Team:Jilin China/RESULT

From 2014.igem.org

(Difference between revisions)
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<h3 >3、DA-PCR </h3>
<h3 >3、DA-PCR </h3>
<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 >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>Procedure of DA-PCR： <br>
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<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>
+
  Mixed primer solutions                   5μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dNTP&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;&nbsp;&nbsp;4&#956;l </p>
+
  Pfu DNA Polymerase 2.5U              0.5μl     <br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10&#215;Pfu&nbsp;buffer（Mg2+）&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5&#956;l </p>
+
  dNTP                                4μl<br>
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<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;50&#956;l </p>
+
  10×Pfu buffer（Mg2+）               5μl<br>
-
<p >DA-PCR的反应程序为： </p>
+
  ddH20add to 50μl<br>
-
 
+
  Procedure of DA-PCR： <br>
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;94&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2min </p>
+
  94℃         2min<br>
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;94&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;30S </p>
+
  94℃         30S<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;47&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;30S&nbsp;&nbsp;&nbsp;&nbsp;25个循环 </p>
+
  50℃         30S     25 cycles<br>
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;72&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1min </p>
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  72℃         1min<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;72&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10min </p>
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  72℃        10min<br>
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;4&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;保存 </p>
+
  4℃preservation<br>
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;End </p>
+
  End<br>
-
<p >DA-PCR拼接反应产物检测采用2％的琼脂糖凝胶电泳，其中 </p>
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  DA-PCR splicing reaction product was  detected in 2% agarose gel electrophoresis,<br>
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<p >DA-PCR产物&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5&#956;l&nbsp; </p>
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  DA-PCR product              5μl <br>
-
<p >10&#215;Loading&nbsp;Buffer&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.6&#956;l&nbsp;&nbsp;&nbsp;混合均匀后点样 </p>
+
  10×Loading Buffer         0.6μl    spotting after mixed<br>
-
<p >100bp&nbsp;Marker&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5&#956;l&nbsp;&nbsp;&nbsp;&nbsp;直接点样 </p>
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  100bp Marker              5μl    spotting directly<br>
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<p >75V电泳1h。 </p>
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75V electrophoress for 1h。 </p>
-
<p >&#9; </p>
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<p ><img src="https://static.igem.org/mediawiki/2014/8/84/Simonsong-result-1.png" ></p>
<p ><img src="https://static.igem.org/mediawiki/2014/8/84/Simonsong-result-1.png" ></p>
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<p>Figure1 DA-PCR  splicing results <br>
-
 
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  Illustration of  the outcome:<br>
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+
  1、A1,  A2, A3, A4 could getintermediates (Block1-4) which were made by six  single-stranded oligonucleotides splicedtogether, but the A3 and A4 groups  could also see by-products which were made by four single-stranded  oligonucleotides splicedtogether , and to be made a whole one after recycling  of Agarose gel.</p>
-
 
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2、A5 could  obtainintermediates(Block5) which were made by four single-stranded  oligonucleotides splicedtogether.
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<p >图1&nbsp;DA-PCR拼接结果 </p>
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-
<p >结果说明： </p>
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-
<p >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。 </p>
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-
<p >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）。 </p>
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-
<p >&nbsp;</p>
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<h3 >4、OE-PCR </h3>
<h3 >4、OE-PCR </h3>
<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 >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>
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<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>
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<p>Block1                       1μl<br>
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<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>
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  Block2                       1μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Block3&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>
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  Block3                       1μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Block4&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>
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  Block4                       1μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Block5&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>
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  Block5                       1μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A1&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;1&#956;l </p>
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  A1                         1μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A4&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;1&#956;l </p>
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  A4                        1μl<br>
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<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;0.5&#956;l&nbsp; </p>
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  <em>Pfu</em> DNA Polymerase 2.5U       0.5μl <br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dNTP&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;4&#956;l </p>
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  dNTP                        4μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10&#215;Pfu&nbsp;buffer（Mg2+）&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5&#956;l </p>
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  10×<em>Pfu</em> buffer（Mg2+）         5μl<br>
-
<p ><img width="349" height="2" src="3_wpsE664.tmp.png" >&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;补齐至&nbsp;&nbsp;50&#956;l </p>
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  <img width="350" height="2" src="Untitled-6_clip_image001.gif">Sterilized  ultrapure water   to 50ul<br>
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<p >OE-PCR反应程序为： </p>
+
  Procedure of OE-PCR： <br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;94&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2min </p>
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  94℃         2min<br>
-
<p ><img width="13" height="64" src="3_wpsE675.tmp.png" >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;94&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;30S </p>
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  <img width="14" height="65" src="Untitled-6_clip_image002.gif">        94℃         30S<br>
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;47&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;30S&nbsp;&nbsp;&nbsp;&nbsp;20个循环 </p>
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  47℃         30S    20 cycles<br>
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;72&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2min </p>
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  72℃        2min<br>
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;72&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10min </p>
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  72℃       10min<br>
-
<p ><img width="349" height="2" src="3_wpsE686.tmp.png" >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;4&#8451;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;保存 </p>
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  <img width="350" height="2" src="Untitled-6_clip_image003.gif">        4℃preservation<br>
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;End </p>
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  End<br>
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<p >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 </p>
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  The full-length gene  spliced by OE-PCR was detected by a 1% agarose gel electrophoresis, specific  programs are as follows<br>
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<p ><img width="13" height="34" src="3_wpsE687.tmp.png" >OE-PCR产物&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5&#956;l&nbsp; </p>
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  <img width="14" height="35" src="Untitled-6_clip_image004.gif">OE-PCR  product           5μl <br>
-
<p >10&#215;Loading&nbsp;Buffer&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.6&#956;l&nbsp;&nbsp;&nbsp;混合均匀后点样 </p>
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  10×Loading Buffer        0.6μl    spotted after mixing well<br>
-
<p ><img width="349" height="2" src="3_wpsE688.tmp.png" >100bp&nbsp;Marker&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5&#956;l&nbsp;&nbsp;&nbsp;&nbsp;直接点样 </p>
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  <img width="350" height="2" src="Untitled-6_clip_image003_0000.gif">100bp Marker              5μl   spotted directly<br>
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<p >80V电泳1h。 </p>
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  80V electrophoresis for  1h.</p>
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<p >&nbsp;</p>
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<p ><img src="https://static.igem.org/mediawiki/2014/2/24/Simonsong-result-2.png" ></p>
<p ><img src="https://static.igem.org/mediawiki/2014/2/24/Simonsong-result-2.png" ></p>
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<p >图2&nbsp;OE-PCR拼接结果 </p>
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<<p>Illustration of  the outcome:</p>
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<ol>
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  <li>L1,  L2, L3 could get mlrA genome which were made by five single-stranded  oligonucleotides splicedtogether.</li>
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  <li>Wide  strip of the tape at 100bp was caused by excessive amount of amplification  primers A1 and A4.</li>
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</ol>
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<p >结果说明： </p>
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<p >1、L1、L2、L3都能得到5条中间产物拼接到一起的mlrA全基因。 </p>
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<p >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。 </p>
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<h3 >5、Constructing and sequencing of subcoloning vector</h3>
<h3 >5、Constructing and sequencing of subcoloning vector</h3>
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<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>
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<p>After double enzyme digestion reaction at 37℃ for 3h by<em> Eco</em>RⅠand <em>Pst</em>Ⅰ, MlrA gene and pSB1C3 vector linked together at 16℃ overnight. And then transformed to<em> E.coli</em> JM109 competent cell, and select the desirable colony by using &ldquo;blue-white selection&rdquo; method. <br>
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<p >Constitute of EcoRⅠand PstⅠdouble enzyme digestion reaction system：： </p>
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  Constitute of <strong><em>Eco</em>R</strong><strong>Ⅰ</strong><strong>and <em>Pst</em></strong><strong>Ⅰdouble enzyme digestion reaction system</strong><strong>：</strong><strong> </strong><br>
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<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>
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  Gene or plasmid                       10μl<br>
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<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>
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  <em>Eco</em>RⅠ                             0.4μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pst&#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;&nbsp;&nbsp;0.2&#956;l </p>
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  <em>Pst</em>Ⅰ                               0.2μl<br>
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<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>
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  10×NEBuffer 3.1                      2μl<br>
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<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>
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  sterilizing ulturapure water         top up to 20μl<br>
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<p >Constitute of linking reaction system： </p>
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  <strong>Constitute of linking reaction system</strong><strong>：</strong><strong> </strong><br>
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<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>
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  mlrA Gene                           10μl<br>
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<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>
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  pSB1C3                               3μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;T4&nbsp;ligase&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;0.5&#956;l </p>
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  T4 ligase                             0.5μl<br>
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<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;10&#215;T4&nbsp;ligase&nbsp;Buffer&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2&#956;l </p>
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  10×T4 ligase Buffer                    2μl<br>
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<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>
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  sterilizing ulturapure water         top up to 20μl<br>
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<p >E.coli&nbsp;JM109感受态细胞制备流程： </p>
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  Preparation process of competent cell <strong><em>E.coli</em>BL21</strong><strong>：</strong><strong> </strong><br>
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<p >(1)&nbsp;E.coli&nbsp;JM109菌株37&#8451;过夜培养以复苏菌种，取过夜培养的菌液600uL加入到30&nbsp;mL&nbsp;LB培养基中，37&#8451;，200&nbsp;r/min振荡培养1-2&nbsp;h，至OD600约为0.3-0.4左右。 </p>
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  (1) Culturing strain <em>E.coli</em>BL21(37℃)overnight  to recovery culture, Adding overnight bacteria culture fluid 600uLto 30 mL LB  culture medium, and 37℃，200  r/min shake culturing 1-2 h, until OD600 is around 0.3-0.4.<br>
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<p >(2)&nbsp;无菌条件下，将30mL菌液转移至离心管中，冰上放置10&nbsp;min，使培养物冷却至0&#8451;。 </p>
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  (2) In the aseptic  condition, transfer 30mLbacteria fluid to the centrifugal tube in the ice 10  min to cooling the culture to 0℃.<br>
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<p >(3)&nbsp;在预冷4&#8451;的离心机上以4000r/min离心10min，弃去上清，加入30mL预冷的0.1mol/L&nbsp;CaCl2溶液重悬沉淀，冰浴上放置10&nbsp;min。 </p>
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  (3) Centrifuging 10 min in precooling centrifugal machine over 4000r/min, throw  supernate, and then add30mLprecooling 0.1mol/L CaCl2 solution to  resuspension precipitation in the ice 10 min.<br>
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<p >(4)&nbsp;以4000r/min在4&#8451;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，200&#956;L/管分装。 </p>
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  (4) Centrifuging 4000r/min  in 4℃10min, throw  supernate,  each 30mL initial culture  resuspension cell precipitation with 1.0mL precooling 0.1mol/LCaCl2  solution, and then 200μL each one.<br>
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<p >热激转化过程： </p>
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  <strong>Heal  shock transformation process</strong><strong>：</strong><strong> </strong><br>
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<p >(1)&nbsp;取新鲜制备或者从-80&#8451;冰箱中取出感受态细胞JM109悬液，冰浴解冻。 </p>
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  (1) Thawing freshly  prepared or -80℃ competentcellBL21suspension.<br>
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<p >(2)&nbsp;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10&#956;l)，轻轻摇匀，冰上放置30分钟后。 </p>
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  (2) Add constructed  recombinant cloning vector plasmidspSB1C3-A(no more than 50ng, 10μl), shake  gently, and then in the ice 30min.<br>
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<p >(3)&nbsp;将该EP管放入预加温至42&#8451;的水浴中，放置90s，快速转移到冰浴中，使细胞冷却1-2&nbsp;min。 </p>
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  (3) Put EP tube in 42℃ water bath90s，and  then transfer it to ice water bath to cool cells1-2 min.<br>
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<p >(4)&nbsp;向EP管加入800&nbsp;&#956;L&nbsp;LB培养基，转移至37&#8451;摇床上，150r/min，温育45&nbsp;min以复苏菌株。&nbsp; </p>
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  (4) add 800μL LB medium  to EP tube，transfer  it to 37℃  table，150r/min，to  recovery strain 45 min.<br>
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<p >平板涂布及培养过程： </p>
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  Spread plate and  Culture<br>
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<p >(1)&nbsp;将37&#8451;培养后的菌体低速离心（5000rpm、5min）浓缩为200&#956;l，涂布到含有氯霉素的LB平板上，设阳性对照。 </p>
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  (1)After culture in 37℃,  centrifuge the cell solution(5000rpm,5min) and concentrate it to 200μl.  Then coat it to LB culture with chloramphenicol and set a positive control.<br>
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<p >(2)&nbsp;将平板置于室温下至液体被完全吸收，倒置平皿，37&#8451;过夜培养； </p>
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  (2) Wait until the  solution in culture is full absorbed by cell, then invert the plate and culture  it in 37℃  overnight.<br>
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<p >实验连接组：连接产物，氯霉素板 </p>
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  Sequence test<br>
-
<p >阳性对照组:&nbsp;氯霉素板，以pSB1C3质粒代替DNA溶液,&nbsp;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 </p>
+
  Replace the fragment(45bp) between EcoR I site  and Pst I site with mlrA(1024bp) on pSB1C3 vector and then we get the  reconstructed plasmid, pSB1C3-A.</p>
-
<p >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。 </p>
+
-
<p >空菌组：感受态细胞，无氯霉素板 </p>
+
-
<p >序列测定 </p>
+
-
<p >在pSB1C3载体上，将EcoR&nbsp;I和Pst&nbsp;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）。 </p>
+
Line 864: Line 843:
-
<p >图3&nbsp;重组载体pSB1C3-A </p>
+
<p >Fig3.Reconstructed vector pSB1C3-A </p>
-
<p >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。 </p>
+
<p >Select the white colony on culture and culture it. Then we extract the plasmid and use it as template in PCR to identify the colony. In theory, the reconstructed vector with mlrA fragment is 1293bp and the empty vector without mlrA fragment is 314bp. So, the result shows that the white colony we select has reconstructed vector with mlrA fragment in it.</p>
<p ><img  src="https://static.igem.org/mediawiki/2014/6/63/Simonsong-result-4.png" ></p>
<p ><img  src="https://static.igem.org/mediawiki/2014/6/63/Simonsong-result-4.png" ></p>
Line 871: Line 850:
-
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;图4&nbsp;重组载体pSB1C3-A的PCR鉴定 </p>
+
<p >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Fig 4. The identification of reconstructed vector pSB1C3-A </p>
-
<p >结果说明： </p>
+
<p >Results: </p>
-
<p >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 </p>
+
<p >1.L1 and L2 is 1300bp and it confirms that the reconstructed vector has mlrA on it. </p>
-
<p >2、M是100bp&nbsp;Ladder&nbsp;Marker </p>
+
<p >2.M is the 100bp Ladde Marker. </p>
-
<p >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。 </p>
+
<p >Sequencing result shows that the sequence of synthetic mlrA gene is exactly same as sequence of designed sequence. </p>
Line 881: Line 860:
<p ><img src="https://static.igem.org/mediawiki/2014/5/5a/Simonsong-result-5.png" ><img src="https://static.igem.org/mediawiki/2014/0/0b/Simonsong-result-6.png" >&nbsp;</p>
<p ><img src="https://static.igem.org/mediawiki/2014/5/5a/Simonsong-result-5.png" ><img src="https://static.igem.org/mediawiki/2014/0/0b/Simonsong-result-6.png" >&nbsp;</p>
-
<p >图5&nbsp;测序结果与设计序列比对 </p>
+
<p > Fig5.Comparison of result of sequencing and designed sequence </p>
<p >&nbsp;</p>
<p >&nbsp;</p>
Line 898: Line 877:
</table>
</table>
<p >&nbsp;</p>
<p >&nbsp;</p>
-
<table >
+
 
-
  <tr >
+
-
    <td width="50" valign="center" ><p >引物编号 </p></td>
+
-
    <td width="456" valign="center" ><p >序列，(5'&nbsp;to&nbsp;3') </p></td>
+
-
    <td width="57" valign="center" ><p >碱基数（bp） </p></td>
+
-
    <td width="57" valign="center" ><p >合成总量(OD) </p></td>
+
-
    <td width="47" valign="center" ><p >分装管数 </p></td>
+
-
    <td width="56" valign="center" ><p >纯化方式 </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A101 </p></td>
+
-
    <td width="456" valign="center" ><p >CCGGAATTCATGCGAGAATTTGTTCGACAACGACCATTATTATGTTTTTATGTTTTAGCT </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A102 </p></td>
+
-
    <td width="456" valign="center" ><p >CTCGTAAAGCATGAGCAGCTAAAGCAATTAAAATAGCTAAAACATAAAAACATAATA </p></td>
+
-
    <td width="57" valign="center" ><p >57 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A103 </p></td>
+
-
    <td width="456" valign="center" ><p >AGCTGCTCATGCTTTACGAGCTATGTCACCAACTCCATTAGATCCAATGTTTAAAATGTT </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A104 </p></td>
+
-
    <td width="456" valign="center" ><p >AGCAGTAATAATATTTAAATGAGCATGAGTTTCTTGTAACATTTTAAACATTGGATCTAA </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A105 </p></td>
+
-
    <td width="456" valign="center" ><p >CTCATTTAAATATTATTACTGCTGTTCGATCAACTTTTGAATATCCAGGAGCTTATACTT </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A106 </p></td>
+
-
    <td width="456" valign="center" ><p >CAGCAAACATTGGAGCAGCTGGAAATAATAATAAAGTATAAGCTCCTGGATATTCA </p></td>
+
-
    <td width="57" valign="center" ><p >56 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A107 </p></td>
+
-
    <td width="456" valign="center" ><p >GCTGCTCCAATGTTTGCTGCTTTAATTGCTACTGGAATTGGATATGGACAAGCTGGATTT </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A108 </p></td>
+
-
    <td width="456" valign="center" ><p >TCGCCATGGAGCACATCGTGATAATAATTCTCGAAATCCAGCTTGTCCATATCCAA </p></td>
+
-
    <td width="57" valign="center" ><p >56 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A109 </p></td>
+
-
    <td width="456" valign="center" ><p >ACGATGTGCTCCATGGCGATCACCAGTTTCATGGCGACAAGGAGTTACTGTTATTGCTGT </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A110 </p></td>
+
-
    <td width="456" valign="center" ><p >CATAATTCCAGTTAAAGCAAAAAAAGCTAAAAAACAAACAGCAATAACAGTAACTCCTTG </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A111 </p></td>
+
-
    <td width="456" valign="center" ><p >TTTTGCTTTAACTGGAATTATGTGGGTTCAAACTTATTTATATGCTCCACCAGGAACTTT </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A112 </p></td>
+
-
    <td width="456" valign="center" ><p >CAACTGGATCTGATCCATATCGTAAAAAAGTTCGATCTAAAGTTCCTGGTGGAGCATATA </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A113 </p></td>
+
-
    <td width="456" valign="center" ><p >CGATATGGATCAGATCCAGTTGCTATTTATGTTATGTTAGCTGCTTCATTATTATTATCA </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A114 </p></td>
+
-
    <td width="456" valign="center" ><p >ATTCTTCTAATAATGGTCCTGGTGATAATAATAATGAAGCAGCT </p></td>
+
-
    <td width="57" valign="center" ><p >44 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A201 </p></td>
+
-
    <td width="456" valign="center" ><p >ATTAGAAGAATTAGGATGGCGAGGATTTGCTTTACCACAATTATTAAAAAAATTTGATCC </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A202 </p></td>
+
-
    <td width="456" valign="center" ><p >CACCACATAATTCCTAAAATAACAGCAGCAGTTAATGGATCAAATTTTTTTAATAATTGT </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A203 </p></td>
+
-
    <td width="456" valign="center" ><p >TGTTATTTTAGGAATTATGTGGTGGGCTTGGCATTTACCACGAGATTTACCAACTTTATT </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A204 </p></td>
+
-
    <td width="456" valign="center" ><p >AACTGACCAAGCAGCTCCTGGAGCTCCTGAAAATAAAGTTGGTAAATCTCGTGGT </p></td>
+
-
    <td width="57" valign="center" ><p >55 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A205 </p></td>
+
-
    <td width="456" valign="center" ><p >AGGAGCTGCTTGGTCAGTTATTGTTAAACAATTAGTTATTACTCCAGGATTTATTGCTTC </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A206 </p></td>
+
-
    <td width="456" valign="center" ><p >CCTAATTTATTACAAACAAAAACAGCAATAATAGTTGAAGCAATAAATCCTGGAGTAATA </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A207 </p></td>
+
-
    <td width="456" valign="center" ><p >TGTTTTTGTTTGTAATAAATTAGGAGGATCAATGTGGGGAGGAGTTTTAACTCATGC </p></td>
+
-
    <td width="57" valign="center" ><p >57 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A208 </p></td>
+
-
    <td width="456" valign="center" ><p >CATTCAGCAGTAACATTAACTCCTAATTCATTATGAATAGCATGAGTTAAAACTCCTCCC </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A209 </p></td>
+
-
    <td width="456" valign="center" ><p >AGGAGTTAATGTTACTGCTGAATGGGCTCCAACTGTTGCTGGATTAGGATGGCGA </p></td>
+
-
    <td width="57" valign="center" ><p >55 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A210 </p></td>
+
-
    <td width="456" valign="center" ><p >ACTAATCCAATAGCAACAGCAAATTCAATTAAATCCCATGGTCGCCATCCTAATCCAGCA </p></td>
+
-
    <td width="57" valign="center" ><p >60 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A211 </p></td>
+
-
    <td width="456" valign="center" ><p >ATTTGCTGTTGCTATTGGATTAGTTTTAATTTGTGGACGATCATTAGGAGCTGCTTC </p></td>
+
-
    <td width="57" valign="center" ><p >57 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A212 </p></td>
+
-
    <td width="456" valign="center" ><p >GTGGAACATTTCCCCAAGCTAATCGAGCATTATCTGGTGAAGCAGCTCCTAATGATCGT </p></td>
+
-
    <td width="57" valign="center" ><p >59 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A213 </p></td>
+
-
    <td width="456" valign="center" ><p >TTAGCTTGGGGAAATGTTCCACCAAAATTACCAGGAGGAGTTGGAGATAAATCAGGAGC </p></td>
+
-
    <td width="57" valign="center" ><p >59 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A214 </p></td>
+
-
    <td width="456" valign="center" ><p >AAGACGTCCTATTAAGCATTAGCTCCTGATTTATCTCCAACTC </p></td>
+
-
    <td width="57" valign="center" ><p >43 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A1 </p></td>
+
-
    <td width="456" valign="center" ><p >CCGGAATTCATGCGAGAATTTGTTCG </p></td>
+
-
    <td width="57" valign="center" ><p >26 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A2 </p></td>
+
-
    <td width="456" valign="center" ><p >ATTCTTCTAATAATGGTCCTGGTGATAATAATAATGAAG </p></td>
+
-
    <td width="57" valign="center" ><p >39 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A3 </p></td>
+
-
    <td width="456" valign="center" ><p >ATTAGAAGAATTAGGATGGCGAGGATTTGC </p></td>
+
-
    <td width="57" valign="center" ><p >30 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A4 </p></td>
+
-
    <td width="456" valign="center" ><p >AAGACGTCCTATTAAGCATTAGCTCCTG </p></td>
+
-
    <td width="57" valign="center" ><p >28 </p></td>
+
-
    <td width="57" valign="center" ><p >1 </p></td>
+
-
    <td width="47" valign="center" ><p >1 </p></td>
+
-
    <td width="56" valign="center" ><p >PAGE </p></td>
+
-
  </tr>
+
-
  <tr >
+
-
    <td width="50" valign="center" ><p >A5 </p></td>
+
-
    <td width="456" valign="center" ><p >AACTGCAGCTATTAAGCATTAGCTCCTG </p></td>
+
-
    <td width="57" valign="center" ><p >28 </p></td>
+
-
    <td width="57" valign="center" ><p >&nbsp;</p></td>
+
-
    <td width="47" valign="center" ><p >&nbsp;</p></td>
+
-
    <td width="56" valign="center" ><p > </p></td>
+
-
  </tr>
+
-
<td bgColor="#FEE5AD"></td>
+
-
</table>
+
</div>
</div>
<td width="100%" rowspan="3" align="left">  
<td width="100%" rowspan="3" align="left">  

Revision as of 02:06, 18 October 2014

Welcome!
Team Jilin China
Top

Retrieved from "http://2014.igem.org/Team:Jilin_China/RESULT"
NOTEBOOK

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

Procedure of DA-PCR：
Mixed primer solutions                  5μl
Pfu DNA Polymerase 2.5U              0.5μl    
dNTP                                4μl
10×Pfu buffer（Mg2+）               5μl
ddH20add to 50μl
Procedure of DA-PCR：
94℃         2min
94℃         30S
50℃         30S    25 cycles
72℃         1min
72℃        10min
4℃preservation
End
DA-PCR splicing reaction product was detected in 2% agarose gel electrophoresis,
DA-PCR product              5μl
10×Loading Buffer         0.6μl   spotting after mixed
100bp Marker              5μl    spotting directly
75V electrophoress for 1h。

Figure1 DA-PCR splicing results
Illustration of the outcome:
1、A1, A2, A3, A4 could getintermediates (Block1-4) which were made by six single-stranded oligonucleotides splicedtogether, but the A3 and A4 groups could also see by-products which were made by four single-stranded oligonucleotides splicedtogether , and to be made a whole one after recycling of Agarose gel.

2、A5 could obtainintermediates(Block5) which were made by four single-stranded oligonucleotides splicedtogether.

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
Sterilized ultrapure water   to 50ul
Procedure of OE-PCR：
94℃         2min
        94℃         30S
47℃         30S   20 cycles
72℃        2min
72℃       10min
        4℃preservation
End
The full-length gene spliced by OE-PCR was detected by a 1% agarose gel electrophoresis, specific programs are as follows
OE-PCR product           5μl
10×Loading Buffer        0.6μl   spotted after mixing well
100bp Marker              5μl   spotted directly
80V electrophoresis for 1h.

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Illustration of the outcome:

  1. L1, L2, L3 could get mlrA genome which were made by five single-stranded oligonucleotides splicedtogether.
  2. Wide strip of the tape at 100bp was caused by excessive amount of amplification primers A1 and A4.

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
sterilizing ulturapure water        top up to 20μl
Constitute of linking reaction system：
mlrA Gene                           10μl
pSB1C3                              3μl
T4 ligase                            0.5μl
10×T4 ligase Buffer                   2μl
sterilizing ulturapure water        top up to 20μl
Preparation process of competent cell E.coliBL21：
(1) Culturing strain E.coliBL21(37℃)overnight to recovery culture, Adding overnight bacteria culture fluid 600uLto 30 mL LB culture medium, and 37℃，200 r/min shake culturing 1-2 h, until OD600 is around 0.3-0.4.
(2) In the aseptic condition, transfer 30mLbacteria fluid to the centrifugal tube in the ice 10 min to cooling the culture to 0℃.
(3) Centrifuging 10 min in precooling centrifugal machine over 4000r/min, throw supernate, and then add30mLprecooling 0.1mol/L CaCl2 solution to resuspension precipitation in the ice 10 min.
(4) Centrifuging 4000r/min in 4℃10min, throw supernate,  each 30mL initial culture resuspension cell precipitation with 1.0mL precooling 0.1mol/LCaCl2 solution, and then 200μL each one.
Heal shock transformation process：
(1) Thawing freshly prepared or -80℃ competentcellBL21suspension.
(2) Add constructed recombinant cloning vector plasmidspSB1C3-A(no more than 50ng, 10μl), shake gently, and then in the ice 30min.
(3) Put EP tube in 42℃ water bath90s，and then transfer it to ice water bath to cool cells1-2 min.
(4) add 800μL LB medium to EP tube，transfer it to 37℃ table，150r/min，to recovery strain 45 min.
Spread plate and Culture
(1)After culture in 37℃, centrifuge the cell solution(5000rpm,5min) and concentrate it to 200μl. Then coat it to LB culture with chloramphenicol and set a positive control.
(2) Wait until the solution in culture is full absorbed by cell, then invert the plate and culture it in 37℃ overnight.
Sequence test
Replace the fragment(45bp) between EcoR I site and Pst I site with mlrA(1024bp) on pSB1C3 vector and then we get the reconstructed plasmid, pSB1C3-A.

 

Fig3.Reconstructed vector pSB1C3-A

Select the white colony on culture and culture it. Then we extract the plasmid and use it as template in PCR to identify the colony. In theory, the reconstructed vector with mlrA fragment is 1293bp and the empty vector without mlrA fragment is 314bp. So, the result shows that the white colony we select has reconstructed vector with mlrA fragment in it.

                   Fig 4. The identification of reconstructed vector pSB1C3-A

Results:

1.L1 and L2 is 1300bp and it confirms that the reconstructed vector has mlrA on it.

2.M is the 100bp Ladde Marker.

Sequencing result shows that the sequence of synthetic mlrA gene is exactly same as sequence of designed sequence.

 

Fig5.Comparison of result of sequencing and designed sequence

 

6、引物合成

     

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