase II: Changing the switching temperature of the RNA thermometer</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''Escherichia coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''Escherichia coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This chapter presents a method that has been used to design RNA thermometer parts that should theoretically switch at a predefined temperature. The method used is based on the data analysis of which the results can be found on the [[Team:TUDelft/Temperature_analysis|analysis page]]. It has been used to design two new parts, one that should theoretically be switched on at 27°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115016 <code>BBa_K115016</code>]), and two that should theoretically be switched on at 32°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115017 <code><del class="diffchange diffchange-inline">BBa:K115017</del></code>]).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This chapter presents a method that has been used to design RNA thermometer parts that should theoretically switch at a predefined temperature. The method used is based on the data analysis of which the results can be found on the [[Team:TUDelft/Temperature_analysis|analysis page]]. It has been used to design two new parts, one that should theoretically be switched on at 27°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115016 <code>BBa_K115016</code>]), and two that should theoretically be switched on at 32°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115017 <code><ins class="diffchange diffchange-inline">BBa_K115017</ins></code>]).</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Secondary structure stability and switching temperature====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Secondary structure stability and switching temperature====</div></td></tr>
</table>Bavandenberghttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=86436&oldid=prevBavandenberg: /* Design phase II: Changing the switching temperature of the RNA thermometer */2008-10-29T08:00:33Z<p><span class="autocomment">Design phase II: Changing the switching temperature of the RNA thermometer</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''Escherichia coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''Escherichia coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This chapter presents a method that has been used to design RNA thermometer parts that should theoretically switch at a predefined temperature. The method used is based on the data analysis of which the results can be found on the [[Team:TUDelft/Temperature_analysis|analysis page]]. It has been used to design two new parts, one that should theoretically be switched on at 27°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115016 <code>BBa_K115016</code>]), and two that should theoretically be switched on at 32°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115017 BBa:K115017]).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This chapter presents a method that has been used to design RNA thermometer parts that should theoretically switch at a predefined temperature. The method used is based on the data analysis of which the results can be found on the [[Team:TUDelft/Temperature_analysis|analysis page]]. It has been used to design two new parts, one that should theoretically be switched on at 27°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115016 <code>BBa_K115016</code>]), and two that should theoretically be switched on at 32°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115017 <ins class="diffchange diffchange-inline"><code></ins>BBa:K115017<ins class="diffchange diffchange-inline"></code></ins>]).</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Secondary structure stability and switching temperature====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Secondary structure stability and switching temperature====</div></td></tr>
</table>Bavandenberghttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=82869&oldid=prevOstassen: /* Design phase II: Changing the switching temperature of the RNA thermometer */2008-10-28T22:31:41Z<p><span class="autocomment">Design phase II: Changing the switching temperature of the RNA thermometer</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Design phase II: <br \><br \>Changing the switching temperature of the RNA thermometer=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Design phase II: <br \><br \>Changing the switching temperature of the RNA thermometer=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''<del class="diffchange diffchange-inline">E. </del>coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''<ins class="diffchange diffchange-inline">Escherichia </ins>coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This chapter presents a method that has been used to design RNA thermometer parts that should theoretically switch at a predefined temperature. The method used is based on the data analysis of which the results can be found on the [[Team:TUDelft/Temperature_analysis|analysis page]]. It has been used to design two new parts, one that should theoretically be switched on at 27°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115016 <code>BBa_K115016</code>]), and two that should theoretically be switched on at 32°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115017 BBa:K115017]).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This chapter presents a method that has been used to design RNA thermometer parts that should theoretically switch at a predefined temperature. The method used is based on the data analysis of which the results can be found on the [[Team:TUDelft/Temperature_analysis|analysis page]]. It has been used to design two new parts, one that should theoretically be switched on at 27°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115016 <code>BBa_K115016</code>]), and two that should theoretically be switched on at 32°C ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K115017 BBa:K115017]).</div></td></tr>
</table>Ostassenhttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=79792&oldid=prevBavandenberg: /* Design phase II: Changing the switching temperature of the RNA thermometer */2008-10-28T17:14:09Z<p><span class="autocomment">Design phase II: Changing the switching temperature of the RNA thermometer</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>=Design phase II: <br \>Changing the switching temperature of the RNA thermometer=</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=Design phase II: <ins class="diffchange diffchange-inline"><br \></ins><br \>Changing the switching temperature of the RNA thermometer=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''E. coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''E. coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td></tr>
</table>Bavandenberghttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=79784&oldid=prevBavandenberg: /* Design phase II: Changing the switching temperature of the RNA thermometer */2008-10-28T17:13:47Z<p><span class="autocomment">Design phase II: Changing the switching temperature of the RNA thermometer</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>=Design phase II: Changing the switching temperature of the RNA thermometer=</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=Design phase II: <ins class="diffchange diffchange-inline"><br \></ins>Changing the switching temperature of the RNA thermometer=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''E. coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Introducing existing RNA thermometers into ''E. coli'' provides us with a number of temperature sensitive switches, all with their own switching temperature. But this only provides a few switching temperatures, which are also relatively close to each other. In order to build a biothermometer, we needed more switching temperatures that have a bigger range. Note, however, that there will always be an upper bound in that the ''E. coli'' cannot survive temperatures above 40°C, and a lower bound in that the activity of the cell will drop at low temperatures.</div></td></tr>
</table>Bavandenberghttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=78477&oldid=prevBavandenberg: /* Result */2008-10-28T15:00:27Z<p><span class="autocomment">Result</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This manual approach has been used to design two RNA thermometers, a 27°C, and a 32°C version (<code>BBa_K115016</code> and <code>BBa_K115017</code>). The secondary structures of the resulting RNA thermometers are shown in [https://2008.igem.org/Image:Design2.png figure 5], together with the stability profiles and the trend line.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This manual approach has been used to design two RNA thermometers, a 27°C, and a 32°C version (<code>BBa_K115016</code> and <code>BBa_K115017</code>). The secondary structures of the resulting RNA thermometers are shown in [https://2008.igem.org/Image:Design2.png figure 5], together with the stability profiles and the trend line.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The stability profiles of the temperature sensitive hairpins off all three RNA thermometers (calculated at their switching temperature) are also displayed in one plot in figure 6. This shows that each of them has a similar stability at their own theoretical switching temperature.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The stability profiles of the temperature sensitive hairpins off all three RNA thermometers (calculated at their switching temperature) are also displayed in one plot in <ins class="diffchange diffchange-inline">[https://2008.igem.org/Image:Design2_1.png </ins>figure 6<ins class="diffchange diffchange-inline">]</ins>. This shows that each of them has a similar stability at their own theoretical switching temperature.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Temperature sensitive hairpin parts====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Temperature sensitive hairpin parts====</div></td></tr>
</table>Bavandenberghttp://2008.igem.org/wiki/index.php?title=Team:TUDelft/Temperature_design2&diff=78471&oldid=prevBavandenberg: /* Result */2008-10-28T14:59:15Z<p><span class="autocomment">Result</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Design2 1.png|thumb|200px|right|'''Figure 6:''' The stability profiles of the original and the two designed RNA thermometers, calculated at their own theoretical switching temperature. This shows that each RNA thermometer has a similar stability at its theoretical switching temperature.]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Design2 1.png|thumb|200px|right|'''Figure 6:''' The stability profiles of the original and the two designed RNA thermometers, calculated at their own theoretical switching temperature. This shows that each RNA thermometer has a similar stability at its theoretical switching temperature.]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This manual approach has been used to design two RNA thermometers, a 27°C, and a 32°C version (<code>BBa_K115016</code> and <code>BBa_K115017</code>). The secondary structures of the resulting RNA thermometers are shown in figure 5, together with the stability profiles and the trend line.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This manual approach has been used to design two RNA thermometers, a 27°C, and a 32°C version (<code>BBa_K115016</code> and <code>BBa_K115017</code>). The secondary structures of the resulting RNA thermometers are shown in <ins class="diffchange diffchange-inline">[https://2008.igem.org/Image:Design2.png </ins>figure 5<ins class="diffchange diffchange-inline">]</ins>, together with the stability profiles and the trend line.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The stability profiles of the temperature sensitive hairpins off all three RNA thermometers (calculated at their switching temperature) are also displayed in one plot in figure 6. This shows that each of them has a similar stability at their own theoretical switching temperature.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The stability profiles of the temperature sensitive hairpins off all three RNA thermometers (calculated at their switching temperature) are also displayed in one plot in figure 6. This shows that each of them has a similar stability at their own theoretical switching temperature.</div></td></tr>
</table>Bavandenberg