Team:Jilin China/RESULT

From 2014.igem.org

(Difference between revisions)
Line 562: Line 562:
<p >Make sure that the synthesis report is consistent to the OD number on the primer label,and check the number of the dispensing tube before the dissolution of oligonucleotides.The volume of water added to make 10umol/L oligonucleotides’ solution is calculated according to the synthetic single report of each primer. Add sterile deionized water and keep it at room temperature for 2min.And reverse the tube to accelerate the progress of solubilization. Finally, collect substances at the bottom of the tube after centrifugation.</p>
<p >Make sure that the synthesis report is consistent to the OD number on the primer label,and check the number of the dispensing tube before the dissolution of oligonucleotides.The volume of water added to make 10umol/L oligonucleotides’ solution is calculated according to the synthetic single report of each primer. Add sterile deionized water and keep it at room temperature for 2min.And reverse the tube to accelerate the progress of solubilization. Finally, collect substances at the bottom of the tube after centrifugation.</p>
<p >Every six primers are combined to one group.Add 4ulbeginning fiprimer, 1ulintermediate primer and 4ul end primerto a new EP tube, then add sterile deionized water to 20ul, mix them up as spare.</p>
<p >Every six primers are combined to one group.Add 4ulbeginning fiprimer, 1ulintermediate primer and 4ul end primerto a new EP tube, then add sterile deionized water to 20ul, mix them up as spare.</p>
-
<table align="center" >
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<table border="1" cellspacing="0" cellpadding="0" width="612">
-
   <tr >
+
   <tr>
-
     <td width="67" valign="center" ><p >组别 </p></td>
+
     <td width="67"><p align="center"><strong>Group</strong></p></td>
-
     <td width="103" valign="center" ><p >引物编号 </p></td>
+
     <td width="103"><p align="center"><strong>Number of primer</strong></p></td>
-
     <td width="65" valign="center" ><p >吸取量 </p></td>
+
     <td width="65"><p align="center"><strong>Uptake</strong></p></td>
-
     <td width="85" valign="center" ><p >灭菌去离子水添加量 </p></td>
+
     <td width="85"><p align="center"><strong>The volume of sterile deionized water</strong></p></td>
-
     <td width="74" valign="center" ><p >总体积 </p></td>
+
     <td width="75"><p align="center"><strong>The total volume</strong></p></td>
-
     <td width="108" valign="top" ><p >每PCR(50ul体系)吸取量 </p></td>
+
     <td width="108" valign="top"><p align="center"><strong>Each PCR (50ul system) uptake</strong></p></td>
-
     <td width="108" valign="center" ><p >终浓度 </p></td>
+
     <td width="108"><p align="center"><strong>Final concentration</strong></p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="67" valign="center" rowspan="6" ><p >A1 </p></td>
+
     <td width="67" rowspan="6"><p align="center">A1</p></td>
-
     <td width="103" valign="center" ><p >A101 </p></td>
+
     <td width="103"><p align="left">A101</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="85" valign="center" rowspan="6" ><p >8 </p></td>
+
     <td width="85" rowspan="6"><p align="center">8</p></td>
-
     <td width="74" valign="center" rowspan="6" ><p >20 </p></td>
+
     <td width="75" rowspan="6"><p align="center"><a name="_GoBack"></a>20</p></td>
-
     <td width="108" valign="center" rowspan="6" ><p >5ul </p></td>
+
     <td width="108" rowspan="6"><p align="center">5ul</p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A102 </p></td>
+
     <td width="103"><p align="left">A102</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="center" ><p >50nM </p></td>
+
     <td width="108"><p align="center">50nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A103 </p></td>
+
     <td width="103"><p align="left">A103</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A104 </p></td>
+
     <td width="103"><p align="left">A104</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A105 </p></td>
+
     <td width="103"><p align="left">A105</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A106 </p></td>
+
     <td width="103"><p align="left">A106</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="67" valign="center" rowspan="6" ><p >A2 </p></td>
+
     <td width="67" rowspan="6"><p align="center">A2</p></td>
-
     <td width="103" valign="center" ><p >A107 </p></td>
+
     <td width="103"><p align="left">A107</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="85" valign="center" rowspan="6" ><p >8 </p></td>
+
     <td width="85" rowspan="6"><p align="center">8</p></td>
-
     <td width="74" valign="center" rowspan="6" ><p >20 </p></td>
+
     <td width="75" rowspan="6"><p align="center">20</p></td>
-
     <td width="108" valign="center" rowspan="6" ><p >5ul </p></td>
+
     <td width="108" rowspan="6"><p align="center">5ul </p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A108 </p></td>
+
     <td width="103"><p align="left">A108</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="center" ><p >50nM </p></td>
+
     <td width="108"><p align="center">50nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A109 </p></td>
+
     <td width="103"><p align="left">A109</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A110 </p></td>
+
     <td width="103"><p align="left">A110</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A111 </p></td>
+
     <td width="103"><p align="left">A111</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A112 </p></td>
+
     <td width="103"><p align="left">A112</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="67" valign="center" rowspan="6" ><p >A3 </p></td>
+
     <td width="67" rowspan="6"><p align="center">A3</p></td>
-
     <td width="103" valign="center" ><p >A113 </p></td>
+
     <td width="103"><p align="left">A113</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="85" valign="center" rowspan="6" ><p >8 </p></td>
+
     <td width="85" rowspan="6"><p align="center">8</p></td>
-
     <td width="74" valign="center" rowspan="6" ><p >20 </p></td>
+
     <td width="75" rowspan="6"><p align="center">20</p></td>
-
     <td width="108" valign="center" rowspan="6" ><p >5ul </p></td>
+
     <td width="108" rowspan="6"><p align="center">5ul </p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A114 </p></td>
+
     <td width="103"><p align="left">A114</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="center" ><p >50nM </p></td>
+
     <td width="108"><p align="center">50nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A201 </p></td>
+
     <td width="103"><p align="left">A201</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A202 </p></td>
+
     <td width="103"><p align="left">A202</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A203 </p></td>
+
     <td width="103"><p align="left">A203</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A204 </p></td>
+
     <td width="103"><p align="left">A204</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="67" valign="center" rowspan="6" ><p >A4 </p></td>
+
     <td width="67" rowspan="6"><p align="center">A4</p></td>
-
     <td width="103" valign="center" ><p >A205 </p></td>
+
     <td width="103"><p align="left">A205</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="85" valign="center" rowspan="6" ><p >8 </p></td>
+
     <td width="85" rowspan="6"><p align="center">8</p></td>
-
     <td width="74" valign="center" rowspan="6" ><p >20 </p></td>
+
     <td width="75" rowspan="6"><p align="center">20</p></td>
-
     <td width="108" valign="center" rowspan="6" ><p >5ul </p></td>
+
     <td width="108" rowspan="6"><p align="center">5ul </p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A206 </p></td>
+
     <td width="103"><p align="left">A206</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="center" ><p >50nM </p></td>
+
     <td width="108"><p align="center">50nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A207 </p></td>
+
     <td width="103"><p align="left">A207</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A208 </p></td>
+
     <td width="103"><p align="left">A208</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A209 </p></td>
+
     <td width="103"><p align="left">A209</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A210 </p></td>
+
     <td width="103"><p align="left">A210</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="67" valign="center" rowspan="4" ><p >A5 </p></td>
+
     <td width="67" rowspan="4"><p align="center">A5</p></td>
-
     <td width="103" valign="center" ><p >A211 </p></td>
+
     <td width="103"><p align="left">A211</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="85" valign="center" rowspan="4" ><p >10 </p></td>
+
     <td width="85" rowspan="4"><p align="center">10</p></td>
-
     <td width="74" valign="center" rowspan="4" ><p >20 </p></td>
+
     <td width="75" rowspan="4"><p align="center">20</p></td>
-
     <td width="108" valign="center" rowspan="4" ><p >5ul </p></td>
+
     <td width="108" rowspan="4"><p align="center">5ul </p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A212 </p></td>
+
     <td width="103"><p align="left">A212</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="center" ><p >50nM </p></td>
+
     <td width="108"><p align="center">50nM</p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A213 </p></td>
+
     <td width="103"><p align="left">A213</p></td>
-
     <td width="65" valign="center" ><p >1 </p></td>
+
     <td width="65"><p align="center">1</p></td>
-
     <td width="108" valign="top" ><p >50nM </p></td>
+
     <td width="108" valign="top"><p align="center">50nM </p></td>
   </tr>
   </tr>
-
   <tr >
+
   <tr>
-
     <td width="103" valign="center" ><p >A214 </p></td>
+
     <td width="103"><p align="left">A214</p></td>
-
     <td width="65" valign="center" ><p >4 </p></td>
+
     <td width="65"><p align="center">4</p></td>
-
     <td width="108" valign="center" ><p >200nM </p></td>
+
     <td width="108"><p align="center">200nM</p></td>
   </tr>
   </tr>
</table>
</table>
Line 736: Line 736:
<h3 >3、DA-PCR </h3>
<h3 >3、DA-PCR </h3>
-
<p >化学合成的单链寡核苷酸,每6条分为一组,通过DA-PCR拼接成为较长的双链中间片段(Block)。DA-PCR的反应体系组成为: </p>
+
<p >Every six primers which are single-stranded oligonucleotidesare chemically synthesized were combined to one group. Then they were going to be made as longer double-stranded fragments of intermediate (Block) by DA-PCR </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Mixed&nbsp;primer&nbsp;solutions&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Mixed&nbsp;primer&nbsp;solutions&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pfu&nbsp;DNA&nbsp;Polymerase&nbsp;2.5U&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.5&#956;l&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pfu&nbsp;DNA&nbsp;Polymerase&nbsp;2.5U&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.5&#956;l&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </p>
Line 774: Line 774:
<p >&nbsp;</p>
<p >&nbsp;</p>
<h3 >4、OE-PCR </h3>
<h3 >4、OE-PCR </h3>
-
<p >以DA-PCR拼接出来的的5条双链中间片段(Block)为模版,进一步利用OE-PCR进行连接,OE-PCR的反应体系组成为: </p>
+
<p >Take the 5 double strand intermediate fragment (Block) spliced by DA-PCR as templates, blocks were further connected by OR-PCR, OE-PCR in a reaction system consisting of: </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Block1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Block1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Block2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Block2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&#956;l </p>
Line 822: Line 822:
-
<h3 >5、亚克隆载体构建与测序 </h3>
+
<h3 >5、Constructing and sequencing of subcoloning vector</h3>
-
<p >合成的mlrA基因与pSB1C3载体经过EcoR&#8544;和Pst&#8544;于37&#8451;双酶切3h后,16&#8451;连接过夜,转化到E.coli&nbsp;JM109感受态细胞中,经蓝白筛选挑取白色菌落。 </p>
+
<p >After double enzyme digestion reaction at 37℃ for 3h by EcoRⅠand PstⅠ, MlrA gene and pSB1C3 vector linked together at 16℃ overnight. And then transformed to E.coli JM109 competent cell, and select the desirable colony by using “blue-white selection” method.</p>
-
<p >EcoR&#8544;和Pst&#8544;双酶切反应体系组成为: </p>
+
<p >Constitute of EcoRⅠand PstⅠdouble enzyme digestion reaction system:: </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gene&nbsp;or&nbsp;plasmid&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gene&nbsp;or&nbsp;plasmid&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;EcoR&#8544;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.4&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;EcoR&#8544;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.4&#956;l </p>
Line 830: Line 830:
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10&#215;NEBuffer&nbsp;3.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10&#215;NEBuffer&nbsp;3.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;灭菌超纯水&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;补齐至&nbsp;&nbsp;20&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;灭菌超纯水&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;补齐至&nbsp;&nbsp;20&#956;l </p>
-
<p >连接反应体系组成为: </p>
+
<p >Constitute of linking reaction system: </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;mlrA&nbsp;Gene&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;mlrA&nbsp;Gene&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pSB1C3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3&#956;l </p>
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pSB1C3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3&#956;l </p>

Revision as of 01:40, 18 October 2014

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Synthesis of gene mlrA

The experimental scheme

1、The amino acid sequence of the protein

MlrA GenBank: AF411068 SOURCE  Sphingomonas sp. ACM-3962

MREFVRQRPLLCFYVLAILIALAAHALRAMSPTPLDPMFKMLQETHAHLNIITAVRSTFEYPGAYTLLLFPAAPMFAALIATGIGYGQAGFRELLSRCAPWRSPVSWRQGVTVIAVCFLAFFALTGIMWVQTYLYAPPGTLDRTFLRYGSDPVAIYVMLAASLLLSPGPLLEELGWRGFALPQLLKKFDPLTAAVILGIMWWAWHLPRDLPTLFSGAPGAAWSVIVKQLVITPGFIASTIIAVFVCNKLGGSMWGGVLTHAIHNELGVNVTAEWAPTVAGLGWRPWDLIEFAVAIGLVLICGRSLGAASPDNARLAWGNVPPKLPGGVGDKSGANA

2、The selection of codons

Lactococcus lactis subsp. cremoris SK11 [gbbct]: 2504 CDS's (696252 codons)

http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=272622

fields: [triplet] [frequency: per thousand] ([number])

UUU 36.1( 25117)  UCU 16.5( 11473)  UAU 28.4( 19782)  UGU  3.9(  2729)

UUC 12.0(  8326)  UCC  3.3(  2266)  UAC  8.1(  5665)  UGC  1.1(   771)

UUA 31.0( 21599)  UCA 21.1( 14698)  UAA  2.5(  1708)  UGA  0.7(   498)

UUG 21.2( 14782)  UCG  3.9(  2685)  UAG  0.4(   298)  UGG 10.1(  7000)

 

CUU 25.2( 17574)  CCU 11.9(  8253)  CAU 13.3(  9269)  CGU 14.6( 10159)

CUC  8.1(  5614)  CCC  2.9(  1990)  CAC  4.5(  3121)  CGC  4.5(  3122)

CUA  8.0(  5591)  CCA 14.5( 10061)  CAA 31.1( 21678)  CGA  5.9(  4140)

CUG  6.4(  4476)  CCG  2.9(  2010)  CAG  6.6(  4596)  CGG  2.3(  1570)

 

AUU 51.0( 35505)  ACU 20.4( 14218)  AAU 40.1( 27903)  AGU 14.7( 10220)

AUC 16.1( 11197)  ACC  7.4(  5135)  AAC 11.1(  7709)  AGC  6.2(  4328)

AUA  8.7(  6023)  ACA 22.1( 15386)  AAA 61.2( 42611)  AGA  8.0(  5557)

AUG 24.7( 17203)  ACG  7.1(  4919)  AAG 13.5(  9375)  AGG  1.7(  1152)

 

GUU 30.8( 21415)  GCU 30.1( 20949)  GAU 37.3( 25965)  GGU 23.4( 16287)

GUC 12.7(  8841)  GCC 12.1(  8400)  GAC 14.4( 10018)  GGC  8.5(  5906)

GUA 12.8(  8921)  GCA 22.3( 15521)  GAA 56.1( 39035)  GGA 24.5( 17046)

GUG  9.2(  6376)  GCG  8.2(  5708)  GAG 13.0(  9070)  GGG  8.2(  5732)

Coding GC 36.75% 1st letter GC 48.61% 2nd letter GC 34.45% 3rd letter GC 27.20%

The codon table used

* TAA 

A GCT

C TGT

D GAT

E GAA

F TTT

G GGA

H CAT

I ATT

K AAA

L TTA

M ATG

N AAT

P CCA

Q CAA

R CGA

S TCA

T ACT

V GTT

W TGG

Y TAT

3、The inverse translation sequences and the selection of restriction enzymes

EcoR I

CCGGAATTCATGCGAGAATTTGTTCGACAACGACCATTATTATGTTTTTATGTTTTAGCTATTTTAATTGCTTTAGCTGCTCATGCTTTACGAGCTATGTCACCAACTCCATTAGATCCAATGTTTAAAATGTTACAAGAAACTCATGCTCATTTAAATATTATTACTGCTGTTCGATCAACTTTTGAATATCCAGGAGCTTATACTTTATTATTATTTCCAGCTGCTCCAATGTTTGCTGCTTTAATTGCTACTGGAATTGGATATGGACAAGCTGGATTTCGAGAATTATTATCACGATGTGCTCCATGGCGATCACCAGTTTCATGGCGACAAGGAGTTACTGTTATTGCTGTTTGTTTTTTAGCTTTTTTTGCTTTAACTGGAATTATGTGGGTTCAAACTTATTTATATGCTCCACCAGGAACTTTAGATCGAACTTTTTTACGATATGGATCAGATCCAGTTGCTATTTATGTTATGTTAGCTGCTTCATTATTATTATCACCAGGACCATTATTAGAAGAATTAGGATGGCGAGGATTTGCTTTACCACAATTATTAAAAAAATTTGATCCATTAACTGCTGCTGTTATTTTAGGAATTATGTGGTGGGCTTGGCATTTACCACGAGATTTACCAACTTTATTTTCAGGAGCTCCAGGAGCTGCTTGGTCAGTTATTGTTAAACAATTAGTTATTACTCCAGGATTTATTGCTTCAACTATTATTGCTGTTTTTGTTTGTAATAAATTAGGAGGATCAATGTGGGGAGGAGTTTTAACTCATGCTATTCATAATGAATTAGGAGTTAATGTTACTGCTGAATGGGCTCCAACTGTTGCTGGATTAGGATGGCGACCATGGGATTTAATTGAATTTGCTGTTGCTATTGGATTAGTTTTAATTTGTGGACGATCATTAGGAGCTGCTTCACCAGATAATGCTCGATTAGCTTGGGGAAATGTTCCACCAAAATTACCAGGAGGAGTTGGAGATAAATCAGGAGCTAATGCTTAATAGCTGCAGTT

4、The sequence analysis

_Base Count : 1008 bp (270 A, 377 T, 158 C, 203 G)
 _Composition : 36% GC, 64% AT

Absent Sites
AarI AatII Acc65I AccI AciI AclI AcuI AfeI AflII AflIII AgeI AhdI AleI ApaI ApaLI AscI AseI AsiSI AsuII AvaI AvrII BaeGI BamHI BanI BbsI BbvCI BceAI BciVI BclI BfaI BfuAI BglI BglII BlpI BmgBI BmrI BmtI Bpu10I BpuEI BsaAI BsaHI BsaI BsaWI BseMII BseYI BsgI BsiEI BsiWI BslI BsmAI BsmBI BsmFI BsmI BsoBI BspCNI BspEI BspHI BspMI BspQI BsrBI BsrDI BsrFI BsrGI BssHII BstAPI BstBI BstEII BstUI BstZ17I Bsu36I BtgZI BtrI BtsI Cac8I ClaI CviQI DdeI DrdI EaeI EagI EarI EciI Eco31I EcoNI EcoO109I EcoRI EcoRV Esp3I FauI FseI FspAI FspI HaeII HaeIII HgaI HhaI HinP1I HincII HindIII HinfI HpaI HpaII Hpy99I HpyAV HpyCH4IV HpyCH4V KasI KpnI MaeI MaeII MfeI MluI MlyI MscI NaeI NarI NciI NdeI NgoMIV NheI NmeAIII NotI NruI NsiI NspI PacI PasI PciI PflFI PflMI PleI PmeI PpuMI PshAI PsiI PspOMI PspXI PstI PvuI RsaI RsrII SacII SalI SanDI SbfI ScaI SexAI SfaNI SfcI SfiI SfoI SgrAI SmaI SmlI SnaBI SpeI SphI SrfI StuI TaiI TatI TauI TfiI TspGWI TspMI TspRI Tth111I XbaI XhoI XmaI ZraI

Unique Sites

XmnI (6) MslI (25)

Tsp45I (89)

SwaI (142) SspI (147)

MspA1I (211)

DraIII (286)

BstXI (309)

BsaBI (439) Hpy188I (447)

Sau96I (501)

MboII (513)

BssSI (619)

SacI (646) XcmI (651) AlwNI (652)

NlaIV (821)

Hpy166II (901)

5、Sequence Split

The maximum allowable assembly oligo length is equal to the target assembly oligo length (60). This may cause some weird behavior, especially in terms of overlap melting temperature.

 

2 building blocks were generated.

Building Block .1   529bp   1..529 
Left  - 5' CCGGAATTCATGCGAGAATTTGTTCG 3'
Rght  - 5' ATTCTTCTAATAATGGTCCTGGTGATAATAATAATGAAG 3'
RghtU - 5' ATTCTTCTAAUAATGGTCCTGGTGATAATAATAATGAAG 3'
Sequence:

CCGGAATTCATGCGAGAATTTGTTCGACAACGACCATTATTATGTTTTTATGTTTTAGCTATTTTAATTGCTTTAGCTGCTCATGCTTTACGAGCTATGTCACCAACTCCATTAGATCCAATGTTTAAAATGTTACAAGAAACTCATGCTCATTTAAATATTATTACTGCTGTTCGATCAACTTTTGAATATCCAGGAGCTTATACTTTATTATTATTTCCAGCTGCTCCAATGTTTGCTGCTTTAATTGCTACTGGAATTGGATATGGACAAGCTGGATTTCGAGAATTATTATCACGATGTGCTCCATGGCGATCACCAGTTTCATGGCGACAAGGAGTTACTGTTATTGCTGTTTGTTTTTTAGCTTTTTTTGCTTTAACTGGAATTATGTGGGTTCAAACTTATTTATATGCTCCACCAGGAACTTTAGATCGAACTTTTTTACGATATGGATCAGATCCAGTTGCTATTTATGTTATGTTAGCTGCTTCATTATTATTATCACCAGGACCATTATTAGAAGAAT

 

Assembly Oligos: average overlap Tm is 47°;average oligo length is 58bp.

 

CCGGAATTCATGCGAGAATTTGTTCGACAACGACCATTATTATGTTTTTATGTTTTAGCTATTTTAATTGCTTTAGCTGCTCATGCTTTACGAGCTATGTCACCAACTCCATTAGATCCAATGTTTAAAATGTTACAAGAAACTCATGCTCATTTAAATATTATTACTGCTGTTCGATCAACTTTTGAATATCCAGGAGCTTATACTTTATTATTATTTCCAGCTGCTCCAATGTTTGCTGCTTTAATTGCTACTGGAATTGGATATGGACAAGCTGGATTTCGAGAATTATTATCACGATGTGCTCCATGGCGATCACCAGTTTCATGGCGACAAGGAGTTACTGTTATTGCTGTTTGTTTTTTAGCTTTTTTTGCTTTAACTGGAATTATGTGGGTTCAAACTTATTTATATGCTCCACCAGGAACTTTAGATCGAACTTTTTTACGATATGGATCAGATCCAGTTGCTATTTATGTTATGTTAGCTGCTTCATTATTATTATCACCAGGACCATTATTAGAAGAAT
CCGGAATTCATGCGAGAATTTGTTCGACAACGACCATTATTATGTTTTTATGTTTTAGCT              AGCTGCTCATGCTTTACGAGCTATGTCACCAACTCCATTAGATCCAATGTTTAAAATGTT              CTCATTTAAATATTATTACTGCTGTTCGATCAACTTTTGAATATCCAGGAGCTTATACTT              GCTGCTCCAATGTTTGCTGCTTTAATTGCTACTGGAATTGGATATGGACAAGCTGGATTT              ACGATGTGCTCCATGGCGATCACCAGTTTCATGGCGACAAGGAGTTACTGTTATTGCTGT               TTTTGCTTTAACTGGAATTATGTGGGTTCAAACTTATTTATATGCTCCACCAGGAACTTT                CGATATGGATCAGATCCAGTTGCTATTTATGTTATGTTAGCTGCTTCATTATTATTATCA                      
                                     ATAATACAAAAATACAAAATCGATAAAATTAACGAAATCGACGAGTACGAAATGCTC                 AATCTAGGTTACAAATTTTACAATGTTCTTTGAGTACGAGTAAATTTATAATAATGACGA              ACTTATAGGTCCTCGAATATGAAATAATAATAAAGGTCGACGAGGTTACAAACGAC                  AACCTATACCTGTTCGACCTAAAGCTCTTAATAATAGTGCTACACGAGGTACCGCT                  GTTCCTCAATGACAATAACGACAAACAAAAAATCGAAAAAAACGAAATTGACCTTAATAC                ATATACGAGGTGGTCCTTGAAATCTAGCTTGAAAAAATGCTATACCTAGTCTAGGTCAAC                TCGACGAAGTAATAATAATAGTGGTCCTGGTAATAATCTTCTTA
GGCCTTAAGTACGCTCTTAAACAAGCTGTTGCTGGTAATAATACAAAAATACAAAATCGATAAAATTAACGAAATCGACGAGTACGAAATGCTCGATACAGTGGTTGAGGTAATCTAGGTTACAAATTTTACAATGTTCTTTGAGTACGAGTAAATTTATAATAATGACGACAAGCTAGTTGAAAACTTATAGGTCCTCGAATATGAAATAATAATAAAGGTCGACGAGGTTACAAACGACGAAATTAACGATGACCTTAACCTATACCTGTTCGACCTAAAGCTCTTAATAATAGTGCTACACGAGGTACCGCTAGTGGTCAAAGTACCGCTGTTCCTCAATGACAATAACGACAAACAAAAAATCGAAAAAAACGAAATTGACCTTAATACACCCAAGTTTGAATAAATATACGAGGTGGTCCTTGAAATCTAGCTTGAAAAAATGCTATACCTAGTCTAGGTCAACGATAAATACAATACAATCGACGAAGTAATAATAATAGTGGTCCTGGTAATAATCTTCTTA 

 

Building Block .2   513bp   519..1031 
Left  - 5' ATTAGAAGAATTAGGATGGCGAGGATTTGC 3'
LeftU - 5' ATTAGAAGAAUTAGGATGGCGAGGATTTGC 3'
Rght  - 5' AAGACGTCCTATTAAGCATTAGCTCCTG 3'
Sequence:

ATTAGAAGAATTAGGATGGCGAGGATTTGCTTTACCACAATTATTAAAAAAATTTGATCCATTAACTGCTGCTGTTATTTTAGGAATTATGTGGTGGGCTTGGCATTTACCACGAGATTTACCAACTTTATTTTCAGGAGCTCCAGGAGCTGCTTGGTCAGTTATTGTTAAACAATTAGTTATTACTCCAGGATTTATTGCTTCAACTATTATTGCTGTTTTTGTTTGTAATAAATTAGGAGGATCAATGTGGGGAGGAGTTTTAACTCATGCTATTCATAATGAATTAGGAGTTAATGTTACTGCTGAATGGGCTCCAACTGTTGCTGGATTAGGATGGCGACCATGGGATTTAATTGAATTTGCTGTTGCTATTGGATTAGTTTTAATTTGTGGACGATCATTAGGAGCTGCTTCACCAGATAATGCTCGATTAGCTTGGGGAAATGTTCCACCAAAATTACCAGGAGGAGTTGGAGATAAATCAGGAGCTAATGCTTAATAGGACGTCTT

Assembly Oligos: average overlap Tm is 49°;average oligo length is 58bp.

ATTAGAAGAATTAGGATGGCGAGGATTTGCTTTACCACAATTATTAAAAAAATTTGATCCATTAACTGCTGCTGTTATTTTAGGAATTATGTGGTGGGCTTGGCATTTACCACGAGATTTACCAACTTTATTTTCAGGAGCTCCAGGAGCTGCTTGGTCAGTTATTGTTAAACAATTAGTTATTACTCCAGGATTTATTGCTTCAACTATTATTGCTGTTTTTGTTTGTAATAAATTAGGAGGATCAATGTGGGGAGGAGTTTTAACTCATGCTATTCATAATGAATTAGGAGTTAATGTTACTGCTGAATGGGCTCCAACTGTTGCTGGATTAGGATGGCGACCATGGGATTTAATTGAATTTGCTGTTGCTATTGGATTAGTTTTAATTTGTGGACGATCATTAGGAGCTGCTTCACCAGATAATGCTCGATTAGCTTGGGGAAATGTTCCACCAAAATTACCAGGAGGAGTTGGAGATAAATCAGGAGCTAATGCTTAATAGGACGTCTT
ATTAGAAGAATTAGGATGGCGAGGATTTGCTTTACCACAATTATTAAAAAAATTTGATCC            TGTTATTTTAGGAATTATGTGGTGGGCTTGGCATTTACCACGAGATTTACCAACTTTATT            AGGAGCTGCTTGGTCAGTTATTGTTAAACAATTAGTTATTACTCCAGGATTTATTGCTTC            TGTTTTTGTTTGTAATAAATTAGGAGGATCAATGTGGGGAGGAGTTTTAACTCATGC               AGGAGTTAATGTTACTGCTGAATGGGCTCCAACTGTTGCTGGATTAGGATGGCGA                 ATTTGCTGTTGCTATTGGATTAGTTTTAATTTGTGGACGATCATTAGGAGCTGCTTC                TTAGCTTGGGGAAATGTTCCACCAAAATTACCAGGAGGAGTTGGAGATAAATCAGGAGC                     
                                    TGTTAATAATTTTTTTAAACTAGGTAATTGACGACGACAATAAAATCCTTAATACACCAC            TGGTGCTCTAAATGGTTGAAATAAAAGTCCTCGAGGTCCTCGACGAACCAGTCAA                 ATAATGAGGTCCTAAATAACGAAGTTGATAATAACGACAAAAACAAACATTATTTAATCC            CCCTCCTCAAAATTGAGTACGATAAGTATTACTTAATCCTCAATTACAATGACGACTTAC            ACGACCTAATCCTACCGCTGGTACCCTAAATTAACTTAAACGACAACGATAACCTAATCA            TGCTAGTAATCCTCGACGAAGTGGTCTATTACGAGCTAATCGAACCCCTTTACAAGGTG               CTCAACCTCTATTTAGTCCTCGATTACGAATTATCCTGCAGAA
TAATCTTCTTAATCCTACCGCTCCTAAACGAAATGGTGTTAATAATTTTTTTAAACTAGGTAATTGACGACGACAATAAAATCCTTAATACACCACCCGAACCGTAAATGGTGCTCTAAATGGTTGAAATAAAAGTCCTCGAGGTCCTCGACGAACCAGTCAATAACAATTTGTTAATCAATAATGAGGTCCTAAATAACGAAGTTGATAATAACGACAAAAACAAACATTATTTAATCCTCCTAGTTACACCCCTCCTCAAAATTGAGTACGATAAGTATTACTTAATCCTCAATTACAATGACGACTTACCCGAGGTTGACAACGACCTAATCCTACCGCTGGTACCCTAAATTAACTTAAACGACAACGATAACCTAATCAAAATTAAACACCTGCTAGTAATCCTCGACGAAGTGGTCTATTACGAGCTAATCGAACCCCTTTACAAGGTGGTTTTAATGGTCCTCCTCAACCTCTATTTAGTCCTCGATTACGAATTATCCTGCAGAA

The experimental procedure and analysis

1、Dissolving of primers

Sterile deionized water whose volume is determined by primer’s molecular weight is used to dilute the solution of the primer to 10um/L. And it is prepared for the following experiment.

Num

Tm

MW(g/mole)

nmol/Tube

Add buffer for 10μM/uL

A101

68.3

18451

1.6

155

A102

65

17588.4

1.4

142

A103

69.7

18359

1.5

155

A104

64.2

18533

1.4

143

A105

66.3

18354

1.6

155

A106

68

17321.2

1.5

151

A107

71.1

18533

1.6

156

A108

70.9

17127.2

1.6

164

A109

73.8

18513

1.6

156

A110

66.3

18440

1.4

137

A111

67.6

18426

1.6

156

A112

69.7

18506

1.5

147

A113

67

18441

1.6

156

A114

64

13568.8

2.0

200

A201

66.3

18568

1.4

143

A202

64.9

18407

1.5

145

A203

68.3

18522

1.5

155

A204

71.8

16968

1.6

162

A205

68.3

18491

1.5

154

A206

64.9

18492

1.4

138

A207

67.9

17753.4

1.6

156

A208

68.3

18305

1.5

151

A209

72.6

17117

1.6

164

A210

70.4

18278

1.5

149

A211

68.6

17622.4

1.7

165

A212

72.6

18145.8

1.6

156

A213

71.9

18356.8

1.5

146

A214

66.9

13072.6

2.2

220

A1

62

8002.2

3.6

356

A2

61

12043.8

2.2

222

A3

62

9375

2.8

281

A4

62

8548.6

3.3

330

A5

62

8548.6

3.3

330

2、Mixing of primers

Oligonucleotides synthesized in powder form need to be centrifuged for 1 min at 10000rpm to assemble powders to the bottom of the EP tube.And be careful to open the cap.

Make sure that the synthesis report is consistent to the OD number on the primer label,and check the number of the dispensing tube before the dissolution of oligonucleotides.The volume of water added to make 10umol/L oligonucleotides’ solution is calculated according to the synthetic single report of each primer. Add sterile deionized water and keep it at room temperature for 2min.And reverse the tube to accelerate the progress of solubilization. Finally, collect substances at the bottom of the tube after centrifugation.

Every six primers are combined to one group.Add 4ulbeginning fiprimer, 1ulintermediate primer and 4ul end primerto a new EP tube, then add sterile deionized water to 20ul, mix them up as spare.

Group

Number of primer

Uptake

The volume of sterile deionized water

The total volume

Each PCR (50ul system) uptake

Final concentration

A1

A101

4

8

20

5ul

200nM

A102

1

50nM

A103

1

50nM

A104

1

50nM

A105

1

50nM

A106

4

200nM

A2

A107

4

8

20

5ul

200nM

A108

1

50nM

A109

1

50nM

A110

1

50nM

A111

1

50nM

A112

4

200nM

A3

A113

4

8

20

5ul

200nM

A114

1

50nM

A201

1

50nM

A202

1

50nM

A203

1

50nM

A204

4

200nM

A4

A205

4

8

20

5ul

200nM

A206

1

50nM

A207

1

50nM

A208

1

50nM

A209

1

50nM

A210

4

200nM

A5

A211

4

10

20

5ul

200nM

A212

1

50nM

A213

1

50nM

A214

4

200nM

3、DA-PCR

Every six primers which are single-stranded oligonucleotidesare chemically synthesized were combined to one group. Then they were going to be made as longer double-stranded fragments of intermediate (Block) by DA-PCR

          Mixed primer solutions                  5μl

          Pfu DNA Polymerase 2.5U              0.5μl     

          dNTP                                4μl

          10×Pfu buffer(Mg2+)               5μl

          灭菌超纯水                  补齐至  50μl

DA-PCR的反应程序为:

        94℃         2min

        94℃         30S

        47℃         30S    25个循环

        72℃         1min

        72℃        10min

        4℃          保存

        End

DA-PCR拼接反应产物检测采用2%的琼脂糖凝胶电泳,其中

DA-PCR产物              5μl 

10×Loading Buffer         0.6μl   混合均匀后点样

100bp Marker              5μl    直接点样

75V电泳1h。

图1 DA-PCR拼接结果

结果说明:

1、A1、A2、A3、A4都能得到6条单链寡核苷酸拼接到一起的中间产物(Block1-4),但是A3和A4组还可看到4条单链寡核苷酸拼接到一起的副产物,需胶回收后再进一步拼全基因。

2、A5组可得到4条单链寡核苷酸拼接到一起的中间产物(Block5)。

 

4、OE-PCR

Take the 5 double strand intermediate fragment (Block) spliced by DA-PCR as templates, blocks were further connected by OR-PCR, OE-PCR in a reaction system consisting of:

      Block1                       1μl

          Block2                       1μl

          Block3                       1μl

          Block4                       1μl

          Block5                       1μl

          A1                          1μl

          A4                          1μl

          Pfu DNA Polymerase 2.5U       0.5μl 

          dNTP                        4μl

          10×Pfu buffer(Mg2+)         5μl

          灭菌超纯水          补齐至  50μl

OE-PCR反应程序为:

        94℃         2min

        94℃         30S

        47℃         30S    20个循环

        72℃        2min

        72℃       10min

        4℃          保存

        End

OE-PCR拼接得到的全长基因采用1%的琼脂糖凝胶电泳进行检测,其中

OE-PCR产物             5μl 

10×Loading Buffer        0.6μl   混合均匀后点样

100bp Marker              5μl    直接点样

80V电泳1h。

 

图2 OE-PCR拼接结果

结果说明:

1、L1、L2、L3都能得到5条中间产物拼接到一起的mlrA全基因。

2、100bp处的宽条带是由于扩增引物A1和A4加入量过多所导致。

5、Constructing and sequencing of subcoloning vector

After double enzyme digestion reaction at 37℃ for 3h by EcoRⅠand PstⅠ, MlrA gene and pSB1C3 vector linked together at 16℃ overnight. And then transformed to E.coli JM109 competent cell, and select the desirable colony by using “blue-white selection” method.

Constitute of EcoRⅠand PstⅠdouble enzyme digestion reaction system::

          Gene or plasmid                      10μl

          EcoRⅠ                             0.4μl

          PstⅠ                               0.2μl

          10×NEBuffer 3.1                     2μl

          灭菌超纯水                  补齐至  20μl

Constitute of linking reaction system:

          mlrA Gene                           10μl

          pSB1C3                              3μl

          T4 ligase                            0.5μl

          10×T4 ligase Buffer                   2μl

          灭菌超纯水                  补齐至  20μl

E.coli JM109感受态细胞制备流程:

(1) E.coli JM109菌株37℃过夜培养以复苏菌种,取过夜培养的菌液600uL加入到30 mL LB培养基中,37℃,200 r/min振荡培养1-2 h,至OD600约为0.3-0.4左右。

(2) 无菌条件下,将30mL菌液转移至离心管中,冰上放置10 min,使培养物冷却至0℃。

(3) 在预冷4℃的离心机上以4000r/min离心10min,弃去上清,加入30mL预冷的0.1mol/L CaCl2溶液重悬沉淀,冰浴上放置10 min。

(4) 以4000r/min在4℃离心10min,弃去上清,每30mL初始培养物用1.0mL预冷的0.1mol/LCaCl2溶液重悬细胞沉淀,200μL/管分装。

热激转化过程:

(1) 取新鲜制备或者从-80℃冰箱中取出感受态细胞JM109悬液,冰浴解冻。

(2) 加入构建好的重组克隆载体质粒pSB1C3-A(含量不超过50ng,体积不超过10μl),轻轻摇匀,冰上放置30分钟后。

(3) 将该EP管放入预加温至42℃的水浴中,放置90s,快速转移到冰浴中,使细胞冷却1-2 min。

(4) 向EP管加入800 μL LB培养基,转移至37℃摇床上,150r/min,温育45 min以复苏菌株。 

平板涂布及培养过程:

(1) 将37℃培养后的菌体低速离心(5000rpm、5min)浓缩为200μl,涂布到含有氯霉素的LB平板上,设阳性对照。

(2) 将平板置于室温下至液体被完全吸收,倒置平皿,37℃过夜培养;

实验连接组:连接产物,氯霉素板

阳性对照组: 氯霉素板,以pSB1C3质粒代替DNA溶液, 其它操作与上面相同。此组正常情况下在含抗生素的LB平板上应产生大量菌落

阴性对照组:氯霉素板,为连接时用水代替酶,其它与实验组相同。

空菌组:感受态细胞,无氯霉素板

序列测定

在pSB1C3载体上,将EcoR I和Pst I之间的45bp片段使用mlrA的1024bp的片段替换,将得到重组的pSB1C3-A质粒(图3)。

 

图3 重组载体pSB1C3-A

挑取白色菌落,经液体培养后,提取的质粒作为模版,以VF2及VR作为扩增引物进行PCR鉴定。有外源基因mlrA插入的重组载体,扩增得到的片段长度为1293bp,而无外源插入的pSB1C3空载体,其扩增产物为314bp。结果(图4)表明,在1300bp处,可见到清晰、特异性的扩增产物条带,所以筛选得到的白斑菌落是含有外源基因的重组载体。

                   图4 重组载体pSB1C3-A的PCR鉴定

结果说明:

1、L1、L2都能扩增得到1300bp的产物,鉴定的重组载体含有外源基因mlrA

2、M是100bp Ladder Marker

将经过PCR鉴定的含有重组载体pSB1C3-A的阳性克隆送到吉林库美生物科技限公司进行测序。结果表明(图5),合成的mlrA基因序列与设计序列一致。

 

图5 测序结果与设计序列比对

 

6、引物合成

     

吉林省库美生物科技有限公司引物合成订购单

 

引物编号

序列,(5' to 3')

碱基数(bp)

合成总量(OD)

分装管数

纯化方式

A101

CCGGAATTCATGCGAGAATTTGTTCGACAACGACCATTATTATGTTTTTATGTTTTAGCT

60

1

1

PAGE

A102

CTCGTAAAGCATGAGCAGCTAAAGCAATTAAAATAGCTAAAACATAAAAACATAATA

57

1

1

PAGE

A103

AGCTGCTCATGCTTTACGAGCTATGTCACCAACTCCATTAGATCCAATGTTTAAAATGTT

60

1

1

PAGE

A104

AGCAGTAATAATATTTAAATGAGCATGAGTTTCTTGTAACATTTTAAACATTGGATCTAA

60

1

1

PAGE

A105

CTCATTTAAATATTATTACTGCTGTTCGATCAACTTTTGAATATCCAGGAGCTTATACTT

60

1

1

PAGE

A106

CAGCAAACATTGGAGCAGCTGGAAATAATAATAAAGTATAAGCTCCTGGATATTCA

56

1

1

PAGE

A107

GCTGCTCCAATGTTTGCTGCTTTAATTGCTACTGGAATTGGATATGGACAAGCTGGATTT

60

1

1

PAGE

A108

TCGCCATGGAGCACATCGTGATAATAATTCTCGAAATCCAGCTTGTCCATATCCAA

56

1

1

PAGE

A109

ACGATGTGCTCCATGGCGATCACCAGTTTCATGGCGACAAGGAGTTACTGTTATTGCTGT

60

1

1

PAGE

A110

CATAATTCCAGTTAAAGCAAAAAAAGCTAAAAAACAAACAGCAATAACAGTAACTCCTTG

60

1

1

PAGE

A111

TTTTGCTTTAACTGGAATTATGTGGGTTCAAACTTATTTATATGCTCCACCAGGAACTTT

60

1

1

PAGE

A112

CAACTGGATCTGATCCATATCGTAAAAAAGTTCGATCTAAAGTTCCTGGTGGAGCATATA

60

1

1

PAGE

A113

CGATATGGATCAGATCCAGTTGCTATTTATGTTATGTTAGCTGCTTCATTATTATTATCA

60

1

1

PAGE

A114

ATTCTTCTAATAATGGTCCTGGTGATAATAATAATGAAGCAGCT

44

1

1

PAGE

A201

ATTAGAAGAATTAGGATGGCGAGGATTTGCTTTACCACAATTATTAAAAAAATTTGATCC

60

1

1

PAGE

A202

CACCACATAATTCCTAAAATAACAGCAGCAGTTAATGGATCAAATTTTTTTAATAATTGT

60

1

1

PAGE

A203

TGTTATTTTAGGAATTATGTGGTGGGCTTGGCATTTACCACGAGATTTACCAACTTTATT

60

1

1

PAGE

A204

AACTGACCAAGCAGCTCCTGGAGCTCCTGAAAATAAAGTTGGTAAATCTCGTGGT

55

1

1

PAGE

A205

AGGAGCTGCTTGGTCAGTTATTGTTAAACAATTAGTTATTACTCCAGGATTTATTGCTTC

60

1

1

PAGE

A206

CCTAATTTATTACAAACAAAAACAGCAATAATAGTTGAAGCAATAAATCCTGGAGTAATA

60

1

1

PAGE

A207

TGTTTTTGTTTGTAATAAATTAGGAGGATCAATGTGGGGAGGAGTTTTAACTCATGC

57

1

1

PAGE

A208

CATTCAGCAGTAACATTAACTCCTAATTCATTATGAATAGCATGAGTTAAAACTCCTCCC

60

1

1

PAGE

A209

AGGAGTTAATGTTACTGCTGAATGGGCTCCAACTGTTGCTGGATTAGGATGGCGA

55

1

1

PAGE

A210

ACTAATCCAATAGCAACAGCAAATTCAATTAAATCCCATGGTCGCCATCCTAATCCAGCA

60

1

1

PAGE

A211

ATTTGCTGTTGCTATTGGATTAGTTTTAATTTGTGGACGATCATTAGGAGCTGCTTC

57

1

1

PAGE

A212

GTGGAACATTTCCCCAAGCTAATCGAGCATTATCTGGTGAAGCAGCTCCTAATGATCGT

59

1

1

PAGE

A213

TTAGCTTGGGGAAATGTTCCACCAAAATTACCAGGAGGAGTTGGAGATAAATCAGGAGC

59

1

1

PAGE

A214

AAGACGTCCTATTAAGCATTAGCTCCTGATTTATCTCCAACTC

43

1

1

PAGE

A1

CCGGAATTCATGCGAGAATTTGTTCG

26

1

1

PAGE

A2

ATTCTTCTAATAATGGTCCTGGTGATAATAATAATGAAG

39

1

1

PAGE

A3

ATTAGAAGAATTAGGATGGCGAGGATTTGC

30

1

1

PAGE

A4

AAGACGTCCTATTAAGCATTAGCTCCTG

28

1

1

PAGE

A5

AACTGCAGCTATTAAGCATTAGCTCCTG

28

 

 

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