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| − | <h2 class="content-subhead">Abstract</h2>
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| − | <p>
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| − | This model is created to evaluate the effectiveness of initial design, and offers guidelines on how the system can (or must) be improved. (You can go to <a href="https://2016.igem.org/Team:NUDT_CHINA/Design">PROJECT. page</a> to see more
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| − | </p>
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| − | <h2 class="content-subhead">Introduction</h2>
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| − | <p>
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| − | We create mathematical models of two aspects of our project, a RCA model and a signal detection model.
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| − | </p>
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| − | <h2 class="content-subhead">Assumption and Justification</h2>
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| − | <h2 class="content-subsub">About model </h2>
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| − | <p>1. MiRNA is not degraded throughout the reaction process.</p>
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| − | <p>2. The two fusion proteins of dCas9 and split-HRP fragments have the same ability to combine with the stem-loop structure, and only when two different proteins next to each other, can they have the ability to catalyze substrate and produce signal.</p>
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| − | <p>3. The number of stem-loop structures in each RCA product is equal under a certain reaction time.</p>
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| − | <p>4. The enzymatic activity remains unchanged with time under the premise of excessive amount of enzymes or a short-time reaction. </p>
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| − | <h2 class="content-subsub">About the data </h2>
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| − | <p>1. The data we obtain from wet-lab experiment are reliable.</p>
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| − | <p>2. All the results are trustworthy in the process of statistical processing and data calculation.</p>
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| − |
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| − | <h2 class="content-subhead">Model</h2>
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| − | <h2 class="content-subsub">Notations</h2>
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| | | | |
| − | <table class="MsoTableGrid" border="1" cellspacing="0" cellpadding="0" style="border:none;">
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| − | <tbody>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">Symbol </span>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">Definition </span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">x</span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <a name="OLE_LINK7"></a><a name="OLE_LINK6"></a><span style="font-family:"">The
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| − | concentration of</span><span style="font-family:""> miRNA (pM)</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">C<sub>1</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">The
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| − | concentration of initiated probe (Abbreviated to iprobe)</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">k<sub>1</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <a name="OLE_LINK8"></a><span style="font-family:"">A constant representing the scale factor</span><span style="font-family:""></span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">K<sub>m </sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">One
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| − | of the characteristic constants of phi29 DNA polymerase</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">V<sub>max</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">One
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| − | of the characteristic constants of phi29 DNA polymerase</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">k<sub>2</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">A
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| − | constant representing the scale factor</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">V</span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">The initial
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| − | speed of RCA </span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <a name="OLE_LINK9"></a><i><span style="font-family:"">n<sub>1</sub></span></i><i><sub><span style="font-family:""></span></sub></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">The
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| − | moles of RCA product</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">n<sub>2</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <a name="OLE_LINK10"></a><span style="font-family:"">The number of stem-loop structures in each RCA product</span><span style="font-family:""></span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">n</span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">The total
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| − | amount of <a name="OLE_LINK23"></a><a name="OLE_LINK22"></a>stem-loop structures</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">N</span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <a name="OLE_LINK41"></a><a name="OLE_LINK16"></a><span style="font-family:"">The
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| − | molecule number of the fusion protein of dCas9 and split-HRP fragments</span><span style="font-family:""></span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">k<sub>3</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">A
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| − | constant representing the scale factor</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">y<sub>1</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">The fluorescence
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| − | intensity of DNA-dye-complex (RFU)</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">N<sub>1</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">The
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| − | molecule number of the fusion protein of dCas9 and split-HRP fragments in the
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| − | solution</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">N<sub>2</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <a name="OLE_LINK45"></a><span style="font-family:"">The molecule number of the fusion protein of dCas9 and
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| − | split-HRP fragments binding with stem-loop structure</span><span style="font-family:""></span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">k<sub>4</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">A
| |
| − | constant representing the scale factor</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">k<sub>5</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">A
| |
| − | constant representing the scale factor</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">ρ</span></i><i><span style="font-family:""></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">Signal
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| − | to noise ratio(Abbreviated to SNR)</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">I</span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">The
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| − | molecule number of formed intact HRP proteins </span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">I<sub>1</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">The
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| − | molecule number of formed intact HRP proteins in the solution</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">I<sub>2</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <a name="OLE_LINK43"></a><span style="font-family:"">The molecule number of formed intact HRP proteins through
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| − | binding with stem-loop structure</span><span style="font-family:""></span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">t</span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">Reaction
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| − | time</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <tr>
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| − | <td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <i><span style="font-family:"">y<sub>2</sub></span></i>
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| − | </p>
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| − | </td>
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| − | <td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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| − | <p class="MsoNormal">
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| − | <span style="font-family:"">The
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| − | signal intensity (OD<sub>450</sub>)</span>
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | </tbody>
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| − | </table>
| |
| − | <div class="pure-g">
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| − | <div class="pure-u-1-1">
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| − | <img class="pure-img-responsive" src="show_test.jpg" alt="Peyto Lake">
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| − | </div>
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| − | </div>
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| − | <p><br>
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| − | <span style="line-height:2;font-family:Perpetua;font-
| |
| − |
| |
| − | size:18px;"><b>Figure 1. Schematic diagram</b></span>
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| − | </p>
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| − |
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| − |
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| − | </div>
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| − | </div>
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| | | | |
| | </div> | | </div> |
