Difference between revisions of "Part:BBa K2170002:Design"
Line 8: Line 8:
 
===Design Notes===
 
===Design Notes===
  
−
'''Related BioBrick:'''
+
'''Related BioBrick:'''<br>
−
<!--*Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part] -->
+
*Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_K2170001 BBa_K2170001]: Secretory eukaryotic biotin binding receptor with enhanced monomeric avidin <br>
−
<!--*Related BioBricks:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part]
+
*Related BioBricks:[https://parts.igem.org/wiki/index.php?title=BBa_K2170003 BBa_K2170003]: Biotinylated receptor with biotin acceptor peptide combined with a secretory BirA
  
 
'''Cloning details:'''<br>
 
'''Cloning details:'''<br>
−
<!--*Designed in RFC10/RFC23/RFC25-->
+
*Designed in RFC25
−
<!--*Mutation C889G to delete XbaI restriction site-->
+
<!--Mutation C889G to delete XbaI restriction site-->
−
<!--*Truncation upstream/downstream compared to template, ?explanation?-->
+
<!--Truncation upstream/downstream compared to template, ?explanation?-->
  
 
'''Quality control measures:'''<br>
 
'''Quality control measures:'''<br>
−
<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
+
*Test digestion using EcorRI & PstI
−
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
+
*Sequencing using VF2
−
<!--*Part was partly sequenced/Part was totally sequenced-->
+
*Part was partly sequenced
  
 
'''Backbone:'''<br>
 
'''Backbone:'''<br>
−
<!--*Backbone name: pSB1C3'/?backbone_name?-->
+
*Backbone name: pSB1C3<br>
−
<!--*Resistance: Amp/Cp/Kan/-->
+
*Resistance: Cp<br>
−
<!--*Copynumber: low/medium/high-->
+
*Copynumber: high
  
 
'''Protein coding:'''<br>
 
'''Protein coding:'''<br>
−
<!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
+
*Protein: Secretory eukaryotic biotin binding receptor with single chain avidin [Nucleotide 633  to 2027]
−
<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
+
 
−
<!--*The protein encoded is posttranslationally modified by ???.-->
+
 
−
<!--*Tag: n-terminally fused/c-terminally fused His5/His6/Strep/Flag/other-->
+
  
 
'''Enzymatic activity:'''
 
'''Enzymatic activity:'''
−
<!--none/EC-number ?.?.?.?-->
+
*none
  
 
'''Cytotoxicity:'''<br>
 
'''Cytotoxicity:'''<br>
−
<!--none/not known/cytotoxic for ''organism name''-->
+
*not known
  
 
'''Safety notes:'''<br>
 
'''Safety notes:'''<br>
−
<!--Known and anticipated sefety issues: none/health_risk/environmental_risk/other_risk-->
+
*Known and anticipated sefety issues: none
−
<!--Known and anticipated security issues: none/other.-->
+
*Known and anticipated security issues: none
  
 
'''Intellectual property:'''
 
'''Intellectual property:'''
Line 57: Line 56:
 
<!--*Preexisting BioBrick ?Bba_number?-->
 
<!--*Preexisting BioBrick ?Bba_number?-->
 
<!--*cDNA Clone: ?clone_name?, ?company_name?-->
 
<!--*cDNA Clone: ?clone_name?, ?company_name?-->
−
<!--*Synthesized by ?company_name?.-->
+
* Parts synthesized by IDT
  
 
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>-->
 
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>-->
Line 63: Line 62:
  
 
'''Organism:'''<br>
 
'''Organism:'''<br>
−
Genesequence derived from ''Escherichia coli''
+
Genesequence designed for:
 
<!--*Codonoptimized for ''?organism_name?''-->
 
<!--*Codonoptimized for ''?organism_name?''-->
−
<!--*Designed for the following Chassis: ''?organism-name?''-->
+
* eucaryotic cells e.g. Mexi or Trex
 
<!--*Statement about functionality in other chassis.-->
 
<!--*Statement about functionality in other chassis.-->
  
Line 74: Line 73:
  
 
'''Literature references:'''<br>
 
'''Literature references:'''<br>
−
<!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]-->
+
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>
  
 
'''Database references:'''<br>
 
'''Database references:'''<br>

Revision as of 13:46, 19 October 2016


Secretory eukaryotic biotin binding receptor with single chain avidin


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 576
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 3719


Design Notes

Related BioBrick:

  • Other versions:BBa_K2170001: Secretory eukaryotic biotin binding receptor with enhanced monomeric avidin
  • Related BioBricks:BBa_K2170003: Biotinylated receptor with biotin acceptor peptide combined with a secretory BirA

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: Secretory eukaryotic biotin binding receptor with single chain avidin [Nucleotide 633 to 2027]


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.]

Database references: