Difference between revisions of "Team:Worldshaper-XSHS/Protocols-methods.html"

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                     <ul class="colul text-left"style="width: 180px;font-size: 15px!important">
                         <li class="colactive mt-1"><a href="#Ourteam">Collaboration with ASTWS-China team and HFLS_ZhejiangUnited team.</a></li>
+
                         <li class="colactive mt-1"><a href="#Ourteam">The main purpose of our experiment</a></li>
 
                         <hr>
 
                         <hr>
                         <li class="mt-1"><a href="#OurSchool">Collaboration with ZJU-China team.</a></li>
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                         <li class="mt-1"><a href="#In the construction of plasmid, we mainly did the following work:">Our main works</a></li>
 
                         <hr>
 
                         <hr>
                         <li class="mt-1"><a href="#Others">Collaborations with social organizations.</a></li>
+
                         <li class="mt-1"><a href="#The Construction of Plasmids">The Construction of Plasmids</a></li>
 +
                        <hr>
 +
                        <li class="mt-1"><a href="#Sensitivity detection">Sensitivity detection</a></li>
 +
                        <hr>
 +
                        <li class="mt-1"><a href="#Appendix">Appendix</a></li>
 +
                        <hr>
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                        <li class="mt-1"><a href="#Experimental system">Experimental system</a></li>
 
                         <!-- 这里是页面定位锚点  href 对应代码的 “id属性  例如 id='xxx'  ”-->
 
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                         <li>
 
                         <li>
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                     <div class="xshs-box3">
 
                         <p class="v1" id="Ourteam" style="text-align:  center; ">
 
                         <p class="v1" id="Ourteam" style="text-align:  center; ">
                             Collaborations with other teams
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                             The main purpose of our experiment is as follows:
 
                         </p>
 
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                    <div>
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                      <p class="itemstyle">
 +
                            1 Screening of Nicotine Inductive Promoter and Construction of the First Version of Nicotine Monitoring System
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ①The construction of plasmids pSB1C3-Pnox + RBS + GFP + ter,pSB1C3-Pnox + RBS + BFP,pSB1C3-Pnox + RBS + RFP + ter,pSB1C3-Pnox.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ②The construction of plasmids pMD-Pnica1 + RBS + GFP + ter,pMD-Pnica2 + RBS + GFP + ter.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            2  The Construction of the Second Version of Nicotine Monitoring System
 +
The construction of plasmid pMD-Pnica2 + RBS + T7RNA poLymerase + PT7 + RBS + GFP + ter.
 +
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            3  The Strengthening of the Promoter Pho that constructed last year
 +
The construction of plasmid pSB1C3-pho + RBS + T7RNA poLymerase + PT7 + RBS + RFP + ter.
 +
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box3">
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                        <p class="v1" id="In the construction of plasmid, we mainly did the following work:" style="text-align:  center; ">
 +
                            In the construction of plasmid, we mainly did the following work:
 +
                        </p>
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                         <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">Collaboration with ASTWS-China team and HFLS_ZhejiangUnited team.</p>
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                         <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">Plasmid DNA extraction</p>
 
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                     </div>
                        
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 +
                    <div>
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                       <p class="itemstyle">
 +
                          ①Transfer 1.5mL of the culture to a Eppendorf tube. Centrifuge at 8000rpm for 5 minutes. Discard the supernatant. Add 280μL of resuspension solution(P1 buffer). Completely resuspent cell pellet.
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                        </p>
 
                         <p class="itemstyle">
 
                         <p class="itemstyle">
                             During the interlab experiment, we cooperated with ASTWS-China team and HFLS_ZhejiangUnited team, we provided the ASTWS-China team with E. coli DH5a and 100μl silicon beads that had better quality as well as gave HFLS_ZhejiangUnited team the transcriptional shaking table bacteria solution and some experimental equipment (chloramphenicol resistance, gun head, etc.). At the same time, we also borrowed the glycerin bacteria we needed from the ASTWS-China team.
+
                             ② Add 200μL of lysis solution(Buffer P2) and mix gently. Set aside for 1 minute.
 
                         </p>
 
                         </p>
                    </div>
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                        <p class="itemstyle">
                    <div class="xshs-box2">
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                             ③Add 200 μL of neutralizing solution(P3 buffer) and mix by inverting the tubes for 5-10 times.
                        <p>
+
                             <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/a/ab/T--worldshaper-XSHS--c001.png" />
+
 
                         </p>
 
                         </p>
                    </div>
 
                    <div class="xshs-box3">
 
 
                         <p class="itemstyle">
 
                         <p class="itemstyle">
                             During the experiment, we lent ASTWS-China team kit1 and kit2, which enables its students to extract the useful DNA.
+
                             ④Centrifuge at 12000rpm for 10 min and carefully transfer the supernatant to a adsorption column. Centrifuge at 8000rpm for 30sec, and remove the supernatant.Add 500μL of DW1 Buffer and centrifuge at 8000rpm for 30sec.
 
                         </p>
 
                         </p>
 
                         <p class="itemstyle">
 
                         <p class="itemstyle">
                             During the Collaborations, our research members visited HFLS_ZhejiangUnited team’s experiments and watched its members’ studying notes.
+
                             ⑤Add 500μL of Wash Solution and centrifuge at 9000rpm for 30sec. Repeat twice.
 
                         </p>
 
                         </p>
                    </div>
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                        <p class="itemstyle">
                    <div class="xshs-box2">
+
                             ⑥Centrifuge for 1min and open the lid for 1min to make the alcohol evaporate completely. Move the adsorption column to a new Eppendorf tube and add 30 μL of TE solution to obtain the plasmid DNA.
                        <p>
+
                             <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/3/35/T--worldshaper-XSHS--c002.png" />
+
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
                     <div class="xshs-box3">
+
 
 +
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 +
                        <div style="
 +
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                            height: 24px;
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                            background-color:  #0c3d0cd9;
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                            /* text-align: left!important; */
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                            margin-left:  0px;
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                            margin-top: 50px;
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                        <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">Transformation</p>
 +
                    </div>
 +
 
 +
                    <div>
 +
                      <p class="itemstyle">
 +
                          ① Thaw 100µL competent E. coli DH5α cells on ice until it is no longer frozen.
 +
                        </p>
 
                         <p class="itemstyle">
 
                         <p class="itemstyle">
                            Because our conversion process——A procedure that obtaining the desired plasmid from the distribution kits—— always failed,we communicated with ASTWS-China team, eliminating the possibilities derived from operate miss and finding the cause of the problem: Homemade E. coli receptive state.
+
                          ②Add 10µL ligation product into 100µL competent E. coli DH5α cells suspension, and then carefully flick the tube 4-5 times to mix cells and DNA.
 
                         </p>
 
                         </p>
                    </div>
+
                        <p class="itemstyle">
                    <div class="xshs-box2">
+
                            ③Place the mixture on ice for 30 minutes.
                         <p>
+
                        </p>
                            <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/b/bb/T--worldshaper-XSHS--c003.png" />
+
                        <p class="itemstyle">
 +
                            ④Heat shock at exactly 42°C for exactly 90 seconds. Then place the mixture on ice for 1 minutes.
 +
                         </p>
 +
                        <p class="itemstyle">
 +
                            ⑤Pipette 1 ml of room temperature LB media into the mixture. Incubate the mixture at 37°C with vigorous shaking for 60 minutes.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑥Plate the mixture onto LB agar media containing antibiotic (ampicillin/ chloramphenicol). Incubate overnight at 37°C with plates upside down.
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
  
 +
                    <div class="xshs-box3">
 +
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                        <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">Preparing electrocompetent bacteria</p>
 +
                    </div>
 +
 +
                    <div>
 +
                      <p class="itemstyle">
 +
                          ◆Before we start: preparing freshly grown E. coli DH5α cells
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ①Preparing the CaCl2 solution at a concentration of 0.1mol/L
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ②Incubate 50µL E. coli DH5α cell suspension into 4ml LB media at 37°C with shaking in centrifugal speed of 200rpm overnight (without antibiotic).
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ③The next day, incubate the 1mL Bacterial suspension at 37°C with shaking in centrifugal speed of 200rpm until the OD600 is approximately 0,5(+-0,1)
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ④Add 25mL above incubated suspension into centrifuge (with gauge of 50mL) tube and centrifuge for 10min at 4 ℃ in centrifugal speed of 4000rpm.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑤Discard the filtrate.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑥Add 21ml of the prepared CaCl2 solution into precipitated bacteria. Incubate the mixture on ice for 20min.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑦Centrifuge the above suspension for 10min at 4 ℃ in centrifugal speed of 4000rpm.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑧Discard the filtrate.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ⑨Add 3.4ml of the prepared CaCl2 solution (precooled) and 0.6mL of pure glycerol into the suspension.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑩Split charge the product into eppendorf tubes, each 100µL, and cryopreservation at -80℃.
 +
                        </p>
 +
                    </div>   
 +
                   
 
                     <div class="xshs-box3">
 
                     <div class="xshs-box3">
                         <p class="v1" id="OurSchool"style="text-align:  center; "> Collaborations with other teams</p>
+
                         <p class="v1" id="The Construction of Plasmids" style="text-align:  center; ">
 +
                            The Construction of Plasmids
 +
                        </p>
 
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                         "><div style="width:20px;">   
 
                         </div>
 
                         </div>
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                        <div class="xshs-box3">
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                        <div style="
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                            height: 24px;
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                            background-color:  #0c3d0cd9;
 +
                            /* text-align: left!important; */
 +
                            margin-left:  0px;
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 +
                        <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;"> Construction of the Series Plasmids of Nox</p>
 +
                    </div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            (1)pSB1C3-Pnox
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/6/62/T--Worldshaper-XSHS--me001.png" />
 +
      </p>
 +
</div>
 +
                   
 +
                    <div class="xshs-box3">
 +
   
 +
    <p class="itemstyle" style="font-size:12px!important;margin-left:209px;text-align: center!important;">
 +
                          Figure 1. pSB1C3-Pnox
 +
    </p>
 +
</div>
 +
                        <div>
 +
                        <p class="itemstyle">
 +
                          ① Expande the newly synthesized pGH-nox plasmid transformed glycerol stocks in 3mL LB media.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                        ②Extract the plasmid from 3mL of the above bacteria suspension and elute with 30µL Elution buffer.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ③Do restriction enzyme digestion of pGH-nox with the restriction enzymes EcoRI and PstI in 50µL system.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ④Run DNA gel electrophoresis of the production of pGH-nox digestion  in 3µL system. Confirm that the restriction enzymes digestion is successful. Get the product of enzyme digestion purified and then eluted by 30µL Elution buffer.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑤Ligate the extractive together with new vector by ligase overnight in temperature of 16℃.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑥Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑦After overnight incubation, inoculate five freshly grown single colony and incubate each with 1.5 mL LB medium overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑧Extract 5 tubes of plasmid from the above bacteria suspension and do restriction enzyme digestion of the plasmid with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑧Extract 5 tubes of plasmid from the above bacteria suspension and do restriction enzyme digestion of the plasmid with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            (2) pSB1C3-Pnox+RBS+BFP、pSB1C3-Pnox+RFP
 +
                        </p>
 
                          
 
                          
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/6/65/T--Worldshaper-XSHS--me002.png" />
 +
      </p>
 +
</div>
 +
<div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/4/46/T--Worldshaper-XSHS--me003.png" />
 +
      </p>
 +
</div>
 +
               
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                          ①Do restriction enzyme digestion of existing plasmids pSB1C3- BFP, pSB1C3- RFP with the restriction enzymes EcoRI and XbaI.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                        ②Do restriction enzyme digestion of the plasmid pGH-nox with the restriction enzymes EcoRI and SPeI.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ③Ligate the extractive together with new vector (digested pSB1C3- BFP、pSB1C3- RFP) by ligase overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ④Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑤After overnight incubation, inoculate five freshly grown single colony and incubate each with 1.5 mL LB medium overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑥Extract 5 tubes of plasmid from the above bacteria suspension and do restriction enzyme digestion of the plasmid with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            (3) The Monitoring of Fluorescence Protein
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            PSB1C3-nox is also induced into fluorescence without nicotine, indicating that nox was a non-inducible promoter.
 +
                        </p>
 +
                    </div>
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/2/29/T--Worldshaper-XSHS--me004.png" />
 +
      </p>
 +
</div>
 +
                    <div class="xshs-box3">
 
                         <div style="
 
                         <div style="
 
                             width: 5px;
 
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                             margin-top: 50px;
 
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                         "></div>
 
                         "></div>
                            <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">Collaboration with ZJU-China team.</p>
+
                        <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;"> Construction of Nica Series plasmids</p>
 +
                    </div>
  
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            (1)the Construction of the first version plasmids of nica(pMD-Pnica1 + RBS + GFP + ter,pMD/pSB1C3-Pnica2 + RBS + GFP + ter)
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ①Design the primer including predictive promoter and RBS, using pSB1C3-GFP plasmid as template, through the polymerase chain reaction amplifying the plasmids containing Pnica1+RBS+GFP+ter (69 ℃ annealing and 72 ℃ extending for 2 minutes) and Pnica2+RBS+GFP+ter (69 ℃ annealing and 72 ℃ extending for 2 minutes) .
 +
                        </p>
 
                         <p class="itemstyle">
 
                         <p class="itemstyle">
                             The aspect about experimental problem: Because of the invalid homemade E. coli receptive state, we did experiments in the ZJU-China team’s laboratories by utilizing its commercial E. coli receptive state. This attempt provided enough opportunities for us to discuss the difference between the experiments, which exerted great advantage to solve such problems in the nest phase.
+
                             ②Purify the genetic segments of Pnica1+RBS+GFP+ter (whose length is about 1Kb) and Pnica2 + RBS + GFP + ter (whose length is about 1Kb).
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
 +
 
                     <div class="xshs-box2">
 
                     <div class="xshs-box2">
                        <p>
+
    <p>
                            <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/7/74/T--worldshaper-XSHS--c004.png" />
+
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/e/ea/T--Worldshaper-XSHS--me005.png" />
 +
      </p>
 +
</div>
 +
 
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            ③Ligate two genetic segments together with T-vector by T4 DNA ligase.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ④Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑤After overnight incubation, inoculate three freshly grown single colony and incubate each with 3 mL LB medium overnight.
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
                     <div class="xshs-box3">
+
 
 +
                     <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/a/a6/T--Worldshaper-XSHS--me006.png" />
 +
      </p>
 +
</div>
 +
 
 +
                    <div>
 
                         <p class="itemstyle">
 
                         <p class="itemstyle">
                             Before carrying out publicity activities, our team made comprehensive discussions with the ZJU-China team like establishing programs of activities, preparing materials, and decorating the venues.
+
                             ⑥Extract plasmids from the above bacteria suspension, each 3 tubes of 1.5mL, and do restriction enzyme digestion of the plasmids with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing.
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
 +
 
                     <div class="xshs-box2">
 
                     <div class="xshs-box2">
                        <p>
+
    <p>
                            <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/e/e1/T--worldshaper-XSHS--c005.png" />
+
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/6/62/T--Worldshaper-XSHS--me007.png" />
 +
      </p>
 +
</div>
 +
 
 +
<div class="xshs-box3">
 +
    <p class="itemstyle" style="font-size:12px!important;margin-left:209px;text-align: center!important;">
 +
                          pMD-Pnica1+RBS+GFP+terand pMD-Pnica2+RBS+GFP+ter Enzyme digestion map 
 +
    </p>
 +
    <p class="itemstyle" style="font-size:12px!important;margin-left:209px;text-align: center!important;">
 +
                          Lane 1:pMD-Pnica1+RBS+GFP+ter-1; Lane 2:pMD-Pnica1+RBS+GFP+ter-2
 +
    </p>
 +
    <p class="itemstyle" style="font-size:12px!important;margin-left:209px;text-align: center!important;">
 +
                          Lane 3:pMD-Pnica1+RBS+GFP+ter-3; Lane4:pMD-Pnica2+RBS+GFP+ter-1
 +
    </p>
 +
    <p class="itemstyle" style="font-size:12px!important;margin-left:209px;text-align: center!important;">
 +
                          Lane 5: blank; Lane 6;pMD-Pnica2+RBS+GFP+ter-2; Lane7:pMD-Pnica2+RBS+GFP+ter-3
 +
    </p>
 +
</div>
 +
 
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            ⑦.The result shows that pMD-Pnica1+RBS+GFP+ter-3 (nica1-3) and pMD-Pnica2+RBS+GFP+ter-1 (nica2-1) sequencing results matched the reference sequences (in which nica2-1 was reverse connected with T-vector).
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑧Using the above bacteria to detect the expression of green fluorescent protein of different colonies. The result as in figure 8, from which we indicated that Pnica1 was a nicotine non-inducible promoter. While the plasmid pMD-Pnica2+RBS+GFP+ter-1  transformed bacteria did not express GFP in the absence of nicotine, suggesting that Pnica2 might be a nicotine inducible promoter.
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
  
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/7/7c/T--Worldshaper-XSHS--me008.png" />
 +
      </p>
 +
</div>
 +
<div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/d/df/T--Worldshaper-XSHS--me009.png" />
 +
      </p>
 +
</div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            ⑨ In order to further verify whether Pnica2 is a nicotine inducible promoter, we compounded a LB agar medium with nicotine concentration of 5g/L, and plated 10µL plasmid pMD-Pnica2-RBS-GFP-ter-1  transformed bacteria suspension (which is produce by bacterial glycerol stock overnight incubation) droplets on it, then incubate it overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ⑩Observe the medium under a fluorescence microscope and we found that there was weak green fluorescence. This result shows that nica2 is a nicotine inducible promoter as shown in the following picture.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/8/8b/T--Worldshaper-XSHS--me010.png" />
 +
      </p>
 +
</div>
 +
 +
                <div>
 +
                        <p class="itemstyle">
 +
                            ⑪Do restriction enzyme digestion of the plasmid pMD-Pnica2 + RBS + GFP + ter with the restriction enzymes EcoRI and PstI in 50µL system.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ⑫.Purify the genetic segment Pnica2 + RBS + GFP + ter (whose length is about 1kb) , and ligate the segments together with linear pSB1C3-vector by T4 DNA ligase.
 +
Successfully complete the construction of the plasmid pSB1C3-Pnica2 + RBS + GFP + ter.
 +
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            (2) the construction of the second version of Nica series plasmid (pMD/pSB1C3-Pnica2+RBS+T7RNA poLymerase +PT7 +RBS +GFP+ter)
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          1.Design the primer including predictive promoter and RBS, using the plasmid pXS-Oxy4 (pSB1C3-Pvgb +RBS+T7RNA poLymerase+ PT7+RBS+GFP+ter) as template, through the polymerase chain reaction amplifying the genetic segment Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            2.Get the genetic segment Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter purified and store the product in single eppendorf tube.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/0/02/T--Worldshaper-XSHS--me011.png" />
 +
      </p>
 +
</div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            3.Ligate the genetic segment Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter together with T-vector by T4 DNA ligase.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          4.Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.
 +
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑤5.After overnight incubation, inoculate twenty four freshly grown single colony and incubate each with 3 mL LB medium overnight.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/d/d0/T--Worldshaper-XSHS--me012.png" />
 +
      </p>
 +
</div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            6.Using the primers T7poLy-F and the universal primer M13-F on the T vector, the PMD-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter plasmid was used as a template PCR to verify whether the reverse insertion was performed. The size of the clone insert 21 does not match and should be about 4 kb. Therefore, the second method (directed insertion) is used to insert Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter into the T vector.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/6/6a/T--Worldshaper-XSHS--me013.png" />
 +
      </p>
 +
</div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            7.Extract plasmid from the above bacteria suspension with gene forward inserted plasmid pMD-Pnica2 + RBS + T7RNA poLymerase + PT7 + RBS + GFP + ter, and do restriction enzyme digestion of the plasmid with the restriction enzymes EcoRI and PstI in 50µL system.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/a/a6/T--Worldshaper-XSHS--me014.png" />
 +
      </p>
 +
</div>
 +
<div class="xshs-box3">
 +
    <p class="itemstyle" style="font-size:12px!important;margin-left:209px;text-align: center!important;">
 +
                          Bottom: Linear T carrier 
 +
    </p>
 +
</div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            10.Purify the genetic segments Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter and linear T-vector and ligate the two segments together by T4 DNA ligase overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            10.Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            10.After overnight incubation, the medium didn't form any bacteria strain. So we decide to take the third method into action:
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ligate the genetic segment Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter together with pUC-19 vector (circular) by T4 DNA ligase.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            11.Transform 1µL of the ligation product into competent E. coli DH5α cells. Plate 100µL of the transformation product onto a LB agar medium and incubate it at 37°C overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            12.After overnight incubation, inoculate four freshly grown single colony and incubate each with 2 mL LB medium overnight.
 +
                        </p>
 +
                    </div>
 +
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/8/8e/T--Worldshaper-XSHS--me015.png" />
 +
      </p>
 +
</div>
 +
 +
                <div>
 +
                    <p class="itemstyle">
 +
                            13.Extract plasmids from the above bacteria suspension, and do restriction enzyme digestion of the plasmid pUC-19 with the restriction enzymes EcoRI and PstI. Then send them for sequencing, confirm that the experimental result is correct.
 +
                        </p>
 +
                </div>
 +
 +
                <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/2/22/T--Worldshaper-XSHS--me016.png" />
 +
      </p>
 +
</div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            14.Purify the genetic segments Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter and ligate the segment together with linear vector pUC-19 and pSB1C3 by T4 DNA ligase overnight at 16℃.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            15.Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            16.After overnight incubation, inoculate five freshly grown single colony and incubate each with 2 mL LB medium overnight.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/5/5e/T--Worldshaper-XSHS--me017.png" />
 +
      </p>
 +
</div>
 +
<div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/d/dd/T--Worldshaper-XSHS--me018.png" />
 +
      </p>
 +
</div>
 +
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            17.Extract plasmids from the above bacteria suspension, each 5 tubes of 1.5mL,  and do restriction enzyme digestion of the plasmids with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing, confirm that the experimental result is correct.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/6/6d/T--Worldshaper-XSHS--me019.png" />
 +
      </p>
 +
</div>
 +
<div class="xshs-box3">
 +
    <p class="itemstyle" style="font-size:12px!important;margin-left:209px;text-align: center!important;">
 +
                          1:pSB1C3-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter Enzyme digestion image
 +
    </p>
 +
    <p class="itemstyle" style="font-size:12px!important;margin-left:209px;text-align: center!important;">
 +
                          2 :pUC-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter Enzyme digestion image
 +
    </p>
 +
</div>
 +
 +
                <div>
 +
                        <p class="itemstyle">
 +
                            18.The LB solid medium having a nicotine concentration of 5 g/L was placed, and the plate was inverted, and 10 μL of pUC-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter glycerol bacteria droplets were placed on the plate and cultured overnight.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ⑲The plate was observed under a fluorescence microscope, and as a result, it was found that the expression level of GFP was significantly increased.
 +
                        </p>
 +
                    </div>
 +
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="​​
 +
https://static.igem.org/mediawiki/2018/e/e7/T--Worldshaper-XSHS--me020.png
 +
​" />
 +
      </p>
 +
</div>
 +
<div class="xshs-box3">
 +
    <p class="itemstyle" style="font-size:12px!important;margin-left:209px;text-align: center!important;">
 +
                          Droplet edge fluorescent protein map (a: under white light b: under blue light excitation)
 +
    </p>
 +
</div>
  
 
                     <div class="xshs-box3">
 
                     <div class="xshs-box3">
                         <p class="v1" id="Others"style="text-align: center;">Collaborations with social organizations</p>
+
                         <p class="v1" id="Sensitivity detection" style="text-align: center; ">
 +
                            Sensitivity detection
 +
                        </p>
 
                         <div style="
 
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                             margin-top: 40px;
                         ">
+
                         "><div style="width:20px;">   
                          
+
                         </div>
                         <div class="xshs-box3">
+
 
                            <div style="
+
                         <div class="xshs-box3">  
 +
                        <div style="
 
                             width: 5px;
 
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                         "></div>
                            <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">Collaboration with Zhejiang Province Science Museum</p>
+
                        <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;"> Experimental purpose</p>
                        </div>
+
                    </div>
                       
+
 
                         <p class="itemstyle" style="margin-left: 0px;width: 1100;">
+
                    <div>
                          We cooperated with Science museum and did some simple experiments in the venue stadium, which is not only appeals visitors, but also facilitates to promote the IGEM project and knowledge about synthetic biology.
+
                         <p class="itemstyle">
 +
                            Experiment sensitivity of the designed monitoring system. In other words, we are going to find the minimum nicotine concentration that can induce the First Version of Monitoring System's (with plasmid pMD-Pnica2 + RBS + GFP + ter transformed) expression by experimenting OD600 and the fluorescence value of the bacteria suspension at the wavelength of 475-530nm in different times by using enzyme-labeled instrument, and compare with that of the Second Version of Monitoring System (with plasmid pMD-Pnica2 + RBS + T7RNA poLymerase + PT7 + RBS + GFP + ter transformed).  
 
                         </p>
 
                         </p>
                        <div class="xshs-box3">
+
                    </div>
                            <div style="
+
 
 +
                    <div class="xshs-box3">  
 +
                        <div style="
 
                             width: 5px;
 
                             width: 5px;
 
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                         "></div>
                            <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">Collaborations with Zhejiang Science and Technology Market</p>
+
                        <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;"> Experimental design</p>
                        </div>
+
                    </div>
                       
+
 
                         <p class="itemstyle" style="margin-left: 0px;width: 1100;">
+
                    <div>
                          During the science and technology week held by Zhejing Science administrators, we collaborated with organizers. In that exhibition, we conducted a questionnaire survey as well as advertised the JGEM project, thus, enriching the program’s content.
+
                         <p class="itemstyle">
 +
                            Activated E. coli
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ①Add 30µL plasmid pMD-Pnica2+RBS+GFP+ter transformed bacterial glycerol stock into a 10ml centrifuge tube containing 3mL LB media with 3µL Amp (in concentration of 1%), incubate at centrifugal speed of 200rpm at 37℃ overnight for 14h,measured that the final OD600=0.8.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ② Add 90µL the above suspension into a 10ml centrifuge tube containing 3mL LB media with 3µL Amp (in concentration of 3%), incubate at centrifugal speed of 200rpm at 37℃ for 5h,measured that the final OD600=0.4.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ③Add 30µL plasmids pMD-Pnica2+RBS+GFP+ter and pMD-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter transformed bacterial glycerol stocks into two 10ml centrifuge tubes containing 3mL LB media with 3µL Amp (in concentration of 1%) respectively, incubate at centrifugal speed of 200rpm at 37℃ overnight for 14h,measured that the final OD600=1.3 and 1.1 respectively.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ④Add 90µL the above suspensions into two 10ml centrifuge tubes containing 3mL LB media with 3µL Amp (in concentration of 3%), incubate at centrifugal speed of 200rpm at 37℃ for approximately 5h,measured that the final OD600 are both approximately 0.4.
 
                         </p>
 
                         </p>
                     
 
 
                     </div>
 
                     </div>
                      
+
 
 +
                     <div class="xshs-box3">
 +
                        <div style="
 +
                            width: 5px;
 +
                            height: 24px;
 +
                            background-color:  #0c3d0cd9;
 +
                            /* text-align: left!important; */
 +
                            margin-left:  0px;
 +
                            border:  none;
 +
                            margin-top: 50px;
 +
                        "></div>
 +
                        <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">  Prepare a nicotine gradient solution</p>
 +
                    </div>
 +
 
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            Purchase the nicotine solution at a concentration of 1.0g/mL. Then dissolve the nicotine solution by LB media with Amp, add 100µL mixture into the 96 hole plate with flat black bottom per well.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            Experiment 1: (of the first version)
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ①.Prepare the nicotine solution at different concentrations of 0 g/mL, 0.02 g/mL, 0.04 g/mL, 0.08 g/mL,0.16 g/mL, 0.32 g/mL, 0.64 g/mL, 1.28 g/mL, 2.56 g/mL, 5.12 g/mL, 10.24 g/mL.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ②Set up three sets of experiments. Add the plasmid MD-Pnica2+RBS+GFP+ter transformed bacteria (whose OD600 is approximately 0.4) in concentration of approximately 3% (3µL) to the 96 hole plate with flat black bottom per well and incubated at centrifugal speed of 150rpm at 37 ℃. Measure the OD600 values and fluorescence values every two hours.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            Experiment 2: (of the first version)
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ①Prepare the nicotine solution at different concentrations of 0 g/mL, 0.001 g/mL, 0.01 g/mL,0.1 g/mL,1 g/mL.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ②Set up five sets of experiments. Add the plasmid MD-Pnica2+RBS+GFP+ter transformed bacteria (whose OD600 is approximately 0.4) in concentration of approximately 3% (3µL) to the 96 hole plate with flat black bottom per well and incubated at centrifugal speed of 150rpm at 37 ℃. Measure the OD600 values and fluorescence values each hour.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            Experiment 3: (the Comparison of the First and the Second Version Monitoring System)
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ①.Prepare the nicotine solution at different concentrations of 0 g/mL, 0.0001 g/mL, 0.001 g/mL,0.01 g/mL.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                            ②Set up five sets of experiments. Add the plasmid MD-Pnica2+RBS+GFP+ter and plasmid pMD-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter transformed bacteria (whose OD600 is approximately 0.4) in concentration of approximately 3% (3µL) to the 96 hole plate with flat black bottom per well and incubated at centrifugal speed of 150rpm at 37 ℃. Measure the OD600 values and fluorescence values every two hours.
 +
                        </p>
 +
                    </div>
 +
 
 +
                    <div class="xshs-box3">
 +
                        <div style="
 +
                            width: 5px;
 +
                            height: 24px;
 +
                            background-color:  #0c3d0cd9;
 +
                            /* text-align: left!important; */
 +
                            margin-left:  0px;
 +
                            border:  none;
 +
                            margin-top: 50px;
 +
                        "></div>
 +
                        <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">  results analysis</p>
 +
                    </div>
 +
 
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            ①The result of the First Experiment shows that high concentration (above 1.28g/L) of nicotine had a strong inhibitory effect on the growth of Escherichia coli, which affected the expression of GFP in Escherichia coli, so we reduce the range of nicotine concentration and carry out the Second Experiment.
 +
                        </p>
 +
                    </div>
 +
 
 
                     <div class="xshs-box2">
 
                     <div class="xshs-box2">
                         <p>
+
    <p>
                             <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/a/a6/T--worldshaper-XSHS--c006.png" />
+
        <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/2/25/T--Worldshaper-XSHS--me021.png
 +
​​
 +
" />
 +
      </p>
 +
</div>
 +
 
 +
                <div>
 +
                         <p class="itemstyle">
 +
                             ② The result of the Second Experiment shows that the fluorescence expression of nicotine when the concentration of nicotine is C=0.01g/L increased steadily within 4 hours, but that of C=0. 001g/L was unstable. In addition, when the concentration of nicotine is within C=0.1g/L and C=1g/L had obvious toxic effect on the bacteria strain.
 +
                        </p>
 +
                    </div>
 +
 
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/1/1b/T--Worldshaper-XSHS--me022.png
 +
​​
 +
" />
 +
      </p>
 +
</div>
 +
 
 +
                <div>
 +
                        <p class="itemstyle">
 +
                            ③The result of the Third Experiment shows that when nicotine concentration was as low as 0.0001g/L, fluorescence expression appears in the second version monitoring system at 1h and steadily increased within 1-3h, while fluorescence expression in the first version monitoring system only appears at 4 h. The result shows that the second version monitoring system greatly improves the induction of nicotine.
 +
                        </p>
 +
                    </div>
 +
 
 +
                    <div class="xshs-box2">
 +
    <p>
 +
        <img class="img-responsive" alt="" src="https://static.igem.org/mediawiki/2018/6/6b/T--Worldshaper-XSHS--me023.png
 +
​​
 +
" />
 +
      </p>
 +
</div>
 +
 
 +
                    <div class="xshs-box3">
 +
                        <p class="v1" id="Appendix" style="text-align:  center; ">
 +
                            Appendix
 +
                        </p>
 +
                        <div style="
 +
                            width: 100%;
 +
                            margin: 0 auto;
 +
                            margin-top: -34px;
 +
                        ">
 +
                        <hr style="
 +
                            height: 3px;
 +
                            background-color: #0c3d0c99!important;
 +
                            margin-top: 40px;
 +
                        "><div style="width:20px;">   
 +
                        </div>
 +
 
 +
                        <div class="xshs-box3">
 +
                        <div style="
 +
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 +
                            height: 24px;
 +
                            background-color:  #0c3d0cd9;
 +
                            /* text-align: left!important; */
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                        <p style="width: 800px;margin-left: 11px;margin-top: -23px;font-size: 22px;margin-bottom: 20px;">  promoter source and sequence</p>
 +
                    </div>
 +
 
 +
                    <div>
 +
                        <p class="itemstyle">
 +
                            ①Promoter nox: gaining from the article 《Cloning of a Novel Nicotine Oxidase Gene from Pseudomonas sp.Strain HZN6 Whose Product NonenantioseLectively Degrades Nicotine to Pseudooxynicotine》
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          From website: https://www.ncbi.nlm.nih.gov/nuccore/JN391188.2
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          Length: about 400bp
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          Note: add the restriction enzymes EcoRI, XbaI restriction enzyme cutting sites at the left end and the SpeI, PstI restriction cutting enzyme sites at the right end.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          Sequence(5'-3'):
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          gagcagcaatacggtttttcaattgcagtcaaggcgggcgggtttctttatatcggtggcgtaacagccgttgataaagagggaaatgaagtatacgccaatgatgctaacaagcaaatgcagcttatttatgagcgtctgggtgcgatcctggccgctcatgatgcagacttcagtaacgttgttagtgaaactatctattataccaccgataatgaaagttacattaaatctGtagacgtcagaactgctgcgtataagggcgtaatagcaccaagtgcatctggcgtcagggttgccgatttcttgagcgacaagacgcttatagaaataacagctgtagcttatctcggcgaataagtgggctgccagtttcatcggttctgtagattcgcaacgatactaaaggtgtcagaca
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ②Promoter nica1/nica2: gaining from the article 《A Novel Gene, Encoding 6-Hydroxy-3-SµccinoyLpyridine Hydroxylase,Involved in Nicotine Degradation by Pseudomonas putida Strain S16》 and with the help of NCBI to predict these two possible promoter
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          From website: https://www.ncbi.nlm.nih.gov/search/?term=+DQ988162
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          Length of nica1: 46bp
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          Length of nica2: 34bp
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          Note: The promoter is designed in the primer, and the ECORI, XbaI restriction enzyme cutting sites is added at the left end and the SpeI, PstI restriction enzyme cutting sites is added at the right end.
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          Sequence of nica1 (5'-3'):
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          ttcagatggcacaggtgcgaaaccctcgttataatccggccactta
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          Sequence of nica2 (5'-3'):
 +
                        </p>
 +
                        <p class="itemstyle">
 +
                          Ttcgtagtacctgtttgtattgggccggtagcat
 
                         </p>
 
                         </p>
 
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                        <p class="v1" id="Experimental system" style="text-align:  center; ">
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                            Experimental system
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Revision as of 17:37, 17 October 2018

Protocols-methods

The main purpose of our experiment is as follows:


1 Screening of Nicotine Inductive Promoter and Construction of the First Version of Nicotine Monitoring System

①The construction of plasmids pSB1C3-Pnox + RBS + GFP + ter,pSB1C3-Pnox + RBS + BFP,pSB1C3-Pnox + RBS + RFP + ter,pSB1C3-Pnox.

②The construction of plasmids pMD-Pnica1 + RBS + GFP + ter,pMD-Pnica2 + RBS + GFP + ter.

2 The Construction of the Second Version of Nicotine Monitoring System The construction of plasmid pMD-Pnica2 + RBS + T7RNA poLymerase + PT7 + RBS + GFP + ter.

3 The Strengthening of the Promoter Pho that constructed last year The construction of plasmid pSB1C3-pho + RBS + T7RNA poLymerase + PT7 + RBS + RFP + ter.

In the construction of plasmid, we mainly did the following work:


Plasmid DNA extraction

①Transfer 1.5mL of the culture to a Eppendorf tube. Centrifuge at 8000rpm for 5 minutes. Discard the supernatant. Add 280μL of resuspension solution(P1 buffer). Completely resuspent cell pellet.

② Add 200μL of lysis solution(Buffer P2) and mix gently. Set aside for 1 minute.

③Add 200 μL of neutralizing solution(P3 buffer) and mix by inverting the tubes for 5-10 times.

④Centrifuge at 12000rpm for 10 min and carefully transfer the supernatant to a adsorption column. Centrifuge at 8000rpm for 30sec, and remove the supernatant.Add 500μL of DW1 Buffer and centrifuge at 8000rpm for 30sec.

⑤Add 500μL of Wash Solution and centrifuge at 9000rpm for 30sec. Repeat twice.

⑥Centrifuge for 1min and open the lid for 1min to make the alcohol evaporate completely. Move the adsorption column to a new Eppendorf tube and add 30 μL of TE solution to obtain the plasmid DNA.

Transformation

① Thaw 100µL competent E. coli DH5α cells on ice until it is no longer frozen.

②Add 10µL ligation product into 100µL competent E. coli DH5α cells suspension, and then carefully flick the tube 4-5 times to mix cells and DNA.

③Place the mixture on ice for 30 minutes.

④Heat shock at exactly 42°C for exactly 90 seconds. Then place the mixture on ice for 1 minutes.

⑤Pipette 1 ml of room temperature LB media into the mixture. Incubate the mixture at 37°C with vigorous shaking for 60 minutes.

⑥Plate the mixture onto LB agar media containing antibiotic (ampicillin/ chloramphenicol). Incubate overnight at 37°C with plates upside down.

Preparing electrocompetent bacteria

◆Before we start: preparing freshly grown E. coli DH5α cells

①Preparing the CaCl2 solution at a concentration of 0.1mol/L

②Incubate 50µL E. coli DH5α cell suspension into 4ml LB media at 37°C with shaking in centrifugal speed of 200rpm overnight (without antibiotic).

③The next day, incubate the 1mL Bacterial suspension at 37°C with shaking in centrifugal speed of 200rpm until the OD600 is approximately 0,5(+-0,1)

④Add 25mL above incubated suspension into centrifuge (with gauge of 50mL) tube and centrifuge for 10min at 4 ℃ in centrifugal speed of 4000rpm.

⑤Discard the filtrate.

⑥Add 21ml of the prepared CaCl2 solution into precipitated bacteria. Incubate the mixture on ice for 20min.

⑦Centrifuge the above suspension for 10min at 4 ℃ in centrifugal speed of 4000rpm.

⑧Discard the filtrate.

⑨Add 3.4ml of the prepared CaCl2 solution (precooled) and 0.6mL of pure glycerol into the suspension.

⑩Split charge the product into eppendorf tubes, each 100µL, and cryopreservation at -80℃.

The Construction of Plasmids


Construction of the Series Plasmids of Nox

(1)pSB1C3-Pnox

Figure 1. pSB1C3-Pnox

① Expande the newly synthesized pGH-nox plasmid transformed glycerol stocks in 3mL LB media.

②Extract the plasmid from 3mL of the above bacteria suspension and elute with 30µL Elution buffer.

③Do restriction enzyme digestion of pGH-nox with the restriction enzymes EcoRI and PstI in 50µL system.

④Run DNA gel electrophoresis of the production of pGH-nox digestion in 3µL system. Confirm that the restriction enzymes digestion is successful. Get the product of enzyme digestion purified and then eluted by 30µL Elution buffer.

⑤Ligate the extractive together with new vector by ligase overnight in temperature of 16℃.

⑥Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.

⑦After overnight incubation, inoculate five freshly grown single colony and incubate each with 1.5 mL LB medium overnight.

⑧Extract 5 tubes of plasmid from the above bacteria suspension and do restriction enzyme digestion of the plasmid with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing.

⑧Extract 5 tubes of plasmid from the above bacteria suspension and do restriction enzyme digestion of the plasmid with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing.

(2) pSB1C3-Pnox+RBS+BFP、pSB1C3-Pnox+RFP

①Do restriction enzyme digestion of existing plasmids pSB1C3- BFP, pSB1C3- RFP with the restriction enzymes EcoRI and XbaI.

②Do restriction enzyme digestion of the plasmid pGH-nox with the restriction enzymes EcoRI and SPeI.

③Ligate the extractive together with new vector (digested pSB1C3- BFP、pSB1C3- RFP) by ligase overnight.

④Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.

⑤After overnight incubation, inoculate five freshly grown single colony and incubate each with 1.5 mL LB medium overnight.

⑥Extract 5 tubes of plasmid from the above bacteria suspension and do restriction enzyme digestion of the plasmid with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing.

(3) The Monitoring of Fluorescence Protein

PSB1C3-nox is also induced into fluorescence without nicotine, indicating that nox was a non-inducible promoter.

Construction of Nica Series plasmids

(1)the Construction of the first version plasmids of nica(pMD-Pnica1 + RBS + GFP + ter,pMD/pSB1C3-Pnica2 + RBS + GFP + ter)

①Design the primer including predictive promoter and RBS, using pSB1C3-GFP plasmid as template, through the polymerase chain reaction amplifying the plasmids containing Pnica1+RBS+GFP+ter (69 ℃ annealing and 72 ℃ extending for 2 minutes) and Pnica2+RBS+GFP+ter (69 ℃ annealing and 72 ℃ extending for 2 minutes) .

②Purify the genetic segments of Pnica1+RBS+GFP+ter (whose length is about 1Kb) and Pnica2 + RBS + GFP + ter (whose length is about 1Kb).

③Ligate two genetic segments together with T-vector by T4 DNA ligase.

④Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.

⑤After overnight incubation, inoculate three freshly grown single colony and incubate each with 3 mL LB medium overnight.

⑥Extract plasmids from the above bacteria suspension, each 3 tubes of 1.5mL, and do restriction enzyme digestion of the plasmids with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing.

pMD-Pnica1+RBS+GFP+terand pMD-Pnica2+RBS+GFP+ter Enzyme digestion map

Lane 1:pMD-Pnica1+RBS+GFP+ter-1; Lane 2:pMD-Pnica1+RBS+GFP+ter-2

Lane 3:pMD-Pnica1+RBS+GFP+ter-3; Lane4:pMD-Pnica2+RBS+GFP+ter-1

Lane 5: blank; Lane 6;pMD-Pnica2+RBS+GFP+ter-2; Lane7:pMD-Pnica2+RBS+GFP+ter-3

⑦.The result shows that pMD-Pnica1+RBS+GFP+ter-3 (nica1-3) and pMD-Pnica2+RBS+GFP+ter-1 (nica2-1) sequencing results matched the reference sequences (in which nica2-1 was reverse connected with T-vector).

⑧Using the above bacteria to detect the expression of green fluorescent protein of different colonies. The result as in figure 8, from which we indicated that Pnica1 was a nicotine non-inducible promoter. While the plasmid pMD-Pnica2+RBS+GFP+ter-1 transformed bacteria did not express GFP in the absence of nicotine, suggesting that Pnica2 might be a nicotine inducible promoter.

⑨ In order to further verify whether Pnica2 is a nicotine inducible promoter, we compounded a LB agar medium with nicotine concentration of 5g/L, and plated 10µL plasmid pMD-Pnica2-RBS-GFP-ter-1 transformed bacteria suspension (which is produce by bacterial glycerol stock overnight incubation) droplets on it, then incubate it overnight.

⑩Observe the medium under a fluorescence microscope and we found that there was weak green fluorescence. This result shows that nica2 is a nicotine inducible promoter as shown in the following picture.

⑪Do restriction enzyme digestion of the plasmid pMD-Pnica2 + RBS + GFP + ter with the restriction enzymes EcoRI and PstI in 50µL system.

⑫.Purify the genetic segment Pnica2 + RBS + GFP + ter (whose length is about 1kb) , and ligate the segments together with linear pSB1C3-vector by T4 DNA ligase. Successfully complete the construction of the plasmid pSB1C3-Pnica2 + RBS + GFP + ter.

(2) the construction of the second version of Nica series plasmid (pMD/pSB1C3-Pnica2+RBS+T7RNA poLymerase +PT7 +RBS +GFP+ter)

1.Design the primer including predictive promoter and RBS, using the plasmid pXS-Oxy4 (pSB1C3-Pvgb +RBS+T7RNA poLymerase+ PT7+RBS+GFP+ter) as template, through the polymerase chain reaction amplifying the genetic segment Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter.

2.Get the genetic segment Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter purified and store the product in single eppendorf tube.

3.Ligate the genetic segment Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter together with T-vector by T4 DNA ligase.

4.Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.

⑤5.After overnight incubation, inoculate twenty four freshly grown single colony and incubate each with 3 mL LB medium overnight.

6.Using the primers T7poLy-F and the universal primer M13-F on the T vector, the PMD-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter plasmid was used as a template PCR to verify whether the reverse insertion was performed. The size of the clone insert 21 does not match and should be about 4 kb. Therefore, the second method (directed insertion) is used to insert Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter into the T vector.

7.Extract plasmid from the above bacteria suspension with gene forward inserted plasmid pMD-Pnica2 + RBS + T7RNA poLymerase + PT7 + RBS + GFP + ter, and do restriction enzyme digestion of the plasmid with the restriction enzymes EcoRI and PstI in 50µL system.

Bottom: Linear T carrier

10.Purify the genetic segments Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter and linear T-vector and ligate the two segments together by T4 DNA ligase overnight.

10.Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.

10.After overnight incubation, the medium didn't form any bacteria strain. So we decide to take the third method into action:

ligate the genetic segment Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter together with pUC-19 vector (circular) by T4 DNA ligase.

11.Transform 1µL of the ligation product into competent E. coli DH5α cells. Plate 100µL of the transformation product onto a LB agar medium and incubate it at 37°C overnight.

12.After overnight incubation, inoculate four freshly grown single colony and incubate each with 2 mL LB medium overnight.

13.Extract plasmids from the above bacteria suspension, and do restriction enzyme digestion of the plasmid pUC-19 with the restriction enzymes EcoRI and PstI. Then send them for sequencing, confirm that the experimental result is correct.

14.Purify the genetic segments Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter and ligate the segment together with linear vector pUC-19 and pSB1C3 by T4 DNA ligase overnight at 16℃.

15.Transform the ligation product into competent E. coli DH5α cells. After centrifugation, discard the supernatant, get the product suspended and concentrated into 100µL, then plate it onto a LB agar medium and incubate at 37°C overnight.

16.After overnight incubation, inoculate five freshly grown single colony and incubate each with 2 mL LB medium overnight.

17.Extract plasmids from the above bacteria suspension, each 5 tubes of 1.5mL, and do restriction enzyme digestion of the plasmids with the restriction enzymes EcoRI and PstI in 10µL system. Then send them for sequencing, confirm that the experimental result is correct.

1:pSB1C3-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter Enzyme digestion image

2 :pUC-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter Enzyme digestion image

18.The LB solid medium having a nicotine concentration of 5 g/L was placed, and the plate was inverted, and 10 μL of pUC-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter glycerol bacteria droplets were placed on the plate and cultured overnight.

⑲The plate was observed under a fluorescence microscope, and as a result, it was found that the expression level of GFP was significantly increased.

Droplet edge fluorescent protein map (a: under white light b: under blue light excitation)

Sensitivity detection


Experimental purpose

Experiment sensitivity of the designed monitoring system. In other words, we are going to find the minimum nicotine concentration that can induce the First Version of Monitoring System's (with plasmid pMD-Pnica2 + RBS + GFP + ter transformed) expression by experimenting OD600 and the fluorescence value of the bacteria suspension at the wavelength of 475-530nm in different times by using enzyme-labeled instrument, and compare with that of the Second Version of Monitoring System (with plasmid pMD-Pnica2 + RBS + T7RNA poLymerase + PT7 + RBS + GFP + ter transformed).

Experimental design

Activated E. coli

①Add 30µL plasmid pMD-Pnica2+RBS+GFP+ter transformed bacterial glycerol stock into a 10ml centrifuge tube containing 3mL LB media with 3µL Amp (in concentration of 1%), incubate at centrifugal speed of 200rpm at 37℃ overnight for 14h,measured that the final OD600=0.8.

② Add 90µL the above suspension into a 10ml centrifuge tube containing 3mL LB media with 3µL Amp (in concentration of 3%), incubate at centrifugal speed of 200rpm at 37℃ for 5h,measured that the final OD600=0.4.

③Add 30µL plasmids pMD-Pnica2+RBS+GFP+ter and pMD-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter transformed bacterial glycerol stocks into two 10ml centrifuge tubes containing 3mL LB media with 3µL Amp (in concentration of 1%) respectively, incubate at centrifugal speed of 200rpm at 37℃ overnight for 14h,measured that the final OD600=1.3 and 1.1 respectively.

④Add 90µL the above suspensions into two 10ml centrifuge tubes containing 3mL LB media with 3µL Amp (in concentration of 3%), incubate at centrifugal speed of 200rpm at 37℃ for approximately 5h,measured that the final OD600 are both approximately 0.4.

Prepare a nicotine gradient solution

Purchase the nicotine solution at a concentration of 1.0g/mL. Then dissolve the nicotine solution by LB media with Amp, add 100µL mixture into the 96 hole plate with flat black bottom per well.

Experiment 1: (of the first version)

①.Prepare the nicotine solution at different concentrations of 0 g/mL, 0.02 g/mL, 0.04 g/mL, 0.08 g/mL,0.16 g/mL, 0.32 g/mL, 0.64 g/mL, 1.28 g/mL, 2.56 g/mL, 5.12 g/mL, 10.24 g/mL.

②Set up three sets of experiments. Add the plasmid MD-Pnica2+RBS+GFP+ter transformed bacteria (whose OD600 is approximately 0.4) in concentration of approximately 3% (3µL) to the 96 hole plate with flat black bottom per well and incubated at centrifugal speed of 150rpm at 37 ℃. Measure the OD600 values and fluorescence values every two hours.

Experiment 2: (of the first version)

①Prepare the nicotine solution at different concentrations of 0 g/mL, 0.001 g/mL, 0.01 g/mL,0.1 g/mL,1 g/mL.

②Set up five sets of experiments. Add the plasmid MD-Pnica2+RBS+GFP+ter transformed bacteria (whose OD600 is approximately 0.4) in concentration of approximately 3% (3µL) to the 96 hole plate with flat black bottom per well and incubated at centrifugal speed of 150rpm at 37 ℃. Measure the OD600 values and fluorescence values each hour.

Experiment 3: (the Comparison of the First and the Second Version Monitoring System)

①.Prepare the nicotine solution at different concentrations of 0 g/mL, 0.0001 g/mL, 0.001 g/mL,0.01 g/mL.

②Set up five sets of experiments. Add the plasmid MD-Pnica2+RBS+GFP+ter and plasmid pMD-Pnica2+RBS+T7RNA poLymerase+PT7+RBS+GFP+ter transformed bacteria (whose OD600 is approximately 0.4) in concentration of approximately 3% (3µL) to the 96 hole plate with flat black bottom per well and incubated at centrifugal speed of 150rpm at 37 ℃. Measure the OD600 values and fluorescence values every two hours.

results analysis

①The result of the First Experiment shows that high concentration (above 1.28g/L) of nicotine had a strong inhibitory effect on the growth of Escherichia coli, which affected the expression of GFP in Escherichia coli, so we reduce the range of nicotine concentration and carry out the Second Experiment.

② The result of the Second Experiment shows that the fluorescence expression of nicotine when the concentration of nicotine is C=0.01g/L increased steadily within 4 hours, but that of C=0. 001g/L was unstable. In addition, when the concentration of nicotine is within C=0.1g/L and C=1g/L had obvious toxic effect on the bacteria strain.

③The result of the Third Experiment shows that when nicotine concentration was as low as 0.0001g/L, fluorescence expression appears in the second version monitoring system at 1h and steadily increased within 1-3h, while fluorescence expression in the first version monitoring system only appears at 4 h. The result shows that the second version monitoring system greatly improves the induction of nicotine.

Appendix


promoter source and sequence

①Promoter nox: gaining from the article 《Cloning of a Novel Nicotine Oxidase Gene from Pseudomonas sp.Strain HZN6 Whose Product NonenantioseLectively Degrades Nicotine to Pseudooxynicotine》

From website: https://www.ncbi.nlm.nih.gov/nuccore/JN391188.2

Length: about 400bp

Note: add the restriction enzymes EcoRI, XbaI restriction enzyme cutting sites at the left end and the SpeI, PstI restriction cutting enzyme sites at the right end.

Sequence(5'-3'):

gagcagcaatacggtttttcaattgcagtcaaggcgggcgggtttctttatatcggtggcgtaacagccgttgataaagagggaaatgaagtatacgccaatgatgctaacaagcaaatgcagcttatttatgagcgtctgggtgcgatcctggccgctcatgatgcagacttcagtaacgttgttagtgaaactatctattataccaccgataatgaaagttacattaaatctGtagacgtcagaactgctgcgtataagggcgtaatagcaccaagtgcatctggcgtcagggttgccgatttcttgagcgacaagacgcttatagaaataacagctgtagcttatctcggcgaataagtgggctgccagtttcatcggttctgtagattcgcaacgatactaaaggtgtcagaca

②Promoter nica1/nica2: gaining from the article 《A Novel Gene, Encoding 6-Hydroxy-3-SµccinoyLpyridine Hydroxylase,Involved in Nicotine Degradation by Pseudomonas putida Strain S16》 and with the help of NCBI to predict these two possible promoter

From website: https://www.ncbi.nlm.nih.gov/search/?term=+DQ988162

Length of nica1: 46bp

Length of nica2: 34bp

Note: The promoter is designed in the primer, and the ECORI, XbaI restriction enzyme cutting sites is added at the left end and the SpeI, PstI restriction enzyme cutting sites is added at the right end.

Sequence of nica1 (5'-3'):

ttcagatggcacaggtgcgaaaccctcgttataatccggccactta

Sequence of nica2 (5'-3'):

Ttcgtagtacctgtttgtattgggccggtagcat

Experimental system


  • Worldshaper-XSHS, Xiaoshan High School

    Adress: No.538,Gongxiu Road,Xiaoshan District,Hangzhou,Zhejiang Province,China