Difference between revisions of "Part:BBa K2170001:Design"
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'''Related BioBrick:'''<br> | '''Related BioBrick:'''<br> | ||
− | Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_K2170002 BBa_K2170002]: Secretory eukaryotic biotin binding receptor with single chain avidin <br> | + | *Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_K2170002 BBa_K2170002]: Secretory eukaryotic biotin binding receptor with single chain avidin <br> |
− | Related BioBricks:[https://parts.igem.org/wiki/index.php?title= | + | *Related BioBricks:[https://parts.igem.org/wiki/index.php?title=Part:BBa_K2170000 BBa_K2170000]: Biotinylated receptor with biotin acceptor peptide combined with a secretory BirA |
'''Cloning details:'''<br> | '''Cloning details:'''<br> | ||
− | Designed in 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 EcorRI & PstI | + | *Test digestion using EcorRI & PstI |
− | Sequencing using VF2 | + | *Sequencing using VF2 |
− | Part was partly sequenced | + | *Part was partly sequenced |
'''Backbone:'''<br> | '''Backbone:'''<br> | ||
− | Backbone name: pSB1C3<br> | + | *Backbone name: pSB1C3<br> |
− | Resistance: Cp<br> | + | *Resistance: Cp<br> |
− | Copynumber: high | + | *Copynumber: high |
'''Protein coding:'''<br> | '''Protein coding:'''<br> | ||
− | Protein: Secretory eukaryotic biotin binding receptor with single chain avidin [Nucleotide 633 to 3314] | + | *Protein: Secretory eukaryotic biotin binding receptor with single chain avidin [Nucleotide 633 to 3314] |
+ | *Tag: internal A3C5 tag/ C terminal ''Strep'' TagII | ||
'''Enzymatic activity:''' | '''Enzymatic activity:''' | ||
− | none | + | *none |
'''Cytotoxicity:'''<br> | '''Cytotoxicity:'''<br> | ||
− | not known | + | *not known |
'''Safety notes:'''<br> | '''Safety notes:'''<br> | ||
− | Known and anticipated sefety issues: none | + | *Known and anticipated sefety issues: none |
− | Known and anticipated security issues: none | + | *Known and anticipated security issues: none |
'''Intellectual property:''' | '''Intellectual property:''' | ||
Line 56: | Line 57: | ||
<!--*Preexisting BioBrick ?Bba_number?--> | <!--*Preexisting BioBrick ?Bba_number?--> | ||
<!--*cDNA Clone: ?clone_name?, ?company_name?--> | <!--*cDNA Clone: ?clone_name?, ?company_name?--> | ||
− | Parts synthesized by IDT | + | * Parts synthesized by IDT |
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>--> | <!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>--> | ||
Line 62: | Line 63: | ||
'''Organism:'''<br> | '''Organism:'''<br> | ||
− | Genesequence | + | Genesequence designed for: |
<!--*Codonoptimized for ''?organism_name?''--> | <!--*Codonoptimized for ''?organism_name?''--> | ||
− | + | * eucaryotic cells e.g. Mexi or Trex | |
<!--*Statement about functionality in other chassis.--> | <!--*Statement about functionality in other chassis.--> | ||
Line 73: | Line 74: | ||
'''Literature references:'''<br> | '''Literature references:'''<br> | ||
− | [http://www.nature.com/nmeth/journal/v2/n2/full/nmeth735.html | + | 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> |
− | [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.] | + | 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> |
− | [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.] | + | 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> |
− | [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.] | + | 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> --> |
<!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]--> | <!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]--> | ||
<!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]--> | <!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]--> |
Latest revision as of 16:11, 19 October 2016
Secretory eukaryotic biotin binding receptor with enhanced monomeric avidin
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 576
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI site found at 2432
Design Notes
Related BioBrick:
- Other versions:BBa_K2170002: Secretory eukaryotic biotin binding receptor with single chain avidin
- Related BioBricks:BBa_K2170000: 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 3314]
- 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.]