Difference between revisions of "Team:IIT Delhi/Notebook"

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.caption {
 
.caption {
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         background-attachment: scroll;
 
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#banner {
 
#banner {
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background: url("https://static.igem.org/mediawiki/2018/3/3e/T--IIT_Delhi--basic_parts.png") ;
  
 
background-position: center;
 
background-position: center;
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</script>
 
</script>
 
<script>
 
<script>
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     /*sr.reveal('.img1', {duration: 700});
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           </div>   
 
           </div>   
 
      
 
      
</div>
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</div>
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+
 
 
 
<!-- Banner -->
 
<!-- Banner -->
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</section>
 
</section>
  
<div class="bgimg-1">
+
  <div class="caption">
+
    <span class="border" >Text anyone?</span>
+
  </div>
+
</div>
+
 
+
+
  
 
<div style="color: #777;background-color:white;text-align:center;padding:50px 80px;text-align: justify;">
 
<div style="color: #777;background-color:white;text-align:center;padding:50px 80px;text-align: justify;">
 
   
 
   
  <p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814001 = pLTL
 
    <br>
 
      </p>
 
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;"> The pLTL (Lac-Tet-Lac) is a hybrid promoter. It is a promoter composed of the operator sequences of pTet and the pLac promoter. There are multiple benefits of using the pLTL promoter.
 
</p>
 
   
 
      <ul style="font-size:20px;" >
 
      <li style="font-family: 'Lato', sans-serif;font-weight:400;">The hybrid pLTL shows almost complete repression on being repressed, and on induction (by IPTG and/or aTc), the hybrid pLTL promoter shows a 1.4-2 times higher expression.</li>
 
      <li style="font-family: 'Lato', sans-serif;font-weight:400;">The hybrid pLTL promoter also permits flexible gene expression because it can be utilized under either or both repression controls (LacI and TetR) simultaneously.</li>
 
   
 
    </ul>
 
<br>
 
  
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814008 = rrnB T1 Terminator + T7Te Terminator
+
<div class="divTable">
    <br>
+
<div class="divTableBody">
      </p>
+
<div class="divTableRow">
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;"> Our part is double terminator composed of rrnB T1 Terminator(BBa B0010) and T7 Te Terminator(BBa B0012). Both of these are forward terminators that are extensively used in E. coli.
+
<div class="divTableCell">&nbsp;S. No</div>
</p>
+
<div class="divTableCell">Part Name&nbsp;</div>
<br>
+
<div class="divTableCell">BioBrick&nbsp;</div>
 
+
<div class="divTableCell">Description&nbsp;</div>
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814009 = mKate2
+
<div class="divTableCell">Part Type&nbsp;</div>
 
+
    <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;"> Mkate2 - mKate2 is a red fluorescent protein derived from Entacmaea quadricolor.  It possesses fluorescence with excitation maxima at 588 nm and emission maxima at 588 and 633 nm, mKate2 is almost 3-fold brighter than mKate. mKate2 can be used in  labelling applications along with blue, cyan, green, yellow, and red fluorescent dyes. Its high pH-stability with pKa=5.4 makes it useful for imaging in acidic organelles, such as late and recycling endosomes and lysosomes.
+
 
+
</p>
+
<br>
+
 
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814010 = rrnB T1 Terminator
+
 
+
    <br>
+
      </p>
+
    <br>
+
 
</div>
 
</div>
 
+
<div class="divTableRow">
<div class="bgimg-2">
+
<div class="divTableCell">1</div>
  <div class="caption">
+
<div class="divTableCell">
    <span class="border" >Text anyone?</span>
+
<p><a href="http://parts.igem.org/Part:BBa_K2814001"><span style="font-weight: 400;">BBa_K2814001</span></a></p>
  </div>
+
 
</div>
 
</div>
 
+
<div class="divTableCell">pLTL&nbsp;</div>
<div style="position:relative;">
+
<div class="divTableCell">Lac-Tet-Lac Hybrid Promoter</div>
  <div style="color: #777;background-color:white;text-align:center;padding:50px 80px;text-align: justify;">
+
<div class="divTableCell">Promoter&nbsp;</div>
 
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814007 = sfGFP_ssrA
+
 
+
 
+
    <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">Our part consists of sfGFP appended with a ssrA(LVA) deg-tag. It has been codon optimised for E. coli.  This part is useful as it has high intensity as compared to other gfp variants as well as faster degradation rates and shorter reporter lifetimes.
+
 
+
 
+
</p>
+
 
+
<p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">Superfolder GFP is a basic (constitutively fluorescent) green fluorescent protein derived from Aequorea victoria. It has an emission wavelength of 510 nm and excitation wavelength of 485nm. It has a robust folding characteristic. The superfolder mutations also make the folding of GFP tolerant of mutations that would otherwise reduce the folding yield of GFP.
+
 
+
 
+
</p>
+
 
+
<p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">Our ssrA degtag is the gfp(LVA) that has a single (A → G) point mutation in nucleotide 349, resulting in an Asp117 → Gly117 (D117G) amino acid change. This point mutation does not appear to change the fluorescence spectrum of gfp(LVA). The LVA tag has been reported to lead to fast protein degradation, degrading GFP with rate -0.018 per minute. This corresponds to in vivo half-lives of mature Gfp(LVA) of approximately 40 min.
+
 
+
 
+
 
+
</p>
+
 
+
<p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">References</p>
+
<ol style="font-size: 20px;">
+
 
+
<li style="font-family: 'Lato', sans-serif;font-weight:400;">Pédelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS. Engineering and characterization of a superfolder green fluorescent protein. Nature biotechnology. 2006 Jan;24(1):79.</li>
+
 
+
<li style="font-family: 'Lato', sans-serif;font-weight:400;">Andersen, J. B. et al. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64, 2240–6 (1998).
+
</li>
+
 
+
 
+
  </ol>
+
 
+
<br>
+
 
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814011 = attP TP901-1
+
 
+
 
+
    <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">AttP TP901-1 - It is the AttP site of TP901-1 integrase (serine based recombinase enzyme). TP901-1 integrase is an enzyme that has been isolated from TP901-1 phage. It is responsible for catalysing site-specific recombination at AttP and AttB sites. The recombination mechanism depends on the orientation of the AttP and AttB sites. These enzymes help the virus integrate its DNA into the bacterial genome. TP901-1 is widely used in the construction of logic gates and modification of DNA sequences.
+
 
+
 
+
</p>
+
 
+
<br>
+
 
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814012 = BxbI Integrase + ssrA(LVA) deg tag
+
 
+
 
+
    <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">BxbI Integrase triggers attP × attB recombination. The product of attP × attB recombination is an integrated prophage flanked by two new recombination sites, attL and attR, each containing half sites derived from attP and attB. In the absence of accessory factors the integrases mediate unidirectional recombination between attP and attB with greater than 80% efficiency. In the presence of a phage-encoded accessory protein, the recombination directionality factor (RDF) the attP × attB recombination is inhibited and the attL × attR recombination is stimulated.
+
Bxb1 integrase yields approximately two-fold more recombinants  and displays about two fold less damage to the recombination sites than other phage-encoded serine integrases.
+
 
+
Our BxbI Integrase has a ssrA deg tag attached to it for faster degradation rates.
+
 
+
 
+
 
+
</p>
+
+
<br>
+
 
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814013 = attB TP901-1
+
 
+
 
+
    <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">AttB TP901-1 -  It is the AttB site of TP901-1 integrase (serine based recombinase enzyme). TP901-1 integrase is an enzyme that has been isolated from TP901-1 phage. It is responsible for catalysing site-specific recombination at AttP and AttB sites. The recombination mechanism depends on the orientation of the AttP and AttB sites. These enzymes help the virus integrate its DNA into the bacterial genome. TP901-1 is widely used in the construction of logic gates and changing DNA sequence.
+
 
+
 
+
 
+
</p>
+
+
<br>
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814014 = complement of B0034, RBS on the antisense strand, twin exists
+
    <br>
+
      </p>
+
<br>
+
 
+
 
+
  </div>
+
 
</div>
 
</div>
 
+
<div class="divTableRow">
<div class="bgimg-3">
+
<div class="divTableCell">2&nbsp;</div>
  <div class="caption">
+
<div class="divTableCell">
    <span class="border">Some random text </span>
+
<p><a href="http://parts.igem.org/Part:BBa_K2814007">BBa_K2814007</a></p>
  </div>
+
</div>
 +
<div class="divTableCell">sfGFP_ssrA&nbsp;</div>
 +
<div class="divTableCell">Reporter gene (codon-optimised for E. coli)&nbsp;</div>
 +
<div class="divTableCell">Coding Sequence&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">3&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814008">BBa_K2814008</a></p>
 +
</div>
 +
<div class="divTableCell">rrnB T1 Terminator + T7Te Terminator&nbsp;</div>
 +
<div class="divTableCell">Double Transcriptional Terminator&nbsp;</div>
 +
<div class="divTableCell">Terminator&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">4&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814009">BBa_K2814009</a></p>
 +
</div>
 +
<div class="divTableCell">mKate2&nbsp;</div>
 +
<div class="divTableCell">Reporter gene (codon-optimised for E. coli)&nbsp;&nbsp;</div>
 +
<div class="divTableCell">Coding Sequence&nbsp;</div>
 
</div>
 
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">5&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814010">BBa_K2814010</a></p>
 +
</div>
 +
<div class="divTableCell">rrnB T1 Terminator&nbsp;</div>
 +
<div class="divTableCell">Transcriptional Terminator</div>
 +
<div class="divTableCell">Terminator&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">6&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814011">BBa_K2814011</a></p>
 +
</div>
 +
<div class="divTableCell">attP TP901-1&nbsp;</div>
 +
<div class="divTableCell">Attachment site for TP901-1 Integrase&nbsp;</div>
 +
<div class="divTableCell">DNA&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">7&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814012">BBa_K2814012</a></p>
 +
</div>
 +
<div class="divTableCell">BxbI Integrase + ssrA(LVA) deg tag&nbsp;</div>
 +
<div class="divTableCell">CDS&nbsp;for Integrase Bxb1&nbsp;&nbsp;</div>
 +
<div class="divTableCell">Coding Sequence&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">8&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814013">BBa_K2814013</a></p>
 +
</div>
 +
<div class="divTableCell">attB TP901-1&nbsp;</div>
 +
<div class="divTableCell">Attachment site for&nbsp;TP901-1 Integrase&nbsp;</div>
 +
<div class="divTableCell">DNA&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">9&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814014">BBa_K2814014</a>&nbsp;</p>
 +
</div>
 +
<div class="divTableCell">complement of B0034, RBS on the antisense strand&nbsp;</div>
 +
<div class="divTableCell">Ribosome Binding Site&nbsp;</div>
 +
<div class="divTableCell">RBS&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">10&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814015">BBa_K2814015</a></p>
 +
</div>
 +
<div class="divTableCell">pLac(lambda) hybrid&nbsp;</div>
 +
<div class="divTableCell">Lac-Lambda Hybrid Promoter&nbsp;</div>
 +
<div class="divTableCell">Promoter</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">11&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814017">BBa_K2814017</a></p>
 +
</div>
 +
<div class="divTableCell">attP Bxb1&nbsp;</div>
 +
<div class="divTableCell">Attachment site for Bxb1 Integrase&nbsp;</div>
 +
<div class="divTableCell">DNA&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">12&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814018">BBa_K2814018</a></p>
 +
</div>
 +
<div class="divTableCell">attB Bxb1&nbsp;</div>
 +
<div class="divTableCell">Attachment site for Bxb1 Integrase&nbsp;</div>
 +
<div class="divTableCell">DNA&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">13&nbsp;</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814019">BBa_K2814019</a></p>
 +
</div>
 +
<div class="divTableCell">P7 Promoter&nbsp;</div>
 +
<div class="divTableCell"><span style="font-weight: 400;">Constitutive P7 promoter</span>&nbsp;</div>
 +
<div class="divTableCell">Promoter</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">14</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814021">BBa_K2814021</a>&nbsp;</p>
 +
</div>
 +
<div class="divTableCell">BxbI-Xis &nbsp;+ ssrA(LVA) deg tag&nbsp;</div>
 +
<div class="divTableCell">CDS for Recombinase Directionality Factor for Integrase Bxb1&nbsp;</div>
 +
<div class="divTableCell">Coding Sequence&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">15</div>
 +
<div class="divTableCell">
 +
<p><a href="http://parts.igem.org/Part:BBa_K2814022">BBa_K2814022</a>&nbsp;</p>
 +
</div>
 +
<div class="divTableCell">attB BxbI (reverse orientation)&nbsp;</div>
 +
<div class="divTableCell">Attachment site for Bxb1 Integrase (Reverse)&nbsp;</div>
 +
<div class="divTableCell">DNA&nbsp;</div>
 +
</div>
 +
<div class="divTableRow">
 +
<div class="divTableCell">16</div>
 +
<div class="divTableCell"><a href="http://parts.igem.org/Part:BBa_K2814025">BBa_K2814025</a>
 +
<p>&nbsp;</p>
 +
</div>
 +
<div class="divTableCell">
 +
<p><span style="font-weight: 400;">TP901-1 Integrase</span>&nbsp;</p>
 +
</div>
 +
<div class="divTableCell">CDS for Integrase TP901-1</div>
 +
<div class="divTableCell">Coding Sequence</div>
 +
</div>
 +
</div>
 +
</div>
 +
<!-- DivTable.com -->
  
<div style="position:relative;">
 
  <div style="color: #777;background-color:white;text-align:center;padding:50px 80px;text-align: justify;">
 
 
      
 
      
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814015 = pLac(lambda) hybrid
+
</div>
  
  
    <br>
 
      </p>
 
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">pLac - Lambda hybrid - is a hybrid promoter consisting of Lac and Lambda operator sites in the core region. This hybrid promoter can be induced in the presence of  IPTG or
 
</p>
 
<br>
 
  
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814017 = attP Bxb1
 
  
 
+
     <div style="background-color: white">
 
+
     <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">AttP Bxb1 - It is the AttP site of Bxb1 integrase (Serine based recombinase). Bxb1 integrase carries out site-specific recombination by catalysing unidirectional recombination to produce AttL and AttR sites from AttP and AttB. This switching capacity allows them to be used in the design of toggle switches.
+
 
+
 
+
</p>
+
<br>
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814018 = attB Bxb1
+
 
+
 
+
    <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">AttB Bxb1 - It is the AttB site of Bxb1 integrase (Serine based recombinase). Bxb1 integrase carries out site-specific recombination by catalysing unidirectional recombination to produce AttL and AttR sites from AttP and AttB. This switching capacity allows them to be used in the design of logic gates.
+
 
+
 
+
</p>
+
<br>
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814019 = P7 Promoter
+
 
+
 
+
 
+
 
+
    <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">Constitutive P7 promoter - It is the complement of the constitutive P7 promoter so as to initiate transcription in the reverse direction. 
+
 
+
</p>
+
 
+
<br>
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814021 = BxbI-Xis  + ssrA(LVA) deg tag------------
+
 
+
 
+
    <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">Xis-BxbI_ssrA deg tag - Consists of bxb1 excisionase followed by ssrA degradation tag. Bxb1-Xis  catalyses the conversion of AttL and AttR sites to AttP and AttB sites when expressed with Bxb1 integrase, thereby reverting the recombination caused by integrase. ssrA deg tag degrades the Bxb1-Xis formed as an increase in the amount of excisionase renders the system inefficient. This property allows Bxb1 to be used in the construction of logic gates.
+
</p>
+
 
+
<br>
+
 
+
<p style="font-size: 30px; font-family: 'Roboto', sans-serif;font-weight:700;">BBa_K2814022 = attB BxbI (reverse orientation)
+
 
+
 
+
    <br>
+
      </p>
+
      <p style="font-size:20px;font-family: 'Lato', sans-serif;font-weight:400;">AttB-BxbI (Reverse Orientation) - Contains AttB site of Bxb1 integrase in the reverse orientation (Reverse of  BBa_K2814018). Bxb1 integrase carries out site-specific recombination by catalysing unidirectional recombination to produce AttL and AttR sites from AttP and AttB. This switching capacity allows them to be used in the design of logic gates.
+
 
+
</p>
+
 
+
<br>
+
 
+
 
+
  </div>
+
</div>
+
 
+
    <!--/**/-->
+
 
+
       
+
<div style="background-color: white">
+
 
         <div  style="background-color: #555;color:black;font-size: 35px;text-align: center;font-family: sans-serif;"><h4 style="color: white">Contact us</h4></div>
 
         <div  style="background-color: #555;color:black;font-size: 35px;text-align: center;font-family: sans-serif;"><h4 style="color: white">Contact us</h4></div>
 
             <div style="text-align: center;margin-bottom: -136px;"><h4 style="color:black;font-size: 50px;"><u class="fx" style="cursor: pointer;text-align: center">Address</u></h4><p style="text-align: center;margin-bottom: 16px">Undergraduate Laboratory<br>
 
             <div style="text-align: center;margin-bottom: -136px;"><h4 style="color:black;font-size: 50px;"><u class="fx" style="cursor: pointer;text-align: center">Address</u></h4><p style="text-align: center;margin-bottom: 16px">Undergraduate Laboratory<br>
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}
 
 
 
  
  

Revision as of 15:33, 17 October 2018

iGEM IIT Delhi

 S. No
Part Name 
BioBrick 
Description 
Part Type 
1
pLTL 
Lac-Tet-Lac Hybrid Promoter
Promoter 
sfGFP_ssrA 
Reporter gene (codon-optimised for E. coli) 
Coding Sequence 
rrnB T1 Terminator + T7Te Terminator 
Double Transcriptional Terminator 
Terminator 
mKate2 
Reporter gene (codon-optimised for E. coli)  
Coding Sequence 
rrnB T1 Terminator 
Transcriptional Terminator
Terminator 
attP TP901-1 
Attachment site for TP901-1 Integrase 
DNA 
BxbI Integrase + ssrA(LVA) deg tag 
CDS for Integrase Bxb1  
Coding Sequence 
attB TP901-1 
Attachment site for TP901-1 Integrase 
DNA 
complement of B0034, RBS on the antisense strand 
Ribosome Binding Site 
RBS 
10 
pLac(lambda) hybrid 
Lac-Lambda Hybrid Promoter 
Promoter
11 
attP Bxb1 
Attachment site for Bxb1 Integrase 
DNA 
12 
attB Bxb1 
Attachment site for Bxb1 Integrase 
DNA 
13 
P7 Promoter 
Constitutive P7 promoter 
Promoter
14
BxbI-Xis  + ssrA(LVA) deg tag 
CDS for Recombinase Directionality Factor for Integrase Bxb1 
Coding Sequence 
15
attB BxbI (reverse orientation) 
Attachment site for Bxb1 Integrase (Reverse) 
DNA 
16

TP901-1 Integrase 

CDS for Integrase TP901-1
Coding Sequence

Contact us

Address

Undergraduate Laboratory
Department of Biotechnology and Biochemical Engineering, IIT Delhi