Difference between revisions of "Team:Oxford/Synbiota"

 
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     <div class="container-fluid page-heading" style="background-image: url(https://static.igem.org/mediawiki/2015/b/b0/OxiGEM_Synbiota_1.jpeg)">
 
         <h3>Synbiota</h3>
 
         <h3>Synbiota</h3>
 
     </div>
 
     </div>
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                     <div class="section" id="synbiota">
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                     <div class="section" id="synbiota_introduction">
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                         <h2> </h2>
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                         <h2>Introduction</h2>
 
                         <p>
 
                         <p>
−
                             We were awarded trailblazer scholarship by <a href="https://synbiota.com">Synbiota</a>, a startup company co-founded by iGEM alumni, and had a chance to test their prototype Rapid DNA Prototyping (RDP) assembly standard including exclusive iGEM kit and <a href="https://gentle-beta.synbiota.com/">RDP part designing software</a>.
+
                             We were awarded trailblazer scholarship by <a href="https://synbiota.com">Synbiota</a>, a startup company co-founded by <a class="definition" title="iGEM" data-content="Students doing something good with synthetic biology. Stands for International Genetically Engineered Machine.">iGEM</a> alumni, and had a chance to test their prototype Rapid <a class="definition" title="DNA" data-content="Contains the genetic code for life, using only four types of molecules. It forms the familiar double helix structure and can self-replicate under certain conditions.">DNA</a> Prototyping (RDP) assembly standard including exclusive iGEM kit and <a href="https://synbiota.com/beta">RDP part designing software</a>.
 
                         </p>
 
                         </p>
 
                         <p>
 
                         <p>
−
                             RDP is a modular approach to synthetic biology that is biobrick compatible, and somewhat similar to standard biobrick approach in a sense that DNA templates can create new RDP parts through PCR. However, each RDP part is defined by each promoter, RBS, coding region, or terminator. Series of RDP parts can be assembled using magnetic anchor under two hours.
+
                             RDP is a modular approach to synthetic biology that is <a class="definition" title="BioBrick" data-content="A specific base sequence that does something you want. Like a lego brick.">BioBrick</a> compatible, and somewhat similar to the standard BioBrick approach in a sense that DNA templates can create new RDP parts through <a class="definition" title="PCR" data-content="Polymerase chain reaction. The technique of amplifying DNA by several orders of magnitude.">PCR</a>. However, each RDP part is defined by each <a class="definition" title="promoter" data-content="The section of DNA that the RNA polymerase enzyme binds to before it starts making the RNA strand - it is needed to start transcription, so it sits in the DNA before a gene. Regulates whether a gene is &quot;on&quot; or &quot;off&quot; and to what extent. They can be made to be sensitive to certain conditions so that if a bacterium senses a change in environment it can up or down regulate the expression of a certain gene (so there will be more or less of the protein encoded by that gene, produced in the cell).">promoter</a>, RBS, coding region, or terminator. Series of RDP parts can be assembled using the magnetic anchor under two hours.
 
                         </p>
 
                         </p>
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                        <div class="image image-full">
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                            <img src="https://static.igem.org/mediawiki/2015/b/b6/OxiGEM_Synbiota2.png" alt="Synbiota image" />
 +
                            <p>
 +
                                Figure 1. Addition of sticky ends at the each strand allows two different RDP parts to be attached.
 +
                            </p>
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                        </div>
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                    </div>
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                    <div id="synbiota_design">
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                        <h2>Design</h2>
 
                         <p>
 
                         <p>
−
                             (Missing Image Here)
+
                             RDP Standard requires addition of two unique sticky ends (X and Z) and their complements (X’ and Z’) onto each part, allowing sequential assembly from promoter to terminator. Figure 1 shows this process.
 
                         </p>
 
                         </p>
 
                         <p>
 
                         <p>
−
                             RDP Standard requires addition of two unique sticky ends (X and Z) and their complements (X’ and Z’) onto each part, allowing sequential assembly from promoter to terminator.
+
                             We have designed two customised RDP parts, pLsr and T4Holin. These RDP parts were designed using <a href="https://gentle-beta.synbiota.com/">GEntle</a> software to contain X-Z’ or Z-X’ sticky ends. Synbiota has provided us with physical RDP parts of pLse and T4Holin, as well as primers to amplify them through PCR. Wetlab notebooks of Synbiota specific PCR can be found <a href="https://2015.igem.org/Team:Oxford/Notebook#syn">here</a>.
 
                         </p>
 
                         </p>
 
                         <p>
 
                         <p>
−
                            We have designed two customised RDP parts, pLsr and T4Holin. These RDP parts were designed using <a href="https://gentle-beta.synbiota.com/">GEntle</a> software to contain X-Z’ or Z-X’ sticky ends. Synbiota has provided us with physical RDP parts of pLse and T4Holin, as well as primers to amplify them through PCR. Wetlab notebooks of Synbiota specific PCR can be found <a href="https://2015.igem.org/Team:Oxford/Notebook#syn">here</a>
+
                             Then pLsr and T4Holin were combined with the provided Anchor RDP part, RBS, terminator and Cap to make a full RDP circuit which is equivalent to <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1659601">BBa_K1659601</a>.
−
                        </p>
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−
                        <p>
+
−
                             Then pLsr and T4Holin were combined with provided Anchor RDP part, RBS, terminator and Cap to make a full RDP circuit which is equivalent to <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1659601">BBa_K1659601</a>.
+
 
                         </p>
 
                         </p>
 
                         <p>
 
                         <p>
 
                             So this is how our part BBa_K1659601 RDP circuit looks like:
 
                             So this is how our part BBa_K1659601 RDP circuit looks like:
 
                         </p>
 
                         </p>
 +
                        <div class="image image-full">
 +
                            <img src="https://static.igem.org/mediawiki/2015/a/a5/OxiGEM_Synbiota3.png" alt="Our BBa_K1659601 RDP circuit" />
 +
                            <p>Our BBa_K1659601 RDP Circuit</p>
 +
                        </div>
 
                         <p>
 
                         <p>
−
                             (Missing Image Here)
+
                             Each ends of Anchor and Cap RDP parts self-assemble to form pSB1C3 backbone that is BioBrick compatible.
 
                         </p>
 
                         </p>
 +
                        <div class="image image-full">
 +
                            <img src="https://static.igem.org/mediawiki/2015/f/f4/Ox_synbiota_img3.png">
 +
                        </div>
 +
                    </div>
 +
                    <div id="synbiota_assembly">
 +
                        <h2>Assembly</h2>
 
                         <p>
 
                         <p>
−
                             Each ends of Anchor and Cap RDP parts self-assemble to form pSB1C3 backbone that is biobrick compatible.
+
                             RDP assembly method is very time-efficient because the assembly starts with a Synbiota Anchor part (DNA anchored to a magnetic bead), and first RDP part (pLsr in our case) is added onto the solution, requiring ligation incubation time of only 8min. Then, an eppendorf tube holder with the magnet pellets Anchor-pLsr component, washing off excess DNA and ligase. The picture below illustrates this very stage.
 
                         </p>
 
                         </p>
 +
                        <div class="image image-full">
 +
                            <img src="https://static.igem.org/mediawiki/2015/4/49/Ox_synbiota_img4.png">
 +
                            <p>Us assembling our construct using the magnet</p>
 +
                        </div>
 
                         <p>
 
                         <p>
−
                             (Missing Image Here)
+
                             Then, next RDP part(RBS 2.1 in this case) resuspends Anchor-pLsr component, repeating the exact same procedure through the assembly of each part.
 
                         </p>
 
                         </p>
 +
                    </div>
 +
                    <div id="synbiota_thanks">
 +
                        <h3>Thanks!</h3>
 
                         <p>
 
                         <p>
−
                             RDP assembly method is very time-efficient because the assembly starts with a Synbiota Anchor part (DNA anchored to a magnetic bead), and first RDP part (pLsr in our case) is added onto the solution, requiring ligation incubation time of only 8min. Then, an eppendorf tube holder with the magnet pellets Anchor-pLsr component, washing off excess DNA and ligase. The picture below illustrates this very stage.
+
                             Throughout rigorous initial interview, webminar introduction to RDP protocol, usability test and final interview, we are grateful to be introduced to expanding assembly methods of synthetic biology. We are also glad that we could provide useful feedbacks to Synbiota, and to watch GEntle software being upgraded from their prototype to current beta version.
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
−
                     <div class="section" id="references">
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                     <div class="section-spacer"></div>
−
                        <h2> References </h2>
+
−
                        (Missing References Here [if any])
+
−
                    </div>
+
 
                 </div>
 
                 </div>
 
             </div>
 
             </div>
 
             <div class="col-md-3 contents-sidebar">
 
             <div class="col-md-3 contents-sidebar">
 
                 <ul id="sidebar" class="nav nav-stacked affix-top sm-hidden xs-hidden" data-spy="affix">
 
                 <ul id="sidebar" class="nav nav-stacked affix-top sm-hidden xs-hidden" data-spy="affix">
−
                     <li>
+
                     <li><a href="#synbiota_introduction">Introduction</a></li>
−
                        <a href="#synbiota">Synbiota</a>
+
                     <li><a href="#synbiota_design">Design</a></li>
−
                     </li>
+
                     <li><a href="#synbiota_assembly">Assembly</a></li>
−
                     <li>
+
                     <li><a href="#synbiota_thanks">Thanks!</a></li>
−
                        <a href="#references">References</a>
+
−
                     </li>
+
 
                 </ul>
 
                 </ul>
 
             </div>
 
             </div>

Latest revision as of 01:08, 19 September 2015

Synbiota

Introduction

We were awarded trailblazer scholarship by Synbiota, a startup company co-founded by iGEM alumni, and had a chance to test their prototype Rapid DNA Prototyping (RDP) assembly standard including exclusive iGEM kit and RDP part designing software.

RDP is a modular approach to synthetic biology that is BioBrick compatible, and somewhat similar to the standard BioBrick approach in a sense that DNA templates can create new RDP parts through PCR. However, each RDP part is defined by each promoter, RBS, coding region, or terminator. Series of RDP parts can be assembled using the magnetic anchor under two hours.

Synbiota image

Figure 1. Addition of sticky ends at the each strand allows two different RDP parts to be attached.

Design

RDP Standard requires addition of two unique sticky ends (X and Z) and their complements (X’ and Z’) onto each part, allowing sequential assembly from promoter to terminator. Figure 1 shows this process.

We have designed two customised RDP parts, pLsr and T4Holin. These RDP parts were designed using GEntle software to contain X-Z’ or Z-X’ sticky ends. Synbiota has provided us with physical RDP parts of pLse and T4Holin, as well as primers to amplify them through PCR. Wetlab notebooks of Synbiota specific PCR can be found here.

Then pLsr and T4Holin were combined with the provided Anchor RDP part, RBS, terminator and Cap to make a full RDP circuit which is equivalent to BBa_K1659601.

So this is how our part BBa_K1659601 RDP circuit looks like:

Our BBa_K1659601 RDP circuit

Our BBa_K1659601 RDP Circuit

Each ends of Anchor and Cap RDP parts self-assemble to form pSB1C3 backbone that is BioBrick compatible.

Assembly

RDP assembly method is very time-efficient because the assembly starts with a Synbiota Anchor part (DNA anchored to a magnetic bead), and first RDP part (pLsr in our case) is added onto the solution, requiring ligation incubation time of only 8min. Then, an eppendorf tube holder with the magnet pellets Anchor-pLsr component, washing off excess DNA and ligase. The picture below illustrates this very stage.

Us assembling our construct using the magnet

Then, next RDP part(RBS 2.1 in this case) resuspends Anchor-pLsr component, repeating the exact same procedure through the assembly of each part.

Thanks!

Throughout rigorous initial interview, webminar introduction to RDP protocol, usability test and final interview, we are grateful to be introduced to expanding assembly methods of synthetic biology. We are also glad that we could provide useful feedbacks to Synbiota, and to watch GEntle software being upgraded from their prototype to current beta version.