Difference between revisions of "Part:BBa K1442027:Design"
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===Design Notes===
 
===Design Notes===
  
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G highlighted in red changed from C to confer the R ---->G substitution indicated in the paper: ttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC114050/  
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G (1390) changed from C to confer the Arginine -> Glycine substitution indicated in the paper: ttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC114050/ which confers 500x increase in colony count.
  
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PstI restriction site CTGCAG → CTCCAG by changing the G at position 168 based on codon bias indicated in: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606. PstI= ctgcag= LQ (they are in frame in the RdRP).
  
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Before CUG=0.04% and CAG= 0.034%, which are indeed the highest. We went with CUC which is 0.02%, half than before remains the best option.
  
 
===Source===
 
===Source===
  
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[1] Blight and Norgard, 2006, Hepatitis C Viruses: Genomes and Molecular Biology, Horizon Biosciences.
 
http://www.ncbi.nlm.nih.gov/books/NBK1616/
 
http://www.ncbi.nlm.nih.gov/books/NBK1616/
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<p></p>
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[2] Schmitt et al., 2011, A Comprehensive Structure-Function Comparison of Hepatitis C Virus Strain JFH1 and J6 Polymerases Reveals a Key Residue Stimulating Replication in Cell Culture across Genotypes, Journal of Virology
 
http://jvi.asm.org/content/85/6/2565.full
 
http://jvi.asm.org/content/85/6/2565.full
  
 
===References===
 
===References===

Latest revision as of 13:25, 4 September 2014

HCV NS5B RDRP


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 289
    Illegal BglII site found at 1334
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 531
    Illegal SapI site found at 560


Design Notes

G (1390) changed from C to confer the Arginine -> Glycine substitution indicated in the paper: ttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC114050/ which confers 500x increase in colony count.

PstI restriction site CTGCAG → CTCCAG by changing the G at position 168 based on codon bias indicated in: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606. PstI= ctgcag= LQ (they are in frame in the RdRP).

Before CUG=0.04% and CAG= 0.034%, which are indeed the highest. We went with CUC which is 0.02%, half than before remains the best option.

Source

[1] Blight and Norgard, 2006, Hepatitis C Viruses: Genomes and Molecular Biology, Horizon Biosciences. http://www.ncbi.nlm.nih.gov/books/NBK1616/

[2] Schmitt et al., 2011, A Comprehensive Structure-Function Comparison of Hepatitis C Virus Strain JFH1 and J6 Polymerases Reveals a Key Residue Stimulating Replication in Cell Culture across Genotypes, Journal of Virology http://jvi.asm.org/content/85/6/2565.full

References