Difference between revisions of "Part:BBa J45992:Design"

(→‎References)
(→‎Design Notes)
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===Design Notes===
 
===Design Notes===
 +
Primers used to PCR this part out of the ''E.coli'' genome:
  
−
Full Forward Primer: 5'- GTT TCT TCG AAT TCG CGG CCG CTT CTA GCTG GCA CAG GAA CGT TAT C - 3'
+
====Forward Primer====
 +
*5'- GTT TCT TCG AAT TCG CGG CCG CTT CTA GCTG GCA CAG GAA CGT TAT C - 3'
 +
*Total Length: 47 bp
 +
*Annealing Length: 19 bp
 +
*GC Content: 52.6%
 +
*Melting Temperature: 53.4 degrees C
 +
*hairpin deltaG: -3.99 kcal/mol
 +
*self dimer deltaG: -98.3 kcal/mol
  
−
Total Length: 47 bp
+
====Reverse Primer====
−
 
+
*5'-GTT TCT TCC TGC AGC GGC CGC TAC TAG TAT TGT TAA ATA TAG ATC ACA ATT TTG- 3'
−
Annealing Length: 19 bp
+
*Total Length: 54 bp
−
 
+
*Annealing Length: 25 bp
−
GC Content: 52.6%
+
*GC Content: 20.0%
−
 
+
*Melting Temperature: 46.4 degrees C
−
Melting Temperature: 53.4 degrees C
+
*hairpin deltaG: -2.86 kcal/mol
−
 
+
*self dimer deltaG: -99.44 kcal/mol
−
hairpin deltaG: -3.99 kcal/mol
+
*heterodimer deltaG with Forward Primer: -99.44 kcal/mol
−
 
+
−
self dimer deltaG: -98.3 kcal/mol
+
−
 
+
−
Reverse Primer: 5'-GTT TCT TCC TGC AGC GGC CGC TAC TAG TAT TGT TAA ATA TAG ATC ACA ATT TTG- 3'
+
−
 
+
−
Total Length: 54 bp
+
−
 
+
−
Annealing Length: 25 bp
+
−
 
+
−
GC Content: 20.0%
+
−
 
+
−
Melting Temperature: 46.4 degrees C
+
−
 
+
−
hairpin deltaG: -2.86 kcal/mol
+
−
 
+
−
self dimer deltaG: -99.44 kcal/mol
+
−
 
+
−
heterodimer deltaG with Forward Primer: -99.44 kcal/mol
+
  
 
===Source===
 
===Source===

Revision as of 05:03, 31 October 2006


Full-length stationary phase osmY promoter


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Primers used to PCR this part out of the E.coli genome:

Forward Primer

  • 5'- GTT TCT TCG AAT TCG CGG CCG CTT CTA GCTG GCA CAG GAA CGT TAT C - 3'
  • Total Length: 47 bp
  • Annealing Length: 19 bp
  • GC Content: 52.6%
  • Melting Temperature: 53.4 degrees C
  • hairpin deltaG: -3.99 kcal/mol
  • self dimer deltaG: -98.3 kcal/mol

Reverse Primer

  • 5'-GTT TCT TCC TGC AGC GGC CGC TAC TAG TAT TGT TAA ATA TAG ATC ACA ATT TTG- 3'
  • Total Length: 54 bp
  • Annealing Length: 25 bp
  • GC Content: 20.0%
  • Melting Temperature: 46.4 degrees C
  • hairpin deltaG: -2.86 kcal/mol
  • self dimer deltaG: -99.44 kcal/mol
  • heterodimer deltaG with Forward Primer: -99.44 kcal/mol

Source

This part was PCRed out of E. coli's genome with the primers listed in the design notes section.

References

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=453110&dopt=GenBank

http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=8282684

http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=9829938

http://www.blackwell-synergy.com/doi/abs/10.1046/j.1365-2958.2002.02746.x

http://www.pubmedcentral.org/articlerender.fcgi?artid=178012

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T3C-456T3CY-3&_coverDate=04%2F25%2F2002&_alid=423325879&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=4943&_sort=d&view=c&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=7d6f4bac2242f1baa6b2b15260904531