http://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&feed=atom&action=historyTeam:Peking R/Project/RNAToolkit1 - Revision history2024-03-29T09:24:00ZRevision history for this page on the wikiMediaWiki 1.16.0http://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=262416&oldid=prevSpring zhq at 03:54, 29 October 20112011-10-29T03:54:43Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">Genetic rheostat aims to fast, flexibly and precisely regulate gene expression. As you can see here, there are two possible approaches. One is regulating transcription strength using inducible promoters. However, due to the lacking of computational tools to effectively describe DNA-protein interaction, it is not ideal. The other approach is regulating translation strength with riboswitches. Because translation process mainly concerns about nucleotide base-paring and RNA unfolding it can be easily simulated and predicted. So we chose to regulate translation strength with riboswitches.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">Genetic rheostat aims to fast, flexibly and precisely regulate gene expression. As you can see here, there are two possible approaches. One is regulating transcription strength using inducible promoters. However, due to the lacking of computational tools to effectively describe DNA-protein interaction, it is not ideal. The other approach is regulating translation strength with riboswitches. Because translation process mainly concerns about nucleotide base-paring and RNA unfolding it can be easily simulated and predicted. So we chose to regulate translation strength with riboswitches.</p></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><p class="mainbody">Hammerhead ribozymes are small self-cleaving RNAs, first discovered in satellite RNAs of plant viruses that catalyze a specific phosphodiester bond isomerization reaction in the course of rolling-circle replication<a href="#r101">[1]</a>. More recently a full-length hammerhead ribozyme from <em> mansoni</em> is being more frequently utilized for application. As shown in <strong>Fig.1-A</strong>, this hammerhead ribozyme can be truncated to a minimal, catalytically active motif consisting of (marked in colors) flanking a central core of 15 mostly invariant nucleotides (marked in frame). And the conserved central bases are essential for the hammerhead ribozyme's catalytic activity<a href="#r102">[1]</a>. <strong>Fig.1-B</strong> indicates that the secondary structure of the <em>Schistosoma</em> hammerhead ribozyme can be distorted into a uridine turn because of distant loop/bulge interaction which induces changes in stem II while simultaneously unwinding stem I. For the basic catalytic function of hammerhead ribozyme, the active site for self-cleaving of <em>Schistosoma</em> hammerhead ribozyme resides between stem III and stem I, as shown in <strong>Fig.1-A.</strong></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="mainbody"><ins class="diffchange diffchange-inline">Riboswitches are structured non-coding RNA elements that control the translation of downstream gene. </ins>Hammerhead ribozymes are small self-cleaving RNAs, first discovered in satellite RNAs of plant viruses that catalyze a specific phosphodiester bond isomerization reaction in the course of rolling-circle replication<a href="#r101">[1]</a>. More recently a full-length hammerhead ribozyme from <em> mansoni</em> is being more frequently utilized for application. As shown in <strong>Fig.1-A</strong>, this hammerhead ribozyme can be truncated to a minimal, catalytically active motif consisting of (marked in colors) flanking a central core of 15 mostly invariant nucleotides (marked in frame). And the conserved central bases are essential for the hammerhead ribozyme's catalytic activity<a href="#r102">[1]</a>. <strong>Fig.1-B</strong> indicates that the secondary structure of the <em>Schistosoma</em> hammerhead ribozyme can be distorted into a uridine turn because of distant loop/bulge interaction which induces changes in stem II while simultaneously unwinding stem I. For the basic catalytic function of hammerhead ribozyme, the active site for self-cleaving of <em>Schistosoma</em> hammerhead ribozyme resides between stem III and stem I, as shown in <strong>Fig.1-A.</strong></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">It has been reported previously that mRNAs encoding enzymes involved in thiamine (vitamin B1) biosynthesis in <em>Escherichia coli</em> can bind derivative without the assistance from protein cofactors<a href="#r201">[2]</a>. These ligand-binding mRNAs actually possess thiamine or pyrophosphate binding domain, called aptamer, in which the binding event can bring about a conformational change which is important for genetic control. This natural thiamine pyrophosphate (TPP) aptamer can bind to TPP specifically and a defined structure is stabilized. As shown in <strong>Fig.1-C</strong>, upon addition of TPP, TPP can bind loop in green. <strong>Fig.1-D</strong> shows the tertiary structure of natural TPP aptamer binding to TPP.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">It has been reported previously that mRNAs encoding enzymes involved in thiamine (vitamin B1) biosynthesis in <em>Escherichia coli</em> can bind derivative without the assistance from protein cofactors<a href="#r201">[2]</a>. These ligand-binding mRNAs actually possess thiamine or pyrophosphate binding domain, called aptamer, in which the binding event can bring about a conformational change which is important for genetic control. This natural thiamine pyrophosphate (TPP) aptamer can bind to TPP specifically and a defined structure is stabilized. As shown in <strong>Fig.1-C</strong>, upon addition of TPP, TPP can bind loop in green. <strong>Fig.1-D</strong> shows the tertiary structure of natural TPP aptamer binding to TPP.</p></div></td></tr>
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</table>Spring zhqhttp://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=261694&oldid=prevSpring zhq at 03:15, 29 October 20112011-10-29T03:15:47Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="left" >Introduction</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="left" >Introduction</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p class="mainbody"><del class="diffchange diffchange-inline">Just as previously stated</del>, <del class="diffchange diffchange-inline">even though proteins fulfill most of biological functions</del>, <del class="diffchange diffchange-inline">such as enzymes as catalysts, receptors as signal transmitters, they have certain drawbacks when used as synthetic biology's modules</del>. One <del class="diffchange diffchange-inline">example </del>is <del class="diffchange diffchange-inline">that they are often coupled with normal biological processes, so their functions depend much on the genetic context</del>. <del class="diffchange diffchange-inline">RNA</del>, <del class="diffchange diffchange-inline">as a large family </del>of <del class="diffchange diffchange-inline">basic biomolecules</del>, <del class="diffchange diffchange-inline">also possesses similar capacities </del>to <del class="diffchange diffchange-inline">those of proteins</del>.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="mainbody"><ins class="diffchange diffchange-inline">Genetic rheostat aims to fast</ins>, <ins class="diffchange diffchange-inline">flexibly and precisely regulate gene expression. As you can see here</ins>, <ins class="diffchange diffchange-inline">there are two possible approaches</ins>. One is <ins class="diffchange diffchange-inline">regulating transcription strength using inducible promoters</ins>. <ins class="diffchange diffchange-inline">However</ins>, <ins class="diffchange diffchange-inline">due to the lacking </ins>of <ins class="diffchange diffchange-inline">computational tools to effectively describe DNA-protein interaction</ins>, <ins class="diffchange diffchange-inline">it is not ideal. The other approach is regulating translation strength with riboswitches. Because translation process mainly concerns about nucleotide base-paring and RNA unfolding it can be easily simulated and predicted. So we chose </ins>to <ins class="diffchange diffchange-inline">regulate translation strength with riboswitches</ins>.</p></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><p class="mainbody">Hammerhead ribozymes are small self-cleaving RNAs, first discovered in satellite RNAs of plant viruses that catalyze a specific phosphodiester bond isomerization reaction in the course of rolling-circle replication<a href="#r101">[1]</a>. More recently a full-length hammerhead ribozyme from <em> mansoni</em> is being more frequently utilized for application. As shown in <strong>Fig.1-A</strong>, this hammerhead ribozyme can be truncated to a minimal, catalytically active motif consisting of (marked in colors) flanking a central core of 15 mostly invariant nucleotides (marked in frame). And the conserved central bases are essential for the hammerhead ribozyme's catalytic activity<a href="#r102">[1]</a>. <strong>Fig.1-B</strong> indicates that the secondary structure of the <em>Schistosoma</em> hammerhead ribozyme can be distorted into a uridine turn because of distant loop/bulge interaction which induces changes in stem II while simultaneously unwinding stem I. For the basic catalytic function of hammerhead ribozyme, the active site for self-cleaving of <em>Schistosoma</em> hammerhead ribozyme resides between stem III and stem I, as shown in <strong>Fig.1-A.</strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">Hammerhead ribozymes are small self-cleaving RNAs, first discovered in satellite RNAs of plant viruses that catalyze a specific phosphodiester bond isomerization reaction in the course of rolling-circle replication<a href="#r101">[1]</a>. More recently a full-length hammerhead ribozyme from <em> mansoni</em> is being more frequently utilized for application. As shown in <strong>Fig.1-A</strong>, this hammerhead ribozyme can be truncated to a minimal, catalytically active motif consisting of (marked in colors) flanking a central core of 15 mostly invariant nucleotides (marked in frame). And the conserved central bases are essential for the hammerhead ribozyme's catalytic activity<a href="#r102">[1]</a>. <strong>Fig.1-B</strong> indicates that the secondary structure of the <em>Schistosoma</em> hammerhead ribozyme can be distorted into a uridine turn because of distant loop/bulge interaction which induces changes in stem II while simultaneously unwinding stem I. For the basic catalytic function of hammerhead ribozyme, the active site for self-cleaving of <em>Schistosoma</em> hammerhead ribozyme resides between stem III and stem I, as shown in <strong>Fig.1-A.</strong></p></div></td></tr>
</table>Spring zhqhttp://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=253388&oldid=prevGrasscliff at 16:29, 28 October 20112011-10-28T16:29:07Z<p></p>
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</table>Grasscliffhttp://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=252714&oldid=prevGrasscliff at 15:08, 28 October 20112011-10-28T15:08:45Z<p></p>
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</table>Grasscliffhttp://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=252536&oldid=prevGrasscliff at 14:45, 28 October 20112011-10-28T14:45:10Z<p></p>
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</table>Grasscliffhttp://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=249916&oldid=prevRobinbin at 03:50, 28 October 20112011-10-28T03:50:09Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <p align="center" class="TITLE2"><strong>High-performance <del class="diffchange diffchange-inline">RNA Controllers </del></strong></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <p align="center" class="TITLE2"><strong>High-performance <ins class="diffchange diffchange-inline">Genetic Rheostats </ins></strong></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" class="TITLE2"><strong>Regulated By TPP</strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="center" class="TITLE2"><strong>Regulated By TPP</strong></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="left" >Introduction</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p align="left" >Introduction</p></div></td></tr>
</table>Robinbinhttp://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=239319&oldid=prevKeyboardKen at 19:19, 19 October 20112011-10-19T19:19:26Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <td width="447" align="left" class="TPP<del class="diffchange diffchange-inline">"><a href="https://2011.igem.org/Team:Peking_R/Project/RNAToolkit1</del>">TPP-regulated hammerhead ribozyme<del class="diffchange diffchange-inline"></a></del></td></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <td width="447" align="left" class="TPP">TPP-regulated hammerhead ribozyme</td></div></td></tr>
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</table>KeyboardKenhttp://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=239290&oldid=prevKeyboardKen at 18:16, 19 October 20112011-10-19T18:16:47Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">Hammerhead ribozymes are small self-cleaving RNAs, first discovered in satellite RNAs of plant viruses that catalyze a specific phosphodiester bond isomerization reaction in the course of rolling-circle replication<a href="#r101">[1]</a>. More recently a full-length hammerhead ribozyme from <em> mansoni</em> is being more frequently utilized for application. As shown in <strong>Fig.1-A</strong>, this hammerhead ribozyme can be truncated to a minimal, catalytically active motif consisting of (marked in colors) flanking a central core of 15 mostly invariant nucleotides (marked in frame). And the conserved central bases are essential for the hammerhead ribozyme's catalytic activity<a href="#r102">[1]</a>. <strong>Fig.1-B</strong> indicates that the secondary structure of the <em>Schistosoma</em> hammerhead ribozyme can be distorted into a uridine turn because of distant loop/bulge interaction which induces changes in stem II while simultaneously unwinding stem I. For the basic catalytic function of hammerhead ribozyme, the active site for self-cleaving of <em>Schistosoma</em> hammerhead ribozyme resides between stem III and stem I, as shown in <strong>Fig.1-A.</strong></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">Hammerhead ribozymes are small self-cleaving RNAs, first discovered in satellite RNAs of plant viruses that catalyze a specific phosphodiester bond isomerization reaction in the course of rolling-circle replication<a href="#r101">[1]</a>. More recently a full-length hammerhead ribozyme from <em> mansoni</em> is being more frequently utilized for application. As shown in <strong>Fig.1-A</strong>, this hammerhead ribozyme can be truncated to a minimal, catalytically active motif consisting of (marked in colors) flanking a central core of 15 mostly invariant nucleotides (marked in frame). And the conserved central bases are essential for the hammerhead ribozyme's catalytic activity<a href="#r102">[1]</a>. <strong>Fig.1-B</strong> indicates that the secondary structure of the <em>Schistosoma</em> hammerhead ribozyme can be distorted into a uridine turn because of distant loop/bulge interaction which induces changes in stem II while simultaneously unwinding stem I. For the basic catalytic function of hammerhead ribozyme, the active site for self-cleaving of <em>Schistosoma</em> hammerhead ribozyme resides between stem III and stem I, as shown in <strong>Fig.1-A.</strong></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">It has been reported previously that mRNAs encoding enzymes involved in thiamine (vitamin B1) biosynthesis in <em>Escherichia coli</em> can bind derivative without the assistance from protein cofactors<a href="#r201">[2]</a>. These ligand-binding mRNAs actually possess thiamine or pyrophosphate binding domain, called aptamer, in which the binding event can bring about a conformational change which is important for genetic control. This natural thiamine pyrophosphate (TPP) aptamer can bind to TPP specifically and a defined structure is stabilized. As shown in <strong>Fig.1-C</strong>, upon addition of TPP, TPP can bind loop in green. <strong>Fig.1-D</strong> shows the tertiary structure of natural TPP aptamer binding to TPP.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">It has been reported previously that mRNAs encoding enzymes involved in thiamine (vitamin B1) biosynthesis in <em>Escherichia coli</em> can bind derivative without the assistance from protein cofactors<a href="#r201">[2]</a>. These ligand-binding mRNAs actually possess thiamine or pyrophosphate binding domain, called aptamer, in which the binding event can bring about a conformational change which is important for genetic control. This natural thiamine pyrophosphate (TPP) aptamer can bind to TPP specifically and a defined structure is stabilized. As shown in <strong>Fig.1-C</strong>, upon addition of TPP, TPP can bind loop in green. <strong>Fig.1-D</strong> shows the tertiary structure of natural TPP aptamer binding to TPP.</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">In fact, the natural aptamer domain of the TPP riboswitch can be exploited to construct very efficient that regulate gene expression, demonstrated by Markus Wieland <em>et.al.</em></a><a href="#r301">[3]</a>. To couple the natural TPP aptamer riboswitch with <em>Schistosoma</em> hammerhead ribozyme, stem III of <em>Schistosoma</em> hammerhead ribozyme and yellow shaded stem of TPP aptamer in <strong>Fig.1-C</strong> were modified to construct linker between hammerhead ribozyme and aptamer. The resulting artificial ribozymes functioned with high performance, </a>whose highest fold reached 1000. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">In fact, the natural aptamer domain of the TPP riboswitch can be exploited to construct very efficient that regulate gene expression, demonstrated by Markus Wieland <em>et.al.</em></a><a href="#r301">[3]</a>. To couple the natural TPP aptamer riboswitch with <em>Schistosoma</em> hammerhead ribozyme, stem III of <em>Schistosoma</em> hammerhead ribozyme and yellow shaded stem of TPP aptamer in <strong>Fig.1-C</strong> were modified to construct linker between hammerhead ribozyme and aptamer. The resulting artificial ribozymes functioned with high performance, </a>whose highest fold reached 1000. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">Markus Wieland <em>et.al.</em> have created several mutants of the constructed ribozyme-based TPP-responsive artificial ribozyme switches (TPP ribozyme)<a href="#r201">[3]</a>. We chose two of the mutants in our project, one of which can activate downstream gene expression upon adding TPP, numbered 1.20, and the other would inhibit downstream gene expression when TPP added, numbered 2.5. The secondary structure of TPP ribozyme 1.20 and 2.5 are shown in <strong>Fig.2</strong>. The lower part of the structure is natural TPP aptamer riboswitch, and the upper part is <em>Schistosoma</em> hammerhead ribozyme. Stem III in green indicates ribozyme, the pairing nucleotides of which is the only distinction between TPP ribozyme 1.20 and 2.5.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">Markus Wieland <em>et.al.</em> have created several mutants of the constructed ribozyme-based TPP-responsive artificial ribozyme switches (TPP ribozyme)<a href="#r201">[3]</a>. We chose two of the mutants in our project, one of which can activate downstream gene expression upon adding TPP, numbered 1.20, and the other would inhibit downstream gene expression when TPP added, numbered 2.5. The secondary structure of TPP ribozyme 1.20 and 2.5 are shown in <strong>Fig.2</strong>. The lower part of the structure is natural TPP aptamer riboswitch, and the upper part is <em>Schistosoma</em> hammerhead ribozyme. Stem III in green indicates ribozyme, the pairing nucleotides of which is the only distinction between TPP ribozyme 1.20 and 2.5.</p></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p class="mainbody">The ribosomal binding site (RBS) of TPP ribozyme locates at the extended stem (shaded red in <strong>Fig.2</strong>). The <em>Schistosoma</em> hammerhead domain in TPP ribozyme could perform self-cleavage when posed in an appropriate conformation, and upon self-cleavage the RBS would be released from pairing, thus ribosome could get access to RBS and initiate translation of the downstream gene. Though similar in secondary structure, TPP ribozyme 1.20 and 2.5 undergo different mechanisms to regulate the translation of downstream gene. Upon addition of TPP, the aptamer domain would bind to TPP; while TPP ribozyme 1.20 would change to a conformation that is suitable for hammerhead domain to cleave itself, TPP ribozyme 2.5 would undergo a conformational change that would decelerate the self-cleaving rate of hammerhead domain. Therefore, upon adding TPP, TPP ribozyme 1.20 would facilitate the translation of downstream gene, whereas TPP ribozyme 2.5 would decrease the translation strength of downstream gene.</p<del class="diffchange diffchange-inline">></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="mainbody">The ribosomal binding site (RBS) of TPP ribozyme locates at the extended stem (shaded red in <strong>Fig.2</strong>). The <em>Schistosoma</em> hammerhead domain in TPP ribozyme could perform self-cleavage when posed in an appropriate conformation, and upon self-cleavage the RBS would be released from pairing, thus ribosome could get access to RBS and initiate translation of the downstream gene. Though similar in secondary structure, TPP ribozyme 1.20 and 2.5 undergo different mechanisms to regulate the translation of downstream gene. Upon addition of TPP, the aptamer domain would bind to TPP; while TPP ribozyme 1.20 would change to a conformation that is suitable for hammerhead domain to cleave itself, TPP ribozyme 2.5 would undergo a conformational change that would decelerate the self-cleaving rate of hammerhead domain. Therefore, upon adding TPP, TPP ribozyme 1.20 would facilitate the translation of downstream gene, whereas TPP ribozyme 2.5 would decrease the translation strength of downstream gene.</p><table width="600" border="0" cellspacing="0" cellpadding="0"></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> the Active Site Prime a Ribozyme for Catalysis. Cell 126, 309-320<br /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> the Active Site Prime a Ribozyme for Catalysis. Cell 126, 309-320<br /></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <strong>[2] </strong>Wade Winkler, Ali Nahvi Ronald R. Breaker. (2002). Thiamine Derivatives Bind Messenger RNAs Directly to Regulate Bacterial Gene Expression. Nature 419, 952-956<br /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <strong>[2] </strong>Wade Winkler, Ali Nahvi Ronald R. Breaker. (2002). Thiamine Derivatives Bind Messenger RNAs Directly to Regulate Bacterial Gene Expression. Nature 419, 952-956<br /></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <strong>[3]</strong> Markus Wieland, Armin Benz, Benedikt Klauser, and Jörg S. Hartig. (2009). Artificial Ribozyme Switches Containing Natural Riboswitch Aptamer Domains. Angew. Chem. 121, 2753-2756 <del class="diffchange diffchange-inline"></p></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <strong>[3]</strong> Markus Wieland, Armin Benz, Benedikt Klauser, and Jörg S. Hartig. (2009). Artificial Ribozyme Switches Containing Natural Riboswitch Aptamer Domains. Angew. Chem. 121, 2753-2756</p></div></td></tr>
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</table>KeyboardKenhttp://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=239287&oldid=prevKeyboardKen at 18:13, 19 October 20112011-10-19T18:13:35Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">In fact, the natural aptamer domain of the TPP riboswitch can be exploited to construct very efficient that regulate gene expression, demonstrated by Markus Wieland <em>et.al.</em></a><a href="#r301">[3]</a>. To couple the natural TPP aptamer riboswitch with <em>Schistosoma</em> hammerhead ribozyme, stem III of <em>Schistosoma</em> hammerhead ribozyme and yellow shaded stem of TPP aptamer in <strong>Fig.1-C</strong> were modified to construct linker between hammerhead ribozyme and aptamer. The resulting artificial ribozymes functioned with high performance, </a>whose highest fold reached 1000. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">In fact, the natural aptamer domain of the TPP riboswitch can be exploited to construct very efficient that regulate gene expression, demonstrated by Markus Wieland <em>et.al.</em></a><a href="#r301">[3]</a>. To couple the natural TPP aptamer riboswitch with <em>Schistosoma</em> hammerhead ribozyme, stem III of <em>Schistosoma</em> hammerhead ribozyme and yellow shaded stem of TPP aptamer in <strong>Fig.1-C</strong> were modified to construct linker between hammerhead ribozyme and aptamer. The resulting artificial ribozymes functioned with high performance, </a>whose highest fold reached 1000. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">Markus Wieland <em>et.al.</em> have created several mutants of the constructed ribozyme-based TPP-responsive artificial ribozyme switches (TPP ribozyme)<a href="#r201">[3]</a>. We chose two of the mutants in our project, one of which can activate downstream gene expression upon adding TPP, numbered 1.20, and the other would inhibit downstream gene expression when TPP added, numbered 2.5. The secondary structure of TPP ribozyme 1.20 and 2.5 are shown in <strong>Fig.2</strong>. The lower part of the structure is natural TPP aptamer riboswitch, and the upper part is <em>Schistosoma</em> hammerhead ribozyme. Stem III in green indicates ribozyme, the pairing nucleotides of which is the only distinction between TPP ribozyme 1.20 and 2.5.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="mainbody">Markus Wieland <em>et.al.</em> have created several mutants of the constructed ribozyme-based TPP-responsive artificial ribozyme switches (TPP ribozyme)<a href="#r201">[3]</a>. We chose two of the mutants in our project, one of which can activate downstream gene expression upon adding TPP, numbered 1.20, and the other would inhibit downstream gene expression when TPP added, numbered 2.5. The secondary structure of TPP ribozyme 1.20 and 2.5 are shown in <strong>Fig.2</strong>. The lower part of the structure is natural TPP aptamer riboswitch, and the upper part is <em>Schistosoma</em> hammerhead ribozyme. Stem III in green indicates ribozyme, the pairing nucleotides of which is the only distinction between TPP ribozyme 1.20 and 2.5.</p></div></td></tr>
</table>KeyboardKenhttp://2011.igem.org/wiki/index.php?title=Team:Peking_R/Project/RNAToolkit1&diff=239286&oldid=prevKeyboardKen at 18:13, 19 October 20112011-10-19T18:13:09Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <td colspan="3"><p align="left"><strong>Figure.1</strong></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <td colspan="3"><p align="left<ins class="diffchange diffchange-inline">" class="picturemark</ins>"><strong>Figure.1</strong></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <span class="picturemark">The schematic structures of ribozyme and natural TPP aptamer. <strong>A) </strong>The secondary structure of <em>Schistosoma</em> hammerhead ribozyme. Three base-pairing stems are shaded in colors. The part in yellow represents stem III, which is later modified to be the linker between hammerhead ribozyme and aptamer. The part in blue represents stem II, and the purple and red ones stand for two parts of stem I. The sequence in frame represents for the conserved nucleotides. The red arrow points to the scissile bond. <strong>B)</strong>The tertiary structure of <em>Schistosoma</em> hammerhead ribozyme. The cyan part indicates the fragment of mRNA after cleavage. The red one indicates the active site for self-cleavage. The linker between hammerhead ribozyme and aptamer is shown in yellow.<strong>C)</strong> The secondary structure of natural TPP aptamer. TPP can bind to loop in green through non-covalent bond and the part marked in yellow indicates the linker between hammerhead ribozyme and apatamer. <strong>D) </strong>The tertiary structure of natural TPP aptamer. The three-dimensional segment in blue is TPP, and the yellow part represents the linker between <em>Schistosoma</em> hammerhead ribozyme and natural TPP aptamer. Nucleotides that bind to TPP are shown in green.</span></p></td></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <span class="picturemark">The schematic structures of ribozyme and natural TPP aptamer. <strong>A) </strong>The secondary structure of <em>Schistosoma</em> hammerhead ribozyme. Three base-pairing stems are shaded in colors. The part in yellow represents stem III, which is later modified to be the linker between hammerhead ribozyme and aptamer. The part in blue represents stem II, and the purple and red ones stand for two parts of stem I. The sequence in frame represents for the conserved nucleotides. The red arrow points to the scissile bond. <strong>B)</strong>The tertiary structure of <em>Schistosoma</em> hammerhead ribozyme. The cyan part indicates the fragment of mRNA after cleavage. The red one indicates the active site for self-cleavage. The linker between hammerhead ribozyme and aptamer is shown in yellow.<strong>C)</strong> The secondary structure of natural TPP aptamer. TPP can bind to loop in green through non-covalent bond and the part marked in yellow indicates the linker between hammerhead ribozyme and apatamer. <strong>D) </strong>The tertiary structure of natural TPP aptamer. The three-dimensional segment in blue is TPP, and the yellow part represents the linker between <em>Schistosoma</em> hammerhead ribozyme and natural TPP aptamer. Nucleotides that bind to TPP are shown in green.</span></p></td></div></td></tr>
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</table>KeyboardKen