Difference between revisions of "Biomod/2013/Tianjin/Designs/Self-assemblyTrack"

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[[Image:TJU-figure2.2.1.png|thumb|center|400px| '''Figure 2.2.1''' the loss of the walker]]
 
[[Image:TJU-figure2.2.1.png|thumb|center|400px| '''Figure 2.2.1''' the loss of the walker]]
  
We must protect the tail, so a second stem-loop structure is needed. And we want the second stem-loop structure remain close when not participate in the polymerization reaction, and be open when became one part of the polymer. At first we want to use 2 DNA strands to make it, because the fewer kinds of DNA strand, the easier the reaction taking place. And then, we find it not goanna work if we want to open the strand in the way like origin HCR, the sequence will make the DNA strand all mess up. So we decide to open the 2<sup>nd<sup> stem-loop structure by itself, just adding a former domain, but this can also change the origin structure like '''Figure 2.2.2''' so we decide to use 4 kinds of DNA strands, and that is or final idea. '''Figure 2.2.3'''  is the final design T1 to T4 and '''Figure2.2.4''' is the structure that stimulated by Nupack.
+
We must protect the tail, so a second stem-loop structure is needed. And we want the second stem-loop structure remain close when not participate in the polymerization reaction, and be open when became one part of the polymer. At first we want to use 2 DNA strands to make it, because the fewer kinds of DNA strand, the easier the reaction taking place. And then, we find it not goanna work if we want to open the strand in the way like origin HCR, the sequence will make the DNA strand all mess up. So we decide to open the 2<sup>nd</sup> stem-loop structure by itself, just adding a former domain, but this can also change the origin structure like '''Figure 2.2.2''' so we decide to use 4 kinds of DNA strands, and that is or final idea. '''Figure 2.2.3'''  is the final design T1 to T4 and '''Figure2.2.4''' is the structure that stimulated by Nupack.
  
 
[[Image:TJU-figure2.2.2.png|thumb|center|284px| '''Figure 2.2.2''' the mismatching]]
 
[[Image:TJU-figure2.2.2.png|thumb|center|284px| '''Figure 2.2.2''' the mismatching]]

Latest revision as of 20:27, 27 October 2013

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               <a href="http://openwetware.org/wiki/Biomod/2013/Tianjin/Designs">Background</a>

<a href="http://openwetware.org/wiki/Biomod/2013/Tianjin/Designs/Self-assemblyTrack">Self-assembly Track</a> <a href="http://openwetware.org/wiki/Biomod/2013/Tianjin/Designs/DeliveryDevice">The Delivery Device</a> </div> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/Tianjin/Experiments &amp; Results" onmouseover="mopen('m4')" onmouseout="mclosetime()" style="height:35px;padding:8px 0px 7px 0px;">Experiments &amp; Results</a>

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<a href="http://openwetware.org/wiki/Biomod/2013/Tianjin/Designs" style="font-size:14px;"><b>Background</b></a> <p>HCR、DNAzyme、DNA-walker、Origami</p> <a href="http://openwetware.org/wiki/Biomod/2013/Tianjin/Designs/Self-assemblyTrack" style="font-size:14px;"><b>Self-assembly Track</b></a> <p>T1-T4、The polymerization reaction</p> <a href="http://openwetware.org/wiki/Biomod/2013/Tianjin/Designs/DeliveryDevice"><b>The Delivery device</b></a> <br/><br/> </div>

<div class="photo rotate_right" style="width:400px;align:center;padding:30px 30px 30px 60px;"> <span style="color:#000;font-size:22px;"><b>Self-assembly Track</b></span> <img src="http://openwetware.org/images/6/60/TJU-figure-1.jpg" alt="" width="300" height="310" /> </div>


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T1-T4

We try to use the mechanism of HCR to design a polymer-track monomer. We set a stem-loop structure just to perform a polymerization reaction just like the HCR. But that is not enough. If we just add a tail to it, which could be cut by the DNAzyme, that will influence the efficiency of the walker. Because when the walker cut it substrate, it perhaps to bind with the track monomer, and that would cause the loss of the walker, as Figure 2.2.1.

Figure 2.2.1 the loss of the walker

We must protect the tail, so a second stem-loop structure is needed. And we want the second stem-loop structure remain close when not participate in the polymerization reaction, and be open when became one part of the polymer. At first we want to use 2 DNA strands to make it, because the fewer kinds of DNA strand, the easier the reaction taking place. And then, we find it not goanna work if we want to open the strand in the way like origin HCR, the sequence will make the DNA strand all mess up. So we decide to open the 2nd stem-loop structure by itself, just adding a former domain, but this can also change the origin structure like Figure 2.2.2 so we decide to use 4 kinds of DNA strands, and that is or final idea. Figure 2.2.3 is the final design T1 to T4 and Figure2.2.4 is the structure that stimulated by Nupack.

Figure 2.2.2 the mismatching
Figure 2.2.3 the matching relation between different monomers. The same color means that the domain could match together.
Figure 2.2.4 structure that stimulated by Nupack

The polymerization reaction

The trigger will open T1’s 1st stem-loop structure, so that T2 could be opened by T1. And then, T3 could attach to the free domain of T2, beside, the preceding domain of T3 will open the 2nd stem-loop structure. T4 can open the 1st stem-loop structure of T1. T1 and T3 could open the 2nd stem-loop structure of each other, using their preceding domain. So could T2 and T4.


<html> <html> <div align:"center;" style="height:318px;width:452px;padding:5px;background:#f9f9f9;border:1px solid #cccccc;"> <div style="height:300px;width:450px;background:#fff;border:1px solid #cccccc;"> <object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#4,0,0,0" width="450px" height="300px"> <param name="SRC" value="http://openwetware.org/images/c/c4/TJU-design2-1.swf"> <param name=quality value=high> <embed src="http://openwetware.org/images/c/c4/TJU-design2-1.swf" quality=high pluginspage="http://www.macromedia.com/shockwave/download/index.cgi?P1_Prod_Version=ShockwaveFlash" type="application/x-shockwave-flash" width="450" height="300"> </embed> </object> </div> <div style="width:450;"> <span style="font-size:14px;"><b>Figure 2.2.5</b> Mechanism of the polymerization reaction</span> </div> </div> </div>


<div class="link"> <p><br /> <br /> E-mail:austinamens@gmail.com | Address:Building No.20, No.92 Weijin Road, Tianjin, China | Zip-code:300072 <br />Copyright 2013 © Tianjin University Biomod Team</p> </div>


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