Biomod/2012/Tianjin/Project/Background: Difference between revisions

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<ul><li> <strong class="selflink">Abstract</strong>
<ul><li> <strong class="selflink">Abstract</strong>
</li><li> <a href="#" title="Team:HokkaidoU Japan/Project/T3SS">What`s T3SS</a><div class="tianjin-description">Detailed information about T3SS and summary of our achievements on iGEM 2010</div>
</li><li> <a href="#" title="#">Title 1</a><div class="tianjin-description">1xxx</div>
</li><li> <a href="#" title="Team:HokkaidoU Japan/Project/Onion">Injection assay using onion cells</a><div class="tianjin-description">Experiments using plant cells are easier to perform than with mammalian ones</div>
</li><li> <a href="#" title="#">Title 2</a><div class="tianjin-description">2xxx</div>
</li><li> <a href="#" title="Team:HokkaidoU Japan/Project/Backbone">Ready-to-inject backbone and Bsa I cloning site</a><div class="tianjin-description">Ready-to-inject backbone and Bsa I cloning site enables easy fusion of T3S signal and protein</div>
</li><li> <a href="#" title="#">Title 3</a><div class="tianjin-description">3xxx</div>
</li><li> <a href="#" title="Team:HokkaidoU Japan/Project/GSK">GSK tag system</a><div class="tianjin-description">A neat injection assay using GSK tag, which can  specifically detect successfully injected proteins</div>
</li><li> <a href="#" title="#">Title 4</a><div class="tianjin-description">4xxx</div>
</li><li> <a href="#" title="Team:HokkaidoU Japan/Project/RFC87">Bsa I cloning site, RFC submission</a><div class="tianjin-description">Detailed documentation of costructing a BioBrick cloning site a BioBrick!</div>
</li><li> <a href="#" title="#">Title 5</a><div class="tianjin-description">5xxx</div>
</li></ul>
</li></ul>
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Revision as of 19:03, 24 October 2012

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<div id="header"> <div class="title" style="height: 180px;"> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin"><img src ="http://openwetware.org/images/7/79/TJU2012-Header.png"></a> <div style="float:right;"><img src="http://openwetware.org/images/c/cd/TJU2012-logo.png"></div> <div class="topsearch" style="position:absolute;top:175px;right:90px;"> <form method="GET" action="http://www.google.com/search"> <input type="hidden" name="hl" value="en"> <input type="hidden" name="sitesearch" value="openwetware.org"> <input type="hidden" name="domains" value="openwetware.org"> <input type="hidden" name="as_epq" value="Tianjin"> <input type="text" name="q" class="frm"><input type="submit" class="btn" value="Search"> </form> </div> </div> </div>

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  	    <li class='active '><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin'><span>Home</span></a></li>
  	    <li class='active '><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Team'><span>Team</span></a>
       </li>
  	    <li class='has-sub'><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Background'><span>Designs</span></a>
  	        <ul>
  	            <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Background'><span>Background</span></a></li>
               <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/LogicGate'><span>The Logic Gate</span></a></li>
               <li><a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/YDNA"><span>Y-DNA</span></a></li>
               <li><a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Origami"><span>The Origami Amplifier</span></a></li>
 	        </ul>

</li>

<li class='has-sub'><a href='#'><span>Experiments and Results</span></a> 

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  	            <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/LogicGate'><span>The Logic Gate</span></a></li>
               <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/YDNA'><span>Y-DNA</span></a></li>
               <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/Origami'><span>The Origami Amplifier</span></a></li>

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  	    <li class='active'><a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Protocol"><span>Protocol</span></a>

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<div id="tianjin-right-content"> <ul><li> <strong class="selflink">Abstract</strong> </li><li> <a href="#" title="#">Title 1</a><div class="tianjin-description">1xxx</div> </li><li> <a href="#" title="#">Title 2</a><div class="tianjin-description">2xxx</div> </li><li> <a href="#" title="#">Title 3</a><div class="tianjin-description">3xxx</div> </li><li> <a href="#" title="#">Title 4</a><div class="tianjin-description">4xxx</div> </li><li> <a href="#" title="#">Title 5</a><div class="tianjin-description">5xxx</div> </li></ul> </div>

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DNAzyme

DNAzymes (also known as deoxyribozymes, DNA enzymes or catalytic DNA, are DNA molecules that have the ability to perform a chemical reaction, such as catalytic action. Since the description of the first DNAzyme for the cleavage of RNA in 1994, many more DNAzymes have been reported to catalyze many different types of chemical transformations, such as porphyrin metalation, DNA phosphorylation, RNA ligation, thymine-thymine dimer repair, carbon-carbon bond formation, and hydrolytic cleavage of DNA. DNA is chemically stable and can be conveniently produced by highly efficient automated DNA synthesis. Therefore, DNAzymes can be quite useful in research and applications in chemical biology, biotechnology, and medical areas.

In our project, we focus on the hydrolytic cleavage of DNA by DNAzyme. Cation-specific DNAzymes are composed of two functional domains: a catalytic loop that recognizes specific ions employed as coenzyme and a binding arm that targets its complementary sequence, or substrate. The sequence of the binding-arms can be altered at will so to adjust to different substrate. On the other hand, the catalytic activity of the DNAzyme relies on the catalytic core sequence which is conservative. The alteration of the conservative sequence will largely affect the catalytic activity. When the DNAzyme is hybridized with its target substrate sequence and the desired cation (cofactor) binds to the catalytic loop, hydrolysis of the target substrate sequences is activated. Because of the lower affinity of the cleaved substrate, the substrate will detach from the DNAzyme.

8-17 is the one of the most comprehensively studied RNA-cleaving DNAzymes and have the ability to carry out sequence-specific cleavage of all-RNA or chimeric RNA/DNA substrate (Figure 1). 8-17 is small in size and composed of a catalytic domain flanked by two substrate binding arms. The catalytic domain of 8-17 has 15 nucleotides composed of a three basepair stem, an AGC triloop, and six unpaired nucleotides. One of the most significant features of 8-17 is the excellent selectivity. For 8-17, Pb2+ can activate it at very low concentration (<1μM) comparing with other ion. The substrate of 8-17 is RNA, at least nucleotide at the cut point should be ribonucleotide. The Cu2+ DNAzyme (Cuzyme) is also an ssDNA that contains a stem-loop of 8 base-pairing. The catalytic domain consists of a conservative sequence of six basepair. The two binding arms flanking the catalytic domain bind with the substrate, one of which forms a DNA triplex of the stem-loop with the substrate. Unlike 8-17, the substrate of Cuzyme is deoxyribonucleotide. When the Cu2+ concentration is <1μM, DNAzyme is still activated. When other ions’ concentration is enormously bigger than Cu2+, the DNAzyme still didn’t recover its full activity, which shows its great selectivity of Cu2+.

There were examples of using DNAzyme to construct logic gate, but their input signals were ssDNA that which required multiple strand replacement. The reaction increases the response time. Due to this, we set out to design an AND gate that uses ion cofactors as input signals, because this mechanism reduced the reaction procedure. Furthermore, the excellent selectivity of metal ion of 8-17 and Cuzyme installs more advantage of our new design.

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