Difference between revisions of "Part:BBa J36848"

(→‎Usage and Biology)
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<b>Possible error in Spring 2008 distribution information</b>
 
<b>Possible error in Spring 2008 distribution information</b>
  
−
The sequence data for this construct suggest it's on plasmid backbone pSB1A3, not pSB1A2 as the 2008 Spring Distribution states. The bases following the PstI site are 5'-tccggcaaaaaa-3' which matches pSB1A3, while the same section of pSB1A2 reads 5'-gcttcctcgctc-3'.  
+
The sequence data for this construct in the 2008 Spring Distribution suggest it's on plasmid backbone pSB1A3, not pSB1A2 as the stated in the documentation. The bases following the PstI site are 5'-tccggcaaaaaa-3' which matches pSB1A3, while the same locus on pSB1A2 reads 5'-gcttcctcgctc-3'.  
  
−
Also, the 'inconsistent' sequence data is due to the fact that, in order to conform to the composite parts format, an 8 base scar is shown in the 'get selected sequence' readout. The sequencing data is checked against this sequence with the 8-base scars, not the 6-base in-frame scars that are part of the sequencing data.
+
Also, the 'inconsistent' sequence data is due to the fact that, in order to conform to the composite parts format, an 8 base scar is shown in the 'get selected sequence' readout. The sequencing data is checked against this sequence with the 8-base scars, not the 6-base in-frame scars that are part of the sequencing data from the actual plasmid.
 
<b>--robere, University of Washington iGEM team, 11 Sept 2009</b>
 
<b>--robere, University of Washington iGEM team, 11 Sept 2009</b>
  
  
 
===Usage and Biology===
 
===Usage and Biology===
−
Characterized by [http://2009.igem.org/Team:Washington Washington 2009 iGEM team]. We sought to use these parts to display streptavidin on the surface of the cell.  We confirmed the expression of these proteins by Western blot using an anti-His detection reagent. We then assayed each part for biotin binding using flow cytometry. Our assay was to incubate cells with a biotinylated fluorophore, wash cells, and then monitor by flow cytometry the retention of fluorophore on the surface of cells that had this part induced with IPTG.  In this experiment, increased florescence would indicate binding interactions between the streptavadin and the biotin. Our results are described below in the histogram, the y-axis is the event frequency (equivalent to the number of cells counted) and the x-axis is the fluorescence intensity (FLA-1) of the cells/beads:
+
Characterized by [http://2009.igem.org/Team:Washington Washington 2009 iGEM team]. We sought to use these parts to display streptavidin on the surface of the cell.  We confirmed the expression of these proteins by Western blot using an anti-His detection reagent. We then assayed each part for biotin binding using flow cytometry. Our assay was to incubate cells with a biotinylated fluorophore, wash cells, and then monitor by flow cytometry the retention of fluorophore on the surface of cells that had this part induced with IPTG.  In this experiment, increased florescence would indicate binding interactions between the streptavadin and the biotin. Our results are described below in the histogram, the y-axis is the event frequency (equivalent to the number of cells counted) and the x-axis is the fluorescence intensity (FL1-A: 488 nm excitation, 515-545 nm emission) of the cells/beads:
  
 
<gallery heights=300px widths=425>
 
<gallery heights=300px widths=425>
−
Image:48.png|'''BBa_J36848''' ''This image shows both the induced and uninduced cells for part 48 in varying levels of flourophore (0nM to 100nM). Expression of the surface display streptavidin in the cells was induced at 1mM IPTG. This data shows that there is no appreciable difference between the induced and uninduced cells at any given level of flourophore.  There is an increase in fluorescence that increases with increased concentration of incubation - we believe this is because there is due to residual fluorophore present in solution after washing.  Fluorescence retention was minimal compared to streptavidin-coated beads (see Control).  For more info please see our [http://2009.igem.org/Team:Washington/Project/Display#Data iGEM 2009 Washington Display Wiki].''
+
Image:48.png|'''BBa_J36848''' ''This image shows both the induced and uninduced cells for part 48 incubated in three levels of flourophore: 0M, 10nM, and 100nM. Expression of the surface display streptavidin in the cells was induced with 1mM IPTG. This data shows that there is no appreciable difference between the induced and uninduced cells at any given level of fluorophore.  There is an increase in fluorescence that increases with increased concentration of incubation - we believe this is because there is due to residual fluorophore present in solution after washing.  Fluorescence retention was minimal compared to streptavidin-coated beads (see Control).  For more info please see our [http://2009.igem.org/Team:Washington/Project/Display#Data iGEM 2009 Washington Display Wiki].''
−
Image:StreptBead cyto.png|'''+ Control''' ''We used streptavidin-coated beads as a positive control for binding of the biotinylated fluorophore to streptavidin.  For this experiment, we treated beads as we treated the cells - incubation in biotinylated fluorophore followed by washing and fluorescence measurement by flow cytometry.  As the concentration of flourophore was increased we could see increased retention between the beads and the flouophore. The black line is beads with no flouophore, the red is with 10 nM, and the blue is 100 nM. These showed a clear difference between the beads without flourophore and the beads with flourophore.  See [http://2009.igem.org/Team:Washington/Notebook iGEM 2009 Washington Protocols] for details.''
+
Image:StreptBead cyto.png|'''+ Control''' ''We used streptavidin-coated beads (SVP-15-5 1.5-1.9 &mu;m polystyrene spheres, [http://www.spherotech.com/coa_pol_par.htm Spherotech]) as a positive control for binding of the biotinylated fluorophore (biotin (5-fluorescein) conjugate, [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=53608|SIGMA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC Sigma Aldrich]) to streptavidin.  For this experiment, we treated beads as we treated the cells - incubation in biotinylated fluorophore followed by washing and fluorescence measurement by flow cytometry.  As the concentration of flourophore was increased we could see increased retention between the beads and the flouophore. The black line is beads with no flouophore, the red is with 10 nM, and the blue is 100 nM. These showed a clear difference between the beads without flourophore and the beads with flourophore.  See [http://2009.igem.org/Team:Washington/Notebook iGEM 2009 Washington Protocols] for details.''
 
</gallery>
 
</gallery>
−
 
−
 
−
 
  
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>

Revision as of 06:05, 20 October 2009

Lac-inducible generator of Lpp-OmpA(46-66)-Streptavidin wild-type + His6tag

This device contains a lac promoter and strong ribosome binding site for lac-inducible expression of the fusion protein of Lpp signal peptide, OmpA aa46-66, and streptavidin wild-type + His6 tag. This expression should display streptavidin on the cell surface of E. coli.

NOTE ABOUT THE SEQUENCE: The mixed site between parts is 'only' six base pairs, ACTAGA. There is no spacer T or G nucleotide. These spacer nucleotides have been placed in the results for "get selected sequence" as an automatic composite-parts addition for the BioBricks mixed site between assembled parts. However, this does not apply for the two spacer nucleotides betweeon R0010 and B0034, and the one spacer nucleotide after B0034, because those were standard BioBricks.

Possible error in Spring 2008 distribution information

The sequence data for this construct in the 2008 Spring Distribution suggest it's on plasmid backbone pSB1A3, not pSB1A2 as the stated in the documentation. The bases following the PstI site are 5'-tccggcaaaaaa-3' which matches pSB1A3, while the same locus on pSB1A2 reads 5'-gcttcctcgctc-3'.

Also, the 'inconsistent' sequence data is due to the fact that, in order to conform to the composite parts format, an 8 base scar is shown in the 'get selected sequence' readout. The sequencing data is checked against this sequence with the 8-base scars, not the 6-base in-frame scars that are part of the sequencing data from the actual plasmid. --robere, University of Washington iGEM team, 11 Sept 2009


Usage and Biology

Characterized by [http://2009.igem.org/Team:Washington Washington 2009 iGEM team]. We sought to use these parts to display streptavidin on the surface of the cell. We confirmed the expression of these proteins by Western blot using an anti-His detection reagent. We then assayed each part for biotin binding using flow cytometry. Our assay was to incubate cells with a biotinylated fluorophore, wash cells, and then monitor by flow cytometry the retention of fluorophore on the surface of cells that had this part induced with IPTG. In this experiment, increased florescence would indicate binding interactions between the streptavadin and the biotin. Our results are described below in the histogram, the y-axis is the event frequency (equivalent to the number of cells counted) and the x-axis is the fluorescence intensity (FL1-A: 488 nm excitation, 515-545 nm emission) of the cells/beads:

  • BBa_J36848 This image shows both the induced and uninduced cells for part 48 incubated in three levels of flourophore: 0M, 10nM, and 100nM. Expression of the surface display streptavidin in the cells was induced with 1mM IPTG. This data shows that there is no appreciable difference between the induced and uninduced cells at any given level of fluorophore. There is an increase in fluorescence that increases with increased concentration of incubation - we believe this is because there is due to residual fluorophore present in solution after washing. Fluorescence retention was minimal compared to streptavidin-coated beads (see Control). For more info please see our [http://2009.igem.org/Team:Washington/Project/Display#Data iGEM 2009 Washington Display Wiki].

  • + Control We used streptavidin-coated beads (SVP-15-5 1.5-1.9 μm polystyrene spheres, [http://www.spherotech.com/coa_pol_par.htm Spherotech]) as a positive control for binding of the biotinylated fluorophore (biotin (5-fluorescein) conjugate, [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=53608|SIGMA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC Sigma Aldrich]) to streptavidin. For this experiment, we treated beads as we treated the cells - incubation in biotinylated fluorophore followed by washing and fluorescence measurement by flow cytometry. As the concentration of flourophore was increased we could see increased retention between the beads and the flouophore. The black line is beads with no flouophore, the red is with 10 nM, and the blue is 100 nM. These showed a clear difference between the beads without flourophore and the beads with flourophore. See [http://2009.igem.org/Team:Washington/Notebook iGEM 2009 Washington Protocols] for details.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 432
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 474
    Illegal AgeI site found at 525
  • 1000
    COMPATIBLE WITH RFC[1000]