Team:DTU-Denmark-2/Project/PlugnplayAssembly

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<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#Making molecular biology easier" class="h1"> Making molecular biology easier</a><br><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#Making molecular biology easier" class="h1"> Making molecular biology easier</a><br><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#How it works" class="h1"> How it works</a><br><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#How it works" class="h1"> How it works</a><br><br>
-
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#The Procedure of assembly" class="h1"> The Procedure of assembly</a><br><br>
+
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#The Procedure of assembly" class="h1"> The procedure of assembly</a><br><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#Plug 'n' Play benefits" class="h1"> Plug 'n' Play benefits</a><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#Plug 'n' Play benefits" class="h1"> Plug 'n' Play benefits</a><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#Improvements of BBF RFC 39"
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#Improvements of BBF RFC 39"
class="h2"> Improvements of BBF RFC 39</a><br>
class="h2"> Improvements of BBF RFC 39</a><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#What you get" class="h2"> What you get</a><br><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#What you get" class="h2"> What you get</a><br><br>
-
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#The Design of The System" class="h1"> The Design of The System</a><br><br>
+
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#The design of the system" class="h1"> The design of the system</a><br><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#References" class="h1">References</a><br><br>
<a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly#References" class="h1">References</a><br><br>
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<a name="Making molecular biology easier"></a><h1><b>Making molecular biology easier</b></h1>
<a name="Making molecular biology easier"></a><h1><b>Making molecular biology easier</b></h1>
<p align="justify">
<p align="justify">
-
We imagine that iGEM should be about assembling BioBricks fast, leaving more time for the actual project. It should be easy to combine any thinkable part, device or existing BioBrick. Unfortunately, classical cloning techniques can cause problems and even PCR can be cumbersome, if you have little or no laboratory experience. <br> <br>  
+
We imagine that iGEM should be about fast assembly of BioBricks, leaving more time for the actual project. It should be easy to combine any thinkable part, device or existing BioBrick. Unfortunately, classical cloning techniques can cause problems and even PCR can be cumbersome, if you have little or no laboratory experience. <br> <br>  
-
Therefore, we introduce a simple and fast way of building new devices and vectors with ready to use PCR products. All that is needed is to select the favorite BioBricks and one of the ready to use backbone vectors, and mix it with USER enzyme. The assembled vector is ready for chemical transformation into competent <i>E. coli</i> cells only 70 minutes later.<br>  
+
Therefore, we introduce a simple and fast way of building new devices and vectors with ready to use PCR products. All that is needed is to select the favorite BioBricks and one of the ready to use backbone vectors, and mix it with USER enzyme. The assembled vector is ready for chemical transformation into competent <i>E. coli</i> cells only 70 minutes later.The 8-9 nucleotide overhangs (linkers) flanking the parts, can hybridize to complementary overhangs without the use of DNA-ligases.<br>  
-
No need to worry if the destination vector has been fully linearized, no need to perform site-directed mutagenesis to remove unwished restriction recognition sites, just simple, fast, and easy.</p>
+
No need to worry whether the destination vector has been fully linearized, no need to perform site-directed mutagenesis to remove unwished restriction recognition sites - just simple, fast, and easy.</p>
<br>
<br>
<p align="justify">
<p align="justify">
-
Successful assembly of six biological parts in one reaction is possible, reducing the plasmid construction time significantly. The upper limit of fragments that efficiently can be assembled has not been delineated yet (1). Owing the 8-9 nucleotide overhangs flanking the parts, they can hybridize to complementary overhangs without the use of DNA-ligases.<br>
+
It is possible to successfully assemble six biological parts in one reaction, reducing the plasmid construction time significantly. The upper limit of fragments that efficiently can be assembled has not yet been delineated (1). <br>
-
In 2009 the first team from DTU to participate in iGEM introduced the USER fusion Assembly standard <a href="http://openwetware.org/wiki/The_BioBricks_Foundation:RFC#BBF_RFC_39:_The_USER_cloning_standard">[BBF RFC 39]</a>. This year we introduce a more standardized version allowing easier use of the system. The Plug 'n' Play assembly standard can be found <a href="http://bbf.openwetware.org/RFC.html#BBF_RFC_80:_Plug_.27n.27_Play_with_DNA"> here</a> (BBF RFC 80).
+
In 2009 the first team from DTU participated in iGEM and introduced the USER fusion Assembly standard <a href="http://openwetware.org/wiki/The_BioBricks_Foundation:RFC#BBF_RFC_39:_The_USER_cloning_standard">[BBF RFC 39]</a>. This year we introduce a standardized version allowing easier use of the system. The Plug 'n' Play assembly standard can be found <a href="http://bbf.openwetware.org/RFC.html#BBF_RFC_80:_Plug_.27n.27_Play_with_DNA"> here</a> (BBF RFC 80).
</p><br>
</p><br>
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-
<a name="The Procedure of assembly"></a><h2><b>The Procedure of assembly</b></h2>
+
<a name="The Procedure of assembly"></a><h2><b>The procedure of assembly</b></h2>
-
Please refer to our Biobrick Assembly Standard <a href="http://bbf.openwetware.org<br>/RFC.html#BBF_RFC_80:_Plug_.27n.27_Play_with_DNA">BBF RFC 80</a> for a detailed protocol.<br><br>
+
Please refer to our Plug 'n' Play with DNA assembly standard <a href="http://bbf.openwetware.org<br>/RFC.html#BBF_RFC_80:_Plug_.27n.27_Play_with_DNA">BBF RFC 80</a> for a detailed protocol.<br><br>
-
1. Pre-produced PCR products are picked from the Plug `n´ Play kit.<br>
+
<dt>
-
2. USER enzyme mix and buffer is added. This will remove the uracil, making sticky end overhangs on all BioBricks.  All BioBricks and backbone plasmid have matching sticky ends, and the BioBricks will self-assemble in the plasmid. <br>
+
<dd><li>Pre-produced PCR products are selected from the Plug 'n' Play kit.</li></dd>
-
3. Transformation in <i>E. coli</i>. Reduced incubation of the transformation mix is obtained when using ampicillin as antibiotic resistance marker. <br>  
+
<dd><li> USER enzyme mix and buffer is added. This will remove the uracils, resulting in sticky ends on all BioBricks.  The BioBricks and the backbone plasmid have matching sticky ends, and will self-assemble. </li></dd>
 +
<dd><li> Chemical transformation of <i>E. coli</i>. The time of the final incubation of the transformation mix can be reduced to 30 min when using ampicillin as antibiotic resistance marker and still results in a high number of transformants.   
-
If a part is not incluede in the Plug `n´ Play kit a simple PCR amplification can performed on the part or BioBricks intended for the assembly. The PCR product should subsequently be gel band purified.
+
 
 +
If a part is not included in the Plug 'n' Play kit a simple PCR amplification can be performed on the part intended for the assembly in accordance to the <a href="https://2011.igem.org/Team:DTU-Denmark-2/Project/PlugnplayAssembly/customization">Customization</a>.</li></dd>
 +
</dt>
<br><br>
<br><br>
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<a name="Improvements of BBF RFC 39"></a><h3><b>Improvements of BBF RFC 39</b></h3>
<a name="Improvements of BBF RFC 39"></a><h3><b>Improvements of BBF RFC 39</b></h3>
-
No need to use a USER cassette, thereby completely avoiding the use of restriction enzymes. <br>
+
<dt>
-
Standardized linkers <br> <br>
+
<dd><li>No need to use a USER cassette, thereby completely avoiding the use of restriction enzymes and increasing the flexibility of the system. </li></dd>
 +
<dd><li>Standardized linkers </li> </dd>
 +
</dt>
 +
<p align="justify">
<a name="What you get"></a><h3><b>What you get</b></h3>
<a name="What you get"></a><h3><b>What you get</b></h3>
-
Rapid assembly of biological parts <br>
+
<dt>
-
A well documented system <br>
+
<dd><li>Rapid assembly of biological parts </li></dd>
-
Assembly of multiple biobricks in one step <br>
+
<dd><li>A well documented system </li></dd>
-
No illegal restrictionsites <br>
+
<dd><li>Assembly of multiple biobricks in one step </li></dd>
-
100% restriction enzyme free <br>
+
<dd><li>No illegal restriction sites </li></dd>
-
100% DNA ligase free <br>
+
<dd><li>100% restriction enzyme free </li></dd>
-
High fidelity ensured by PfuTurbo® 7x Hotstart DNA polymerase <br>
+
<dd><li>100% DNA ligase free </li></dd>
-
Directionality of inserts are supported <br>
+
<dd><li>High fidelity ensured by PfuTurbo® 7x Hotstart DNA polymerase </li></dd>
-
Any vector can be made Plug’n’Play compatible <br>
+
<dd><li>Directionality of inserts are supported </li></dd>
-
Suitable for large scale high throughput projects <br><br>
+
<dd><li>Any vector can be made Plug’n’Play compatible </li></dd>
 +
<dd><li>Suitable for large scale high throughput projects </li></dd>
 +
</dt>
</p>
</p>
-
 
+
<br><br>
-
<p align="justify">
+
-
Vectors for Plug `n´ Play have been prepared by PCR ensuring 100% linear fragments. This means that the occurrences of false positives due to the presence uncut vector can be completely avoided (2).<br><br>
+
-
</p>
+
-
 
+
<p align="justify">
<p align="justify">
-
Drawbacks of the USER cassette (2):<br>
+
Vectors for Plug 'n' Play have been prepared by PCR ensuring 100% linear fragments. This means that the occurrence of false positives after bacterial transformation can be completely avoided (2).<br><br>
-
• The USER cassette has to be inserted into the vector of choice, which has to be done by classical cloning.<br>
+
-
• Fragments can only be inserted at the site of the USER cassette making it inflexible<br>
+
-
• The USER cassette has to be digested by a restriction endonuclease and a nicking enzyme<br><br>
+
</p>
</p>
<p align="justify">
<p align="justify">
The USER compatible backbone vectors were made by PCR amplification with primers containing the standardized linkers 6 and 1.  
The USER compatible backbone vectors were made by PCR amplification with primers containing the standardized linkers 6 and 1.  
-
For all the PCR reactions it is important to remove the template vector, to ensure assembly in USER reaction and avoid inauspicious transformation and false positive. The template can simply be removed by DpnI treatment (2). However, a gel band purification was instead performed, when preparing the vector to further ensure a high degree a purification of our BioBricks.</p><br>
+
For all the PCR reactions it is important to remove the template vector before utilizing it in the USER reaction to avoid inauspicious transformations and false positives. The template can be removed by DpnI treatment or by gel band purification(2). </p><br>
<p align="justify">
<p align="justify">
-
Previous studies have demonstrated a high level of correct assembly and directionality of fragments (2,3) and although we did not make such analysis ourselves it was in general our perception that this was the case, of the more than 25 different Plug `n´ Play assemblies we performed we encountered no more than 2 false-positives.</p><br>
+
Previous studies have demonstrated a high level of correct assembly and directionality of fragments (2,3) and although we did not make such analysis ourselves it was in general our perception that this was the case, as of the more than 25 different Plug 'n' Play assemblies performed we encountered no more than two false-positives.</p><br>
<p align="justify">
<p align="justify">
-
It is well known that mutations can be introduced during PCR. To minimize mutations the X7 proof-reading polymerases (4) are used which are fully compatible with the Plug `n´ Play standard. The x7 proof-reading polymerase helps lowering the risk of introducing mutations. The concern for introduction mutations is specially regarding the gene of interest (GOI), because mutations occurring in the vector backbone or resistance cassette would in worst case scenario mean the vector might not be able to propagate.</p>
+
It is well known that mutations can be introduced during PCR. To minimize mutations the x7 proof-reading polymerase (4) that are fully compatible with the Plug 'n' Play standard should be used. The x7 proof-reading polymerase helps lowering the risk of introducing mutations.</p>
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-
<a name="The Design of The System"></a><h2><b>The Design of The System</b></h2>
+
<a name="The Design of The System"></a><h2><b>The design of the system</b></h2>
<p align="justify">
<p align="justify">
-
The system is designed in order to assemble BioBricks from the categories promotor, a gene of interest (GOI), a targeting signal (TS), a terminator, a marker cassette and a vector backbone. The marker cassette consist of a promoter, a resistance gene, and a terminator. Ribosome binding site (RBS) is integrated in the promoter. However, a RBS can if needed be integrated in the reverse primer of the promoter when amplifying by PCR. This was the case when constructing the BioBricks and devices for the iGEM team <a href="https://2011.igem.org/Team:DTU-Denmark-2/results/Copenhagen"> Copenhagen</a>. </p>
+
The system was designed based on the most common categories of biological part in the order; promotor, gene of interest (GOI), tail sequence (TS), terminator, marker cassette, and vector backbone. The standard marker cassette consists of a promoter, a gene, and a terminator. Short sequences are such as ribosomal binding sites (RBS) are meant to be integrated in the forward or reverse primer of the desired part when amplifying it by PCR. An example of this can be found on <a href="https://2011.igem.org/Team:DTU-Denmark-2/results/Copenhagen"> this page</a>. </p>
<br>
<br>
<p align="justify">
<p align="justify">
-
The system is depending on custom-made overhangs on each part to be assembled. The parts with overhangs is formed by PCR amplifying the target DNA using primers designed with an upstream extension of 8-9 additional nucleotides that ends in a single deoxyuridine residue. In order to assembled multiple parts and having a flexible system the final DNA extension is preferred to consist of a adenine in the 5' end and a thymine in the 3' end.
+
The system is dependent on the assembly of the custom-made linkers on each part. The parts with linkers are synthesized by PCR amplification of template DNA using primers designed with an upstream extension of 8-9 additional nucleotides with a single deoxyuridine residue directly upstream the part. In order to assemble multiple parts while having a flexible system the linkers have an adenine in the 5' end and a thymine in the 3' end.
-
Furthermore, the it is important that the overhangs (tails) of the different parts are not identical to ensure directionality and correct order of the biobricks.<br><br>
+
Furthermore, it is important that the linkers of the different parts are not identical to ensure the directionality and correct order of the biobricks.<br><br>
-
Illustrated below, the sequence of linkers between the parts, which are generated from the overhangs(tail) on the PCR products.   
+
Illustrated below, are the sequences of linkers between the parts, which are generated from the overhangs (linkers) on the PCR products.   
</p>
</p>
<br>
<br>
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<br>
<br>
<p align="justify">
<p align="justify">
-
The linkers are making the whole system flexible in that it is possible use any promoter, since it will all ways end up have the same overhang generated in the PCR reaction. In the Plug `n´ Play system we are distinguishing between having a gene of interest where a targeting signal or reporter is wanted or not. Therefore, a GOI is a a gene of interest without any reporter or targeting signal, which can be assembled with a TS targeting signal or reporter. However, if the gene of interest is wanted without any reporter or targeting signal, we call it a module. A module can also include a gene of interest where the a targeting signal is included already or if it is a reporter by itself. </p>
+
The linkers are responsible for the flexibility of the system in that it for instance is possible use any promoter, since they will always have the same linkers. In the Plug 'n' Play system the coding sequence(s) can either consist of one gene of interest (GOI), called a module, or a GOI and a tail sequence, which could be any given DNA sequence of interest. </p>
<br>
<br>

Latest revision as of 21:19, 21 September 2011




Plug 'n' Play with DNA assembly standard



Making molecular biology easier

We imagine that iGEM should be about fast assembly of BioBricks, leaving more time for the actual project. It should be easy to combine any thinkable part, device or existing BioBrick. Unfortunately, classical cloning techniques can cause problems and even PCR can be cumbersome, if you have little or no laboratory experience.

Therefore, we introduce a simple and fast way of building new devices and vectors with ready to use PCR products. All that is needed is to select the favorite BioBricks and one of the ready to use backbone vectors, and mix it with USER enzyme. The assembled vector is ready for chemical transformation into competent E. coli cells only 70 minutes later.The 8-9 nucleotide overhangs (linkers) flanking the parts, can hybridize to complementary overhangs without the use of DNA-ligases.
No need to worry whether the destination vector has been fully linearized, no need to perform site-directed mutagenesis to remove unwished restriction recognition sites - just simple, fast, and easy.


It is possible to successfully assemble six biological parts in one reaction, reducing the plasmid construction time significantly. The upper limit of fragments that efficiently can be assembled has not yet been delineated (1).
In 2009 the first team from DTU participated in iGEM and introduced the USER fusion Assembly standard [BBF RFC 39]. This year we introduce a standardized version allowing easier use of the system. The Plug 'n' Play assembly standard can be found here (BBF RFC 80).


How it works

We have demonstrated that successful assembly of up to six biological parts in one reaction is possible e.g. (BBa_K678068). The entire process of combining six BioBricks is illustrated in the figure below. The number of BioBricks can be adjusted as preferred and for instance mutations can easily be introduced by customizing the standard.



The procedure of assembly

Please refer to our Plug 'n' Play with DNA assembly standard BBF RFC 80 for a detailed protocol.

  • Pre-produced PCR products are selected from the Plug 'n' Play kit.
  • USER enzyme mix and buffer is added. This will remove the uracils, resulting in sticky ends on all BioBricks. The BioBricks and the backbone plasmid have matching sticky ends, and will self-assemble.
  • Chemical transformation of E. coli. The time of the final incubation of the transformation mix can be reduced to 30 min when using ampicillin as antibiotic resistance marker and still results in a high number of transformants. If a part is not included in the Plug 'n' Play kit a simple PCR amplification can be performed on the part intended for the assembly in accordance to the Customization.


  • Plug 'n' Play benefits

    Improvements of BBF RFC 39

  • No need to use a USER cassette, thereby completely avoiding the use of restriction enzymes and increasing the flexibility of the system.
  • Standardized linkers
  • What you get

  • Rapid assembly of biological parts
  • A well documented system
  • Assembly of multiple biobricks in one step
  • No illegal restriction sites
  • 100% restriction enzyme free
  • 100% DNA ligase free
  • High fidelity ensured by PfuTurbo® 7x Hotstart DNA polymerase
  • Directionality of inserts are supported
  • Any vector can be made Plug’n’Play compatible
  • Suitable for large scale high throughput projects


  • Vectors for Plug 'n' Play have been prepared by PCR ensuring 100% linear fragments. This means that the occurrence of false positives after bacterial transformation can be completely avoided (2).

    The USER compatible backbone vectors were made by PCR amplification with primers containing the standardized linkers 6 and 1. For all the PCR reactions it is important to remove the template vector before utilizing it in the USER reaction to avoid inauspicious transformations and false positives. The template can be removed by DpnI treatment or by gel band purification(2).


    Previous studies have demonstrated a high level of correct assembly and directionality of fragments (2,3) and although we did not make such analysis ourselves it was in general our perception that this was the case, as of the more than 25 different Plug 'n' Play assemblies performed we encountered no more than two false-positives.


    It is well known that mutations can be introduced during PCR. To minimize mutations the x7 proof-reading polymerase (4) that are fully compatible with the Plug 'n' Play standard should be used. The x7 proof-reading polymerase helps lowering the risk of introducing mutations.


    The design of the system

    The system was designed based on the most common categories of biological part in the order; promotor, gene of interest (GOI), tail sequence (TS), terminator, marker cassette, and vector backbone. The standard marker cassette consists of a promoter, a gene, and a terminator. Short sequences are such as ribosomal binding sites (RBS) are meant to be integrated in the forward or reverse primer of the desired part when amplifying it by PCR. An example of this can be found on this page.


    The system is dependent on the assembly of the custom-made linkers on each part. The parts with linkers are synthesized by PCR amplification of template DNA using primers designed with an upstream extension of 8-9 additional nucleotides with a single deoxyuridine residue directly upstream the part. In order to assemble multiple parts while having a flexible system the linkers have an adenine in the 5' end and a thymine in the 3' end. Furthermore, it is important that the linkers of the different parts are not identical to ensure the directionality and correct order of the biobricks.

    Illustrated below, are the sequences of linkers between the parts, which are generated from the overhangs (linkers) on the PCR products.




    The linkers are responsible for the flexibility of the system in that it for instance is possible use any promoter, since they will always have the same linkers. In the Plug 'n' Play system the coding sequence(s) can either consist of one gene of interest (GOI), called a module, or a GOI and a tail sequence, which could be any given DNA sequence of interest.


    References

    (1) Hansen, B.G.; Salomonsen, B.; Nielsen, M. T.; Nielsen, J. B.; Hansen, N. B.; Nielsen, K. F.; Regueira, T. B.; Nielsen, J.; Patil, K. R.; Mortensen, U. F.; “Versatile enzyme expression and Characterization system for Aspergillus, with the Penicillium brevicompactum Polyketide Synthase Gene from the Mycophenolic Acid Gene Cluster as a Test Case.” American Society for Microbiology, 2011, 3044-3051.

    (2) Hansen, B. G.; Holm, D. K.; Nielsen M.T.; Mortensen, U.H. PCR based USER cloning for restriction enzyme and ligase-independent vector construction. Manuscript.

    (3) Frandsen, R. J. N.; Andersson, J.A.; Kristensen, M. B.; Giese, H. Efficient four fragment cloning for the construction of vectors for targeted gene replacement in filamentous fungi.
 BMC Molecular Biology 2008, 9:70.

    (4) Nørholm, M. H. H. A mutant Pfu DNA polymerase designed for advanced uracil-excision DNA engineering. BMC Biotechnol. 10, 21 (2010).