Difference between revisions of "Part:BBa K3425021"
 
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Type IIS iGEM standard allows for fast and efficient construction of transcriptional units (TU) and multi-transcriptional units (MTU) in groups of four components. These components are needed in Level 1 assemblies (promoter, RBS, CDS and terminator) but might not be needed in higher level assemblies if the amount of transcriptional units in your system is not a multiple of four.
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<p>Type IIS iGEM standard allows for fast and efficient construction of transcriptional units (TU) and multi-transcriptional units (MTU) in groups of four components. These components are needed in Level 1 assemblies (promoter, RBS, CDS and terminator) but might not be needed in higher level assemblies if the amount of transcriptional units in your system is not a multiple of four.</p>
  
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For this reason, placeholders called dummy parts were created based on an existing Modular Assembly method [1]. These parts mimic a basic Type IIS part or a transcriptional unit and can be included in the assembly whenever needed.  
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<p>For this reason, placeholders called dummy parts were created based on an existing Modular Assembly method [1]. These parts mimic a basic Type IIS part or a transcriptional unit and can be included in the assembly whenever needed. </p>
  
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This page corresponds to TU-DY which was cloned to all pOdd plasmids (pSB1K0#) and mimics transcriptional units. Not present in the part would be BsaI recognition sites, which are positioned so the fusion sites are cut in the proper way. The part with these sites can be found in Team Uppsala 2020's <a href="https://2020.igem.org/Team:UofUppsala/Parts#Collection">Parts page</a>.
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<p>This page corresponds to TU-DY which was cloned to all pOdd plasmids (<a href="https://parts.igem.org/Part:pSB1K01">pSB1K0#</a>) and mimics transcriptional units. Not present in the part would be the BsaI recognition sites, which are positioned so that the fusion sites are cut in the proper way. The part with these sites can be found in Team Uppsala 2020's <a href="https://2020.igem.org/Team:UofUppsala/Parts#Collection">Parts page</a>. Sequencing results of this part cloned in all pOdd plasmids can be found in the Sequence Analysis section and the trace files are in the <a href="https://parts.igem.org/Collections/iGEM_Type_IIS_Collections">iGEM Type IIS standard collection page</a> as well as our Parts page.</p>
  
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More information about this cloning standard and dummy parts can be found in Team Uppsala 2020's <a href="https://2020.igem.org/Team:UofUppsala/Engineering#TypeIIS">iGEM Type IIS standard guidebook</a>
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<p>More information about this cloning standard and dummy parts can be found in Team Uppsala 2020's <a href="https://2020.igem.org/Team:UofUppsala/Engineering#TypeIIS">iGEM Type IIS standard guidebook</a>.</p>
 
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This part is part of iGEM Uppsala 2020's <html><a href="https://parts.igem.org/Collections/iGEM_Type_IIS_Collections">iGEM Type IIS standard collection</a></html>.
  
 
===Usage and Biology===
 
===Usage and Biology===
 
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Experiments with cloning the original dummy sequences TU-DY (<a href="parts.igem.org/Part:BBa_K3425021">BBa_K3425021</a>) and MTU-DY (<a href="parts.igem.org/Part:BBa_K3425022">BBa_K3425022</a>) together (<a href="parts.igem.org/Part:BBa_K3425064">BBa_K3425064</a> and <a href="parts.igem.org/Part:BBa_K3425065">BBa_K3425065</a>) showed that these parts should be longer than 4bp and different from each other. This is reflected in the design of the new set of dummies, where each dummy is 8bp long and all of them are different.
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<p>Experiments with cloning together all four TU-DY mimicking four TUs in pSB3C11 showed that most clones contain deletions or insertions of various sizes in the area of the "multi-dummy" sequence. </p>
  
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<p>This is probably due to the short and repetitive sequence generated by the dummies, since all of them contain the same fusion sites and spacer in between. More information can be found in the composite part </html><partinfo>BBa_K3425071</partinfo><html>.</p>
  
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<p>Dummy parts are only supposed to be fillers that allow the cloning reaction to ligate properly when you have less than four parts to assemble. In this sense, this dummy sequence works as intended. However, it is not ideal to have unpredictable mutations occurring systematically. Longer dummy parts with different sequences from each other were designed <i>in silico</i> as a better alternative.</p>
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<p>The following table details the part numbers and names of these new dummies (which contain the plasmid they should be cloned into), along with the transcriptional unit they are mimicking.</p>
 
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<th>Registry Number</th>
 
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<partinfo>BBa_K3425021 parameters</partinfo>
 
<partinfo>BBa_K3425021 parameters</partinfo>
 
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===References===
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1. Binder, A., Lambert, J., Morbitzer, R., Popp, C., Ott, T., Lahaye, T., and Parniske, M. (2014) A Modular Plasmid Assembly Kit for Multigene Expression, Gene Silencing and Silencing Rescue in Plants. PLOS ONE. 9, e88218

Latest revision as of 17:43, 26 October 2020


iGEM Type IIS standard Level 1 Dummy (TU-DY)

Type IIS iGEM standard allows for fast and efficient construction of transcriptional units (TU) and multi-transcriptional units (MTU) in groups of four components. These components are needed in Level 1 assemblies (promoter, RBS, CDS and terminator) but might not be needed in higher level assemblies if the amount of transcriptional units in your system is not a multiple of four.

For this reason, placeholders called dummy parts were created based on an existing Modular Assembly method [1]. These parts mimic a basic Type IIS part or a transcriptional unit and can be included in the assembly whenever needed.

This page corresponds to TU-DY which was cloned to all pOdd plasmids (pSB1K0#) and mimics transcriptional units. Not present in the part would be the BsaI recognition sites, which are positioned so that the fusion sites are cut in the proper way. The part with these sites can be found in Team Uppsala 2020's Parts page. Sequencing results of this part cloned in all pOdd plasmids can be found in the Sequence Analysis section and the trace files are in the iGEM Type IIS standard collection page as well as our Parts page.

More information about this cloning standard and dummy parts can be found in Team Uppsala 2020's iGEM Type IIS standard guidebook.

This part is part of iGEM Uppsala 2020's iGEM Type IIS standard collection.

Usage and Biology

Experiments with cloning together all four TU-DY mimicking four TUs in pSB3C11 showed that most clones contain deletions or insertions of various sizes in the area of the "multi-dummy" sequence.

This is probably due to the short and repetitive sequence generated by the dummies, since all of them contain the same fusion sites and spacer in between. More information can be found in the composite part BBa_K3425071.

Dummy parts are only supposed to be fillers that allow the cloning reaction to ligate properly when you have less than four parts to assemble. In this sense, this dummy sequence works as intended. However, it is not ideal to have unpredictable mutations occurring systematically. Longer dummy parts with different sequences from each other were designed in silico as a better alternative.

The following table details the part numbers and names of these new dummies (which contain the plasmid they should be cloned into), along with the transcriptional unit they are mimicking.

Registry Number Name Mimics
BBa_K3425023 pSB1K01-DY TU1
BBa_K3425024 pSB1K02-DY TU2
BBa_K3425025 pSB1K03-DY TU3
BBa_K3425026 pSB1K04-DY TU4

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


References

1. Binder, A., Lambert, J., Morbitzer, R., Popp, C., Ott, T., Lahaye, T., and Parniske, M. (2014) A Modular Plasmid Assembly Kit for Multigene Expression, Gene Silencing and Silencing Rescue in Plants. PLOS ONE. 9, e88218