Rules of siRNA design for RNA interference (RNAi)
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Rules of siRNA design for RNA interference (RNAi) |
Source: Protocol Online |
Abstract: Summarize both Tom Tuschl's motif siRNA design rules and siRNA rational design. |
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General Guidelines
Tom Tuschl's rules
Rational siRNA design By experimentally analyzing the silencing efficiency of 180 siRNAs targeting the mRNA of two genes and correlating it with various sequence features of individual siRNAs, Reynolds et al at Dharmacon, Inc identified eight characteristics associated with siRNA functionality. These characteristics are used by rational siRNA design algorithm to evaluate potential targeted sequences and assign scores to them. Sequences with higher scores will have higher chance of success in RNAi. The table below lists the 8 criteria and the methods of score assignment.
<center>
<table>
<tbody>
<tr>
<td>
<p>
<b><font>Criteria</font> </b></p>
</td>
<td>
<p>
<b><font>Description</font> </b></p>
</td>
<td>
<p>
<b><font>Score</font> </b></p>
</td>
</tr>
<tr>
<td>
<p>
<font>Yes</font></p>
</td>
<td>
<p>
<font>No</font></p>
</td>
</tr>
<tr>
<td>
<font>1</font></td>
<td>
<p>
<font>Moderate to low (30%-52%) GC Content</font></p>
</td>
<td>
<p>
<font>1 point</font></p>
</td>
<td>
<p>
<font> </font></p>
</td>
</tr>
<tr>
<td>
<font>2</font></td>
<td>
<p>
<font>At least 3 A/Us at positions 15-19 (sense)</font></p>
</td>
<td>
<p>
<font>1 point /per A or U</font></p>
</td>
<td>
<p>
<font> </font></p>
</td>
</tr>
<tr>
<td>
<font>3</font></td>
<td>
<p>
<font>Lack of internal repeats (Tundefined<20¡ãC)</font></p>
</td>
<td>
<p>
<font>1 point</font></p>
</td>
<td>
<p>
<font> </font></p>
</td>
</tr>
<tr>
<td>
<font>4</font></td>
<td>
<p>
<font>A at position 19 (sense)</font></p>
</td>
<td>
<p>
<font>1 point</font></p>
</td>
<td>
<p>
<font> </font></p>
</td>
</tr>
<tr>
<td>
<font>5</font></td>
<td>
<p>
<font>A at position 3 (sense)</font></p>
</td>
<td>
<p>
<font>1 point</font></p>
</td>
<td>
<p>
<font> </font></p>
</td>
</tr>
<tr>
<td>
<font>6</font></td>
<td>
<p>
<font>U at position 10 (sense)</font></p>
</td>
<td>
<p>
<font>1 point</font></p>
</td>
<td>
<p>
<font> </font></p>
</td>
</tr>
<tr>
<td>
<font>7</font></td>
<td>
<p>
<font>No G/C at position 19 (sense)</font></p>
</td>
<td>
<p>
<font> </font></p>
</td>
<td>
<p>
<font>-1 point</font></p>
</td>
</tr>
<tr>
<td>
<font>8</font></td>
<td>
<p>
<font>No G at position 13 (sense)</font></p>
</td>
<td>
<p>
<font> </font></p>
</td>
<td>
<p>
<font>-1 point</font></p>
</td>
</tr>
</tbody>
</table>
</center>
There are two siRNA design tools which implement this siRNA design algorithm: one is offered by Dharmacon, Inc; the other is a downloadable Excel template, written by Maurice Ho at http://boz094.ust.hk/RNAi/siRNA.
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