Difference between revisions of "Part:BBa K4452025:Design"

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===Design Notes===
 
===Design Notes===
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<p>These three genes and a synthetic spacer (BBa_K4452009) were assembled into BBa_K4452025 using Golden Braid assembly, specifically level omega assembly with BsmBI.</p>
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<p>The three genes (BBa_K4452015, BBa_K4452017, BBa_K4452018) and a synthetic spacer (BBa_K4452009) were assembled into BBa_K4452025 using Golden Braid assembly, specifically level omega assembly with BsmBI.</p>
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<table>
 +
  <tr>
 +
    <th>Part</th>
 +
    <th>Description</th>
 +
    <th>BsmBI site</th>
 +
  </tr>
 +
  <tr>
 +
    <td>BBa_K4452015</td>
 +
    <td>Ferritin</td>
 +
    <td>GGAG / AATG</td>
 +
  </tr>
 +
  <tr>
 +
    <td>BBa_K4452017</td>
 +
    <td>RUBY reporter</td>
 +
    <td>AATG / AGCC</td>
 +
  </tr>
 +
  <tr>
 +
    <td>BBa_K4452018</td>
 +
    <td>nptII Antibiotic Resistance</td>
 +
    <td>AGCC / TTCG</td>
 +
  </tr>
 +
  <tr>
 +
    <td>BBa_K4452009</td>
 +
    <td>M13R primer</td>
 +
    <td>TTCG / CGCT</td>
 +
  </tr>
 +
  <tr>
 +
    <td>BBa_K4452010</td>
 +
    <td>pLX-B3(omega)1</td>
 +
    <td>GGAG / CGCT</td>
 +
  </tr>
 +
</table>  
  
 
<p>GoldenBraid is a standardized assembly system based on type IIS restriction enzymes “that allows the indefinite growth of composite parts through the succession of iterative assembling steps.” This criteria is important for us because our cloning plan requires assembling basic parts into three distinct genes and then assembling those genes together. Additionally, GoldenBraid was designed with the intention of being an assembly standard for plant synthetic biology [1], so it would be an appropriate method for our project.</p>
 
<p>GoldenBraid is a standardized assembly system based on type IIS restriction enzymes “that allows the indefinite growth of composite parts through the succession of iterative assembling steps.” This criteria is important for us because our cloning plan requires assembling basic parts into three distinct genes and then assembling those genes together. Additionally, GoldenBraid was designed with the intention of being an assembly standard for plant synthetic biology [1], so it would be an appropriate method for our project.</p>

Latest revision as of 04:33, 10 October 2022


Ferritin with prSSG1 transit peptide + RUBY + nptII


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 95
    Illegal BglII site found at 527
    Illegal BglII site found at 3119
    Illegal BglII site found at 7127
    Illegal BglII site found at 8211
    Illegal BamHI site found at 5776
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 3712
    Illegal NgoMIV site found at 4291
    Illegal NgoMIV site found at 6004
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 2430
    Illegal BsaI site found at 7522
    Illegal BsaI site found at 9457
    Illegal BsaI.rc site found at 2709
    Illegal BsaI.rc site found at 7801
    Illegal BsaI.rc site found at 9736


Design Notes

The three genes (BBa_K4452015, BBa_K4452017, BBa_K4452018) and a synthetic spacer (BBa_K4452009) were assembled into BBa_K4452025 using Golden Braid assembly, specifically level omega assembly with BsmBI.

Part Description BsmBI site
BBa_K4452015 Ferritin GGAG / AATG
BBa_K4452017 RUBY reporter AATG / AGCC
BBa_K4452018 nptII Antibiotic Resistance AGCC / TTCG
BBa_K4452009 M13R primer TTCG / CGCT
BBa_K4452010 pLX-B3(omega)1 GGAG / CGCT

GoldenBraid is a standardized assembly system based on type IIS restriction enzymes “that allows the indefinite growth of composite parts through the succession of iterative assembling steps.” This criteria is important for us because our cloning plan requires assembling basic parts into three distinct genes and then assembling those genes together. Additionally, GoldenBraid was designed with the intention of being an assembly standard for plant synthetic biology [1], so it would be an appropriate method for our project.

Implementation of GoldenBraid requires (1) specific type IIS restriction sites on basic parts and (2) specific destination plasmids with type IIS restriction sites positioned inside the vectors to allow for “braiding” parts binarily in indefinite successive iterations.

Basic parts are flanked with BsaI recognition-cleavage sites using distinct 4 bp cleavage sequences for neighboring basic parts such that the parts can be assembled in a specified sequence. When the parts are ligated with the correct destination plasmid that is flanked by BsaI sites in divergent orientation, all BsaI recognition sites disappear from the resulting expression plasmid. This process of putting the parts into a destination plasmid with BsaI digestion is referred to as level alpha assembly.

To assemble parts from level alpha plasmids into another destination plasmid requires BsmBI digestion, this is referred to as level omega assembly. The level alpha plasmids and the level omega destination plasmid will be flanked by complementary 4 bp BsmBI cleavage sites.

Source

none

References

[1] Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juárez P, Fernández-del-Carmen A, et al. (2011) GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules. PLOS ONE 6(7): e21622. https://doi.org/10.1371/journal.pone.0021622