Difference between revisions of "Part:BBa K896002:Design"

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===Design Notes===
 
===Design Notes===
  
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1. Endogenious EcoRI site are at 1636bp and 4143bp, and PstI is at 121bp.  
+
1. Endogenious EcoRI sites are at 1636bp and 4143bp, and PstI sites are at 826bp and 3833bp.
  
−
2. Instead of mutant ctting site, we created a smart pSB1C3 plasmid (MfeI-XbaI -pSB1C3-SbfI-SpeI)for CysI cloning.
+
2. Endogenious BglII sites are at 1091bp and 4098bp, and NgoMIV sites are at 1741bp and 4748bp.
 +
 
 +
3. Endogenious AgeI sites are at 406bp, 1261bp, 3413bp, 4268bp.
 +
 
 +
4. We used BamHI(at 3008bp) to combine DsrI and DsrII gene, and produced Dsr gene.
 +
 
 +
5. Instead of mutant ctting site, we created a smart pSB1C3 plasmid (MfeI-XbaI -pSB1C3-SbfI-SpeI)for Dsr cloning.
 
   
 
   
−
3. Taking advantage of MfeI and EcoRI are compatible; SbfI and XbaI are compatible.
+
6. Taking advantage of MfeI and EcoRI are compatible; SbfI and XbaI are compatible.
 
   
 
   
−
4. Vector: MfeI-XbaI -pSB1C3-SbfI-SpeI, cut with MfeI and SbfI  
+
7. Vector: MfeI-XbaI -pSB1C3-SbfI-SpeI, cut with MfeI and SbfI  
  
−
5. Insert: CysI, cut with EcoRI and XbaI
+
8. Insert: Dsr, cut with EcoRI and XbaI
  
 
===Source===
 
===Source===
  
−
YES
+
Wildtype sulfite reductase which is originatal from Desulfovibrio desulfuricans w/o engineered.
  
 
===References===
 
===References===
 +
 +
1.[http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=27774&Template=bacteria Desulfovibrio desulfuricans subsp. desulfuricans ]
 +
 +
2.Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20, Hauser L.J., Land M.L., NUCLEOTIDE SEQUENCE LARGE SCALE GENOMIC DNA.
 +
 +
3.Dissimilatory Sulfite Reductase (Desulfoviridin) of the Taurine-Degrading, Non-Sulfate-Reducing Bacterium
 +
Bilophila wadsworthia RZATAU Contains a Fused DsrB-DsrD Subunit, HEIKE LAUE, MICHAEL FRIEDRICH et al, Journal of Bacteriology 183 (2001), 5, pp. 1727-1733.
 +
 +
4.Growth Yields and Growth Rates of. Desulfovibrio  vulgaris (Marburg) Growing on Hydrogen plus Sulfate and Hydrogen plus Thiosulfate as the Sole Energy Sources, Werner Badziong and Rudolf K. Thauer, Arch. Microbiol. 117, 209-214 [1978].
 +
 +
5.The Genus Desulfovibrio: The Centennial, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, GERRIT VOORDOUW, Aug. 1995, p. 2813–2819.
 +
 +
6.Microvolume turbidimetry for rapid and sensitive determination of the acid labile sulfide fraction in waters after headspace single-drop microextraction with in situ generation of volatile hydrogen sulfide, I. Lavilla, F. Pena-Pereira et al, Analytica Chimica Acta 647 (2009) 112–116.

Latest revision as of 19:51, 26 September 2012

Dsr (sulfite reductase)


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 1636
    Illegal EcoRI site found at 4648
    Illegal PstI site found at 826
    Illegal PstI site found at 3838
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 1636
    Illegal EcoRI site found at 4648
    Illegal PstI site found at 826
    Illegal PstI site found at 3838
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 1636
    Illegal EcoRI site found at 4648
    Illegal BglII site found at 1091
    Illegal BglII site found at 4103
    Illegal BamHI site found at 3007
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 1636
    Illegal EcoRI site found at 4648
    Illegal PstI site found at 826
    Illegal PstI site found at 3838
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 1636
    Illegal EcoRI site found at 4648
    Illegal PstI site found at 826
    Illegal PstI site found at 3838
    Illegal NgoMIV site found at 1741
    Illegal NgoMIV site found at 4753
    Illegal AgeI site found at 406
    Illegal AgeI site found at 1261
    Illegal AgeI site found at 3418
    Illegal AgeI site found at 4273
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

1. Endogenious EcoRI sites are at 1636bp and 4143bp, and PstI sites are at 826bp and 3833bp.

2. Endogenious BglII sites are at 1091bp and 4098bp, and NgoMIV sites are at 1741bp and 4748bp.

3. Endogenious AgeI sites are at 406bp, 1261bp, 3413bp, 4268bp.

4. We used BamHI(at 3008bp) to combine DsrI and DsrII gene, and produced Dsr gene.

5. Instead of mutant ctting site, we created a smart pSB1C3 plasmid (MfeI-XbaI -pSB1C3-SbfI-SpeI)for Dsr cloning.

6. Taking advantage of MfeI and EcoRI are compatible; SbfI and XbaI are compatible.

7. Vector: MfeI-XbaI -pSB1C3-SbfI-SpeI, cut with MfeI and SbfI

8. Insert: Dsr, cut with EcoRI and XbaI

Source

Wildtype sulfite reductase which is originatal from Desulfovibrio desulfuricans w/o engineered.

References

1.[http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=27774&Template=bacteria Desulfovibrio desulfuricans subsp. desulfuricans ]

2.Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20, Hauser L.J., Land M.L., NUCLEOTIDE SEQUENCE LARGE SCALE GENOMIC DNA.

3.Dissimilatory Sulfite Reductase (Desulfoviridin) of the Taurine-Degrading, Non-Sulfate-Reducing Bacterium Bilophila wadsworthia RZATAU Contains a Fused DsrB-DsrD Subunit, HEIKE LAUE, MICHAEL FRIEDRICH et al, Journal of Bacteriology 183 (2001), 5, pp. 1727-1733.

4.Growth Yields and Growth Rates of. Desulfovibrio vulgaris (Marburg) Growing on Hydrogen plus Sulfate and Hydrogen plus Thiosulfate as the Sole Energy Sources, Werner Badziong and Rudolf K. Thauer, Arch. Microbiol. 117, 209-214 [1978].

5.The Genus Desulfovibrio: The Centennial, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, GERRIT VOORDOUW, Aug. 1995, p. 2813–2819.

6.Microvolume turbidimetry for rapid and sensitive determination of the acid labile sulfide fraction in waters after headspace single-drop microextraction with in situ generation of volatile hydrogen sulfide, I. Lavilla, F. Pena-Pereira et al, Analytica Chimica Acta 647 (2009) 112–116.