Difference between revisions of "Team:SZU China/Orthogonal system"

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             <h2 class="blog-post-title">Sample blog post</h2>
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             <h2 class="blog-post-title">Orthogonal system</h2>
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            <p class="blog-post-meta">January 1, 2014 by <a href="#">Mark</a></p>
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             <p>This blog post shows a few different types of content that's supported and styled with Bootstrap. Basic typography, images, and code are all supported.</p>
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             <p>Parallel and independent orthogonal system is one of the foundations of synthetic biology. This system has no or little cross with the natural biological system. The orthogonal system is composed of unnatural base pair,shift code,unnatural amino acid,orthogonal aaRS(aminoacyl tRNA synthetase), orthogonal RNA synthetase,promoter and the orthogonal ribosome.These components work corporately or separately in the organism, programming cells with new functions, and also providing new techniques for researchers.</p>
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            <p>Cum sociis natoque penatibus et magnis <a href="#">dis parturient montes</a>, nascetur ridiculus mus. Aenean eu leo quam. Pellentesque ornare sem lacinia quam venenatis vestibulum. Sed posuere consectetur est at lobortis. Cras mattis consectetur purus sit amet fermentum.</p>
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          <img src="" alt="">
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            <blockquote>
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    <h3>Biological UAA Orthogonal genectical system：</h3>
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  <h4>What is UAA?</h4>
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            </blockquote>
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            <p>UAA is short for Unnatural Amino Acids.In most organisms,there are 20 kinds of amino acids in DNA encoding,which form the vast majority of proteins in the present life.Part of the ancient bacteria (Archaea) and (eubacteria) can encoding selenium (selenocysteine) or the pyrrolysine.The amino acids which do not exist in the natural protein sequence are called UAA.The unnatural amino acids used in the system must be stable, and can be stable in the cell.</p>
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             <p>Etiam porta <em>sem malesuada magna</em> mollis euismod. Cras mattis consectetur purus sit amet fermentum. Aenean lacinia bibendum nulla sed consectetur.</p>
 
             <p>Etiam porta <em>sem malesuada magna</em> mollis euismod. Cras mattis consectetur purus sit amet fermentum. Aenean lacinia bibendum nulla sed consectetur.</p>
 
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             <p>If the unnatural amino acids were inserted into the  proteins expressed by the genetic system of encoding,the new physical and chemical properties of the proteins will expand the space of protein operation.</p>
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             <h3>Sub-heading</h3>
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             <h4>The UAA using in our system:Acetyllysine(ACK)</h4>
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             <p>Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.</p>
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             <p>Acetyllysine(ACK) is one of unnatural amino acid and only corresponds to a special aminoacyl-tRNA(tRNA). It can be added to the protein by Semantic coding of termination codon(UAG).</p>
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            <pre><code>Example code block</code></pre>
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             <p>Aenean lacinia bibendum nulla sed consectetur. Etiam porta sem malesuada magna mollis euismod. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa.</p>
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      <h4>Use UAA as a switch to start the translation of proteins:</h4>
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             <h3>Sub-heading</h3>
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             <p>To transmit the genetic information of mRNAs to proteins,after aa-tRNAs were synthesized by natural amino acids and tRNA via aaRS,they entered, and then entered the protein or peptide.To expand the genetic code and to lead new amino acids into the biosynthetic system,we need to identify the unnatural orthogonal codon,the tRNA with blank codon,the aaRS which can load UAA onto the tRNA specifically,the orthogonal mRNA,which can identify and highly efficient orthogonal translation,appropriate ribosome-binding site (RBS). These components need to satisfy the following conditions: (1) the only code must be recognized by the new tRNA, and has a link-coupled aaRS; (2) the aaRS/tRNA combination must be highly specific for unnatural amino acids in the host cells; (3) aaRs/tRNA pairs must be orthogonal differentiating endogenous aaRS/tRNA pairs(That is not cross in using).</p>
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            <p>Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Aenean lacinia bibendum nulla sed consectetur. Etiam porta sem malesuada magna mollis euismod. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa justo sit amet risus.</p>
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              <li>Praesent commodo cursus magna, vel scelerisque nisl consectetur et.</li>
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             <h3>About our Bladder Cancer Sniper:</h3>
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              <li>Donec id elit non mi porta gravida at eget metus.</li>
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      <h4>Methodology</h4>
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              <li>Nulla vitae elit libero, a pharetra augue.</li>
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      <img src="" alt="">
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            </ul>
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  <h4>How the sniper was formed?</h4>
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             <p>Donec ullamcorper nulla non metus auctor fringilla. Nulla vitae elit libero, a pharetra augue.</p>
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    <h4><em>(1)The construction of Orthogonal system:</em></h4>
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            <ol>
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            <p>In our project,when AND gate operates the tRNA as well as AckRS are desperately synthesized.The certain tRNA can identify and combine terminations codon UAG. AckRS can achieve the attachment between unnatural amino acid Ack and the tRNA. Then the tRNA charged with unnatural amino acid Ack is able to specifically promote a certain protein translation. Eventually the certain mRNA can be translate successfully and output some effectors to regulate tumors growth, motility and apoptosis. The benefits of our UAA orthogonal system is that it can only working in our bladder while unable to interfere our regular genetic system.</p>
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              <li>Vestibulum id ligula porta felis euismod semper.</li>
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                <img src="" alt="">
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              <li>Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.</li>
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             <p>Bladder cell specific promoters hUPII and hTERT are the receptors that respond to the endogenous transcription signals sent by bladder cancer cells. When two promoters are activated at the same time , the expression of downstream effector genes will start. HUPII and hTERT promoters only work in bladder cancer cells rather than normal cells or other tumor cells with its capability to identify and intervent bladder cancer cells selectively. The effector genes was mutated in amber mutation, where a kind of unnatural amino acid Acetyllysine(Ack) is added. This process enable the effector genes to continue the translation of protein.</p>
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              <li>Maecenas sed diam eget risus varius blandit sit amet non magna.</li>
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          <h4><em>(1)The combination of AND gate and Orthogonal system:</em></h4>
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            </ol>
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            <p>2015 SZU-iGEM constructed SV40(with Enhancer) and Rluc with one codon being amber mutated in the same plasmid. This plasmid, together with two other plasmids, are inserted into the cell. Only when the three plasmids work simultanuously can our orthogonal system behave its function, specifically recognise bladder cancer cells and kill them.Our unnatural amino acid orthogonal system consists of three devices(plasmids)..</p>
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            <p>Cras mattis consectetur purus sit amet fermentum. Sed posuere consectetur est at lobortis.</p>
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    <p>(1)hUPll+AckRS(BBa_K1722007): hUPll is a bladder-cell specific promoter. when it's activated, AckRS, a tRNA synthetase, will be produced. </p>
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          </div><!-- /.blog-post -->
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  <p> (2)hTERT+tRNA(BBa_K1722010)/ shTERT+tRNA(BBa_K1722011): hTERT and shTERT are cancer-cell specific promoters. tRNA can be expressed out when the promoter is activated.</p>
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  <p> (3)SV40+Rluc(BBa_K1722012): SV40 is a widely used strong promoter. Rluc is a reporter that can produce RLUC which is a kind of luciferase.
  
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            <h2 class="blog-post-title">Another blog post</h2>
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            <p class="blog-post-meta">December 23, 2013 by <a href="#">Jacob</a></p>
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            <p>Cum sociis natoque penatibus et magnis <a href="#">dis parturient montes</a>, nascetur ridiculus mus. Aenean eu leo quam. Pellentesque ornare sem lacinia quam venenatis vestibulum. Sed posuere consectetur est at lobortis. Cras mattis consectetur purus sit amet fermentum.</p>
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            <p>Vivamus sagittis lacus vel augue laoreet rutrum faucibus dolor auctor. Duis mollis, est non commodo luctus, nisi erat porttitor ligula, eget lacinia odio sem nec elit. Morbi leo risus, porta ac consectetur ac, vestibulum at eros.</p>
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            <h2 class="blog-post-title">New feature</h2>
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            <p class="blog-post-meta">December 14, 2013 by <a href="#">Chris</a></p>
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            <p>Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Aenean lacinia bibendum nulla sed consectetur. Etiam porta sem malesuada magna mollis euismod. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa justo sit amet risus.</p>
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Revision as of 04:39, 18 September 2015



Orthogonal system




Orthogonal system

Parallel and independent orthogonal system is one of the foundations of synthetic biology. This system has no or little cross with the natural biological system. The orthogonal system is composed of unnatural base pair,shift code,unnatural amino acid,orthogonal aaRS(aminoacyl tRNA synthetase), orthogonal RNA synthetase,promoter and the orthogonal ribosome.These components work corporately or separately in the organism, programming cells with new functions, and also providing new techniques for researchers.

Biological UAA Orthogonal genectical system：

What is UAA?

UAA is short for Unnatural Amino Acids.In most organisms,there are 20 kinds of amino acids in DNA encoding,which form the vast majority of proteins in the present life.Part of the ancient bacteria (Archaea) and (eubacteria) can encoding selenium (selenocysteine) or the pyrrolysine.The amino acids which do not exist in the natural protein sequence are called UAA.The unnatural amino acids used in the system must be stable, and can be stable in the cell.

Etiam porta sem malesuada magna mollis euismod. Cras mattis consectetur purus sit amet fermentum. Aenean lacinia bibendum nulla sed consectetur.

Heading

If the unnatural amino acids were inserted into the proteins expressed by the genetic system of encoding,the new physical and chemical properties of the proteins will expand the space of protein operation.

The UAA using in our system:Acetyllysine(ACK)

Acetyllysine(ACK) is one of unnatural amino acid and only corresponds to a special aminoacyl-tRNA(tRNA). It can be added to the protein by Semantic coding of termination codon(UAG).

Use UAA as a switch to start the translation of proteins:

To transmit the genetic information of mRNAs to proteins,after aa-tRNAs were synthesized by natural amino acids and tRNA via aaRS,they entered, and then entered the protein or peptide.To expand the genetic code and to lead new amino acids into the biosynthetic system,we need to identify the unnatural orthogonal codon,the tRNA with blank codon,the aaRS which can load UAA onto the tRNA specifically,the orthogonal mRNA,which can identify and highly efficient orthogonal translation,appropriate ribosome-binding site (RBS). These components need to satisfy the following conditions: (1) the only code must be recognized by the new tRNA, and has a link-coupled aaRS; (2) the aaRS/tRNA combination must be highly specific for unnatural amino acids in the host cells; (3) aaRs/tRNA pairs must be orthogonal differentiating endogenous aaRS/tRNA pairs(That is not cross in using).

About our Bladder Cancer Sniper:

Methodology

How the sniper was formed?

(1)The construction of Orthogonal system:

In our project,when AND gate operates the tRNA as well as AckRS are desperately synthesized.The certain tRNA can identify and combine terminations codon UAG. AckRS can achieve the attachment between unnatural amino acid Ack and the tRNA. Then the tRNA charged with unnatural amino acid Ack is able to specifically promote a certain protein translation. Eventually the certain mRNA can be translate successfully and output some effectors to regulate tumors growth, motility and apoptosis. The benefits of our UAA orthogonal system is that it can only working in our bladder while unable to interfere our regular genetic system.

Bladder cell specific promoters hUPII and hTERT are the receptors that respond to the endogenous transcription signals sent by bladder cancer cells. When two promoters are activated at the same time , the expression of downstream effector genes will start. HUPII and hTERT promoters only work in bladder cancer cells rather than normal cells or other tumor cells with its capability to identify and intervent bladder cancer cells selectively. The effector genes was mutated in amber mutation, where a kind of unnatural amino acid Acetyllysine(Ack) is added. This process enable the effector genes to continue the translation of protein.

(1)The combination of AND gate and Orthogonal system:

2015 SZU-iGEM constructed SV40(with Enhancer) and Rluc with one codon being amber mutated in the same plasmid. This plasmid, together with two other plasmids, are inserted into the cell. Only when the three plasmids work simultanuously can our orthogonal system behave its function, specifically recognise bladder cancer cells and kill them.Our unnatural amino acid orthogonal system consists of three devices(plasmids)..

(1)hUPll+AckRS(BBa_K1722007): hUPll is a bladder-cell specific promoter. when it's activated, AckRS, a tRNA synthetase, will be produced.

(2)hTERT+tRNA(BBa_K1722010)/ shTERT+tRNA(BBa_K1722011): hTERT and shTERT are cancer-cell specific promoters. tRNA can be expressed out when the promoter is activated.

(3)SV40+Rluc(BBa_K1722012): SV40 is a widely used strong promoter. Rluc is a reporter that can produce RLUC which is a kind of luciferase.