Difference between revisions of "Part:BBa K2170000:Design"

 
Line 7: Line 7:
  
 
===Design Notes===
 
===Design Notes===
−
none
 
  
 +
'''Related BioBrick:'''<br>
 +
*Related BioBricks:<br>
 +
[https://parts.igem.org/wiki/index.php?title=Part:BBa_K2170002 BBa_K2170002]: Secretory eukaryotic biotin binding receptor with single chain avidin <br>
 +
[https://parts.igem.org/wiki/index.php?title=Part:BBa_K2170001 BBa_K2170001]: Secretory eukaryotic biotin binding receptor with enhanced monomeric avidin
  
 +
 +
'''Cloning details:'''<br>
 +
*Designed in RFC25
 +
<!--Mutation C889G to delete XbaI restriction site-->
 +
<!--Truncation upstream/downstream compared to template, ?explanation?-->
 +
 +
'''Quality control measures:'''<br>
 +
*Test digestion using EcorRI & PstI
 +
*Sequencing using VF2
 +
*Part was partly sequenced
 +
 +
'''Backbone:'''<br>
 +
*Backbone name: pSB1C3<br>
 +
*Resistance: Cp<br>
 +
*Copynumber: high
 +
 +
'''Protein coding:'''<br>
 +
*Protein:
 +
Biotinylated receptor with biotin acceptor peptid [Nucleotide 633  to 2204]
 +
Secretory BirA [Nucleotide 2605  to 3672]
 +
*Tag: internal A3C5 tag/ C terminal ''Strep'' TagII
 +
 +
 +
 +
'''Enzymatic activity:'''
 +
*none
 +
 +
'''Cytotoxicity:'''<br>
 +
*not known
 +
 +
'''Safety notes:'''<br>
 +
*Known and anticipated sefety issues: none
 +
*Known and anticipated security issues: none
 +
 +
'''Intellectual property:'''
 +
<!--Information on patent situation.-->
 +
<!--Intellectual property claims made by the authors.-->
 +
 +
'''Corresponding part author/authors:'''
 +
<!--https://igem.org/User_Information.cgi?user_id=????/email-->
  
 
===Source===
 
===Source===
  
−
assembly
+
'''Source:'''<br>
 +
<!--*Commercial system: plasmid name, system name, company name-->
 +
<!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
 +
<!--*Preexisting BioBrick ?Bba_number?-->
 +
<!--*cDNA Clone: ?clone_name?, ?company_name?-->
 +
* Parts synthesized by IDT
 +
 
 +
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>-->
 +
<!--'''Reverse Primer:'''<br><code>5'- ??? - 3'</code><br>-->
 +
 
 +
'''Organism:'''<br>
 +
Genesequence designed for:
 +
<!--*Codonoptimized for ''?organism_name?''-->
 +
* eucaryotic cells e.g. Mexi or Trex
 +
<!--*Statement about functionality in other chassis.-->
 +
 
 +
<!--Thank you very much for using BBF RFC 82 to describe the present BioBrick. If you have any remarks or recommendations concerning this RFC we would highly appreciate to get your feedback on: []-->
  
 
===References===
 
===References===
 +
<!-- Here you find templates to insert references to literature and different databases-->
 +
 +
'''Literature references:'''<br>
 +
1. [http://www.nature.com/nmeth/journal/v2/n2/full/nmeth735.html Chen, I., Howarth, M., Lin, W., & Ting, A. Y. (2005). Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase. Nature methods, 2(2), 99-104.]<br>
 +
2. [http://jcb.rupress.org/content/108/2/229.short Kozak, M. (1989). The scanning model for translation: an update. The Journal of cell biology, 108(2), 229-241.]<br>
 +
3. [http://nar.oxfordjournals.org/content/15/20/8125.short Kozak, M. (1987). An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic acids research, 15(20), 8125-8148.]<br>
 +
4. [http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1701.html Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature methods, 8(10), 785-786.]<br>
 +
5. [http://content.iospress.com/articles/human-antibodies/hab5-1-2-11  Alexander, H., Harpprecht, J., Podzuweit, H. G., Rautenberg, P., & Müller-Ruchholtz, W. (1994). Human monoclonal antibodies recognize early and late viral proteins of human cytomegalovirus. Human Antibodies, 5(1-2), 81-90. 6. ]<br>
 +
7. [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.000439 Kredel, S., Oswald, F., Nienhaus, K., Deuschle, K., Röcker, C., Wolff, M., ... & Wiedenmann, J. (2009). mRuby, a bright monomeric red fluorescent protein for labeling of subcellular structures. PloS one, 4(2), e4391.]<br>
 +
8. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754705/ Bajar, B. T., Wang, E. S., Lam, A. J., Kim, B. B., Jacobs, C. L., Howe, E. S., ... & Chu, J. (2016). Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting. Scientific reports, 6.]<br>
 +
9. [http://www.nature.com/nprot/journal/v2/n6/abs/nprot.2007.209.html Schmidt, T. G., & Skerra, A. (2007). The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins. Nature protocols, 2(6), 1528-1535.]<br>

Revision as of 16:20, 19 October 2016


Biotinylated receptor with biotin acceptor peptide combined with a secretory BirA


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 576
    Illegal BglII site found at 3529
    Illegal BamHI site found at 2597
    Illegal XhoI site found at 761
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 2372
    Illegal BsaI site found at 4077
    Illegal BsaI.rc site found at 743
    Illegal SapI site found at 2529


Design Notes

Related BioBrick:

  • Related BioBricks:

BBa_K2170002: Secretory eukaryotic biotin binding receptor with single chain avidin
BBa_K2170001: Secretory eukaryotic biotin binding receptor with enhanced monomeric avidin


Cloning details:

  • Designed in RFC25

Quality control measures:

  • Test digestion using EcorRI & PstI
  • Sequencing using VF2
  • Part was partly sequenced

Backbone:

  • Backbone name: pSB1C3
  • Resistance: Cp
  • Copynumber: high

Protein coding:

  • Protein:

Biotinylated receptor with biotin acceptor peptid [Nucleotide 633 to 2204] Secretory BirA [Nucleotide 2605 to 3672]

  • Tag: internal A3C5 tag/ C terminal Strep TagII


Enzymatic activity:

  • none

Cytotoxicity:

  • not known

Safety notes:

  • Known and anticipated sefety issues: none
  • Known and anticipated security issues: none

Intellectual property:

Corresponding part author/authors:

Source

Source:

  • Parts synthesized by IDT


Organism:
Genesequence designed for:

  • eucaryotic cells e.g. Mexi or Trex


References

Literature references:
1. [http://www.nature.com/nmeth/journal/v2/n2/full/nmeth735.html Chen, I., Howarth, M., Lin, W., & Ting, A. Y. (2005). Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase. Nature methods, 2(2), 99-104.]
2. [http://jcb.rupress.org/content/108/2/229.short Kozak, M. (1989). The scanning model for translation: an update. The Journal of cell biology, 108(2), 229-241.]
3. [http://nar.oxfordjournals.org/content/15/20/8125.short Kozak, M. (1987). An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic acids research, 15(20), 8125-8148.]
4. [http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1701.html Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature methods, 8(10), 785-786.]
5. [http://content.iospress.com/articles/human-antibodies/hab5-1-2-11 Alexander, H., Harpprecht, J., Podzuweit, H. G., Rautenberg, P., & Müller-Ruchholtz, W. (1994). Human monoclonal antibodies recognize early and late viral proteins of human cytomegalovirus. Human Antibodies, 5(1-2), 81-90. 6. ]
7. [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.000439 Kredel, S., Oswald, F., Nienhaus, K., Deuschle, K., Röcker, C., Wolff, M., ... & Wiedenmann, J. (2009). mRuby, a bright monomeric red fluorescent protein for labeling of subcellular structures. PloS one, 4(2), e4391.]
8. Bajar, B. T., Wang, E. S., Lam, A. J., Kim, B. B., Jacobs, C. L., Howe, E. S., ... & Chu, J. (2016). Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting. Scientific reports, 6.
9. [http://www.nature.com/nprot/journal/v2/n6/abs/nprot.2007.209.html Schmidt, T. G., & Skerra, A. (2007). The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins. Nature protocols, 2(6), 1528-1535.]