Difference between revisions of "Team:Gifu/modeling-page"
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− | <h6><font size=" | + | <h6><font size="4" face="Century"> 【Method of calculation】</font><br></h6> |
<font size="3"> | <font size="3"> | ||
<p> We make following two assumptions, and calculate the efficiency of circularization in each phenomenon.</p><br> | <p> We make following two assumptions, and calculate the efficiency of circularization in each phenomenon.</p><br> | ||
<p>Ⅰ.In structure of mRNA indicated in fig.1, we assume that stability of all combinations between 3’ and 5’ side of the intron is a correlation with their possibility (possibility of being close to each other). Therefore we assume that stability of these combinations is a correlation with possibility of circularization.</p> | <p>Ⅰ.In structure of mRNA indicated in fig.1, we assume that stability of all combinations between 3’ and 5’ side of the intron is a correlation with their possibility (possibility of being close to each other). Therefore we assume that stability of these combinations is a correlation with possibility of circularization.</p> | ||
− | <p>Ⅱ.We assume that distance of both splicing sites in structure of RNA indicated in | + | <p>Ⅱ.We assume that distance of both splicing sites in structure of RNA indicated in Fig.1 is a correlation with possibility of circularization.</p> |
</font> | </font> | ||
+ | <br> | ||
<h6><font size="4" face="Century"> About phenomenon of Ⅰ</font><br></h6> | <h6><font size="4" face="Century"> About phenomenon of Ⅰ</font><br></h6> | ||
<font size="3"> | <font size="3"> | ||
− | <p> Each base’s colors of | + | <p> Each base’s colors of Fig.1 indicate probability of binding base pairs complementary (we call it probability) and we express it in figure of 0~1. In this time, we calculate value of Ⅰ by using this parameter. Concretely, we divide color into 66 equal and assign the probability value to these colors (table1). And we make color (stability) of all combinations between 3’ and 5’ side of the intron correspond to the value and evaluate in system of addition.</p> |
<p>nbsp; The range of sequence applying possibility of all combinations between 3’ and 5’ side of the intron is these following sections in devices. </p> | <p>nbsp; The range of sequence applying possibility of all combinations between 3’ and 5’ side of the intron is these following sections in devices. </p> | ||
<p> | <p> | ||
− | <b> | + | <b> |
+ | <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_K1332003" > BBa_K1332003</a> | ||
+ | and | ||
+ | <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_K1332005" > BBa_K1332005</a> | ||
+ | / | ||
+ | <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_K1859015" > BBa_K1859015</a> | ||
+ | and | ||
+ | <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_K1859016" > BBa_K1859016</a> | ||
+ | / | ||
+ | <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_K1859001" > BBa_K1859001</a> | ||
+ | and | ||
+ | <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_K1859003" > BBa_K1859003</a> | ||
+ | (Please look at fig.3-6)</b> | ||
− | <p><img src="https://static.igem.org/mediawiki/2015/8/8f/Gifu_blue_red.png" width=" | + | <p><center><img src="https://static.igem.org/mediawiki/2015/8/8f/Gifu_blue_red.png" width="80px"></img></center></p> |
− | <center><b>Fig.2 the color using in | + | <center><b>Fig.2 the color using in Fig.1</b></center> |
+ | <br><br> | ||
+ | <center> | ||
+ | <p>Table1. Probability value of each color</p> | ||
+ | <p><img src="https://static.igem.org/mediawiki/2015/7/77/Gifu_possibility_value.png" width="300px"></img></p> | ||
+ | </center> | ||
+ | |||
+ | <br><br> | ||
+ | |||
+ | <p><center><img src="https://static.igem.org/mediawiki/2015/a/ae/%E5%8E%BB%E5%B9%B4_%E4%B8%8A%E5%88%87%E3%82%8A%E5%8F%96%E3%82%8A%E5%9B%B3_%E6%94%B9.png" width="15%"></img></center></p> | ||
+ | <br clear="all"> | ||
+ | <center><b>Fig.3 The upper part of (1) and applied sections of calculation</b> </center> | ||
<br> | <br> | ||
+ | <p><center><img src="https://static.igem.org/mediawiki/2015/1/18/%E5%A4%96%E5%81%B4_%E4%B8%8A%E5%88%87%E3%82%8A%E5%8F%96%E3%82%8A%E5%9B%B3_%E6%94%B9.png" width="220px"></img></center></p> | ||
+ | <br clear="all"> | ||
+ | <center><b>Fig.4 The upper part of (2) and applied sections of calculation</b> </center> | ||
+ | <br> | ||
+ | <p><center><img src="https://static.igem.org/mediawiki/2015/8/89/%E5%86%85%E5%81%B4_3-1_%E4%B8%8A%E5%88%87%E3%82%8A%E5%8F%96%E3%82%8A_%E6%94%B9.png" width="280px"></img></center></p> | ||
+ | <br clear="all"> | ||
+ | <center><b>Fig.5 The upper part of (3) and applied sections of calculation</b> </center> | ||
+ | <br> | ||
+ | <p><center><img src="https://static.igem.org/mediawiki/2015/f/f0/%E5%86%85%E5%81%B4_1-3_%E4%B8%8A%E5%88%87%E3%82%8A%E5%8F%96%E3%82%8A%E5%9B%B3_%E6%94%B9.png" width="300px"></img></center></p> | ||
+ | <br clear="all"> | ||
+ | <center><b>Fig.6 The upper part of (4) and applied sections of calculation</b></center> | ||
+ | <br><br> | ||
+ | <p> About each RNA of (1)-(4), we calculate the sum of value of probability in applied sections mentioned above.</p> | ||
+ | <p> And we evaluate stability of structure in each mRNA when we set the value of (1) for 1.</p> | ||
+ | </font> | ||
+ | <br> | ||
+ | <h6><font size="4" face="Century">【Result of calculation】</font><br></h6> | ||
+ | <p> | ||
+ | <div class="center"> | ||
+ | <b>Table 2. Efficiency of circularizationⅠin each mRNA</b> | ||
+ | </div> | ||
+ | <table align="center" class="partsjump"> | ||
+ | <tr> | ||
+ | <th></th><th>(1)</th><th>(2)</th><th>(3)</th><th>(4)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>The sum of probability value</td><td>23.7</td><td>35.1</td><td>34.3</td><td>31.8</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Efficiency of circularizationⅠ(relativity value)</td><td>1.00</td><td>1.48</td><td>1.45</td><td>1.34</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </p> | ||
− | < | + | <blockquote><blockquote> |
− | < | + | <br> |
+ | <h6><font size="4" face="Century">【Consideration】 </font><br></h6> | ||
+ | <font size="3"><p> | ||
+ | The value of efficiency of circularization calculated in our experiment become like table3. (And please look at our RESULT page)</blockquote></blockquote> | ||
+ | </p> | ||
+ | <p> | ||
+ | <div class="center"> | ||
+ | <b>Table 3. Efficiency of circularization in experiment value</b> | ||
+ | </div> | ||
+ | <table align="center" class="partsjump"> | ||
+ | <tr> | ||
+ | <th></th><th>(1)</th><th>(2)</th><th>(3)</th><th>(4)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Efficiency of circularization (relativity value)</td><td>1.00</td><td>2.05</td><td>1.22</td><td>1.34</td> | ||
+ | </tr> | ||
</table> | </table> | ||
+ | </p> | ||
+ | <br><blockquote><blockquote> | ||
− | < | + | <p> When we compare the value of modeling with that of experiment, their tendency is similar. </p> |
− | < | + | |
+ | <br><br> <h6><font size="4" face="Century"> About phenomenon of Ⅱ </font><br></h6> | ||
+ | <font size="3"> | ||
+ | <p> Splicing site in mRNA combine with each other and mRNA cyclize by nucleophilic substitution reaction. As described above, the nearer distance of splicing site, the stronger the force of two splicing sites pulling against each, so the cyclization will be easier. </p> | ||
+ | </blockquote> | ||
+ | </blockquote> | ||
+ | <p><center><img src="https://static.igem.org/mediawiki/2015/1/1f/RNA4%E7%A8%AE_%E8%B7%9D%E9%9B%A2_%E6%94%B92.png" width="800px"></img></center></p> | ||
+ | <blockquote> | ||
+ | <blockquote> | ||
+ | <b>Fig.7 Distance of both splicing sites in each mRNA</b> | ||
+ | <p> In this figure, the arrows show distance of splicing site in each mRNA.</p> | ||
+ | <p>We calculate the relativity distance of both splicing sites in each mRNA when we set the value of (1) for 1(significant figures are three columns.). | ||
+ | At the moment, we intend to adopt the value that took these numerical reciprocal numbers as the magnification. | ||
+ | </p> | ||
+ | </blockquote></blockquote> | ||
+ | <p> | ||
+ | <div class="center"> | ||
+ | <b>Table 4. Efficiency of circularization in each mRNA</b> | ||
+ | </div> | ||
+ | <table align="center" class="partsjump"> | ||
+ | <tr> | ||
+ | <th></th><th>(1)</th><th>(2)</th><th>(3)</th><th>(4)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>The distance (relativity value)</td><td>1.000</td><td>0.998</td><td>0.278</td><td>0.493</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Efficiency of circularization Ⅱ(relativity value)</td><td>1.00</td><td>1.00</td><td>3.60</td><td>2.03</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </p> | ||
+ | </font> | ||
+ | <blockquote><blockquote> | ||
+ | <br> | ||
+ | <h6><font size="4" face="Century"> 【consideration】 </font><br></h6> | ||
+ | </blockquote></blockquote> | ||
+ | <font size="3"> | ||
+ | <p> | ||
+ | <div class="center"> | ||
+ | <b>Table 5. Efficiency of circularization in experiment value (the same one mentioned above)</b> | ||
+ | </div> | ||
+ | <table align="center" class="partsjump"> | ||
+ | <tr> | ||
+ | <th></th><th>(1)</th><th>(2)</th><th>(3)</th><th>(4)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Efficiency of circularization (relativity value)</td><td>1.00</td><td>2.05</td><td>1.22</td><td>1.34</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </p> | ||
+ | |||
+ | <blockquote><blockquote> | ||
+ | <p>When we compare the value of modeling with that of experiment, they are quite different.</p> | ||
+ | <p> | ||
+ | Why did we get data like this? We consider what points were wrong in modeling when we regard experiment value as correct. The reasons which we can consider are following two contents.</p> | ||
+ | <p>As mentioned above, real shape of mRNA is tertiary structure. But we use RNA models of secondary structure as reference, because to predict RNA models of tertiary structure is too difficult for us. The RNA models of secondary structure and tertiary structure are quite different, so complementary sequences combining each other are different. Therefore the reliability of circularize efficiency of Ⅱ is quite low. And we consider that this is the worst point.</p></font> | ||
+ | <br><br> | ||
+ | <h6><font size="4" face="Century"> 【Conclusion】 </font><br></h6> | ||
+ | <font size="3"> | ||
+ | <p>The value of phenomenonⅡdoesn’t correlate with the value calculated from the experiment. However, we may say that the value of phenomenonⅠ correlate with result the value calculated from the experiment. | ||
+ | From this result, stability of the hydrogen bonding of RNA can become one of the factor when we think of efficiency of splicing reaction by ribozyme. | ||
+ | </p> | ||
+ | </blockquote></blockquote> | ||
+ | <br><br> | ||
</blockquote> | </blockquote> | ||
</blockquote> | </blockquote> |
Latest revision as of 21:32, 18 September 2015
(1) | (2) | (3) | (4) | |
---|---|---|---|---|
The sum of probability value | 23.7 | 35.1 | 34.3 | 31.8 |
Efficiency of circularizationⅠ(relativity value) | 1.00 | 1.48 | 1.45 | 1.34 |
【Consideration】
The value of efficiency of circularization calculated in our experiment become like table3. (And please look at our RESULT page)
(1) | (2) | (3) | (4) | |
---|---|---|---|---|
Efficiency of circularization (relativity value) | 1.00 | 2.05 | 1.22 | 1.34 |
When we compare the value of modeling with that of experiment, their tendency is similar.
About phenomenon of Ⅱ
Splicing site in mRNA combine with each other and mRNA cyclize by nucleophilic substitution reaction. As described above, the nearer distance of splicing site, the stronger the force of two splicing sites pulling against each, so the cyclization will be easier.
Fig.7 Distance of both splicing sites in each mRNAIn this figure, the arrows show distance of splicing site in each mRNA.
We calculate the relativity distance of both splicing sites in each mRNA when we set the value of (1) for 1(significant figures are three columns.). At the moment, we intend to adopt the value that took these numerical reciprocal numbers as the magnification.
(1) | (2) | (3) | (4) | |
---|---|---|---|---|
The distance (relativity value) | 1.000 | 0.998 | 0.278 | 0.493 |
Efficiency of circularization Ⅱ(relativity value) | 1.00 | 1.00 | 3.60 | 2.03 |
【consideration】
(1) | (2) | (3) | (4) | |
---|---|---|---|---|
Efficiency of circularization (relativity value) | 1.00 | 2.05 | 1.22 | 1.34 |
When we compare the value of modeling with that of experiment, they are quite different.
Why did we get data like this? We consider what points were wrong in modeling when we regard experiment value as correct. The reasons which we can consider are following two contents.
As mentioned above, real shape of mRNA is tertiary structure. But we use RNA models of secondary structure as reference, because to predict RNA models of tertiary structure is too difficult for us. The RNA models of secondary structure and tertiary structure are quite different, so complementary sequences combining each other are different. Therefore the reliability of circularize efficiency of Ⅱ is quite low. And we consider that this is the worst point.
【Conclusion】
The value of phenomenonⅡdoesn’t correlate with the value calculated from the experiment. However, we may say that the value of phenomenonⅠ correlate with result the value calculated from the experiment. From this result, stability of the hydrogen bonding of RNA can become one of the factor when we think of efficiency of splicing reaction by ribozyme.