Difference between revisions of "Part:BBa K203109:Design"

(→‎Design Notes)
(→‎Design Notes)
 
Line 8: Line 8:
  
 
We performed [http://2009.igem.org/Team:Heidelberg/Project_Synthetic_promoters RA-PCR] with oligos containing binding sites for some well known generally activating transcription factors (Sp1, Ap1, CREB, NF-Y) which we identified from literature search [1],[2],[3]. We also added NF-κB responsive oligos as NF-κB has non-specific activity and is therefore used by a variety of viral constitutive promoters, e.g. the HIV promoter [4]. We then cloned the construct into [[Part:BBa_K203112]] by SpeI and HindIII to obtain a core promoter. We picked 24 colonies, two of which we dismissed after a test digest. This promoter corresponds to clone S5.  
 
We performed [http://2009.igem.org/Team:Heidelberg/Project_Synthetic_promoters RA-PCR] with oligos containing binding sites for some well known generally activating transcription factors (Sp1, Ap1, CREB, NF-Y) which we identified from literature search [1],[2],[3]. We also added NF-κB responsive oligos as NF-κB has non-specific activity and is therefore used by a variety of viral constitutive promoters, e.g. the HIV promoter [4]. We then cloned the construct into [[Part:BBa_K203112]] by SpeI and HindIII to obtain a core promoter. We picked 24 colonies, two of which we dismissed after a test digest. This promoter corresponds to clone S5.  
 +
 
[[Image:Rapcr.jpg|thumb|none|600px]]
 
[[Image:Rapcr.jpg|thumb|none|600px]]
  

Latest revision as of 13:31, 20 October 2009

Constitutive promoter; 2.5 REU


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

We performed [http://2009.igem.org/Team:Heidelberg/Project_Synthetic_promoters RA-PCR] with oligos containing binding sites for some well known generally activating transcription factors (Sp1, Ap1, CREB, NF-Y) which we identified from literature search [1],[2],[3]. We also added NF-κB responsive oligos as NF-κB has non-specific activity and is therefore used by a variety of viral constitutive promoters, e.g. the HIV promoter [4]. We then cloned the construct into Part:BBa_K203112 by SpeI and HindIII to obtain a core promoter. We picked 24 colonies, two of which we dismissed after a test digest. This promoter corresponds to clone S5.

Rapcr.jpg
Oligo name Oligo Sequence µL of Oligo used
NFkB responsive forward 1 GCGATCGGCAGATCAGGGGACTTTGCCGGGTGACGGGTTCA 0,5
NFkB responsive forward 2 GCGATCGGCAGATCAGGGGRWYYCCCGGGTGACGGGTTCA 0,5
NFkB responsive reverse TGATCTGCCGATCGCCCGTTTCAGGGGTGAACCCGTCACCC 1
Spacer reverse TGATCTGCCGATCGCNNNNNNNNNNTGAACCCGTCACCC 3
Sp1 responsive GCGATCGGCAGATCAGGGGCGGGGCGGGTGACGGGTTCA 2
Ap1 responsive GCGATCGGCAGATCATGACTCAGGGTGACGGGTTCA 1
CREB responsive GCGATCGGCAGATCABNBVNTGACGTCAGGGTGACGGGTTCA 1
NF-Y responsive GCGATCGGCAGATCANNCCAATNNGGGTGACGGGTTCA 1
Stop 5' CAGTACTAGTGGGTGACGGGTTCA 1
Stop 3' TGACAAGCTTAGTGAACCCGTCACCC 1

Source

Generated in our laboratory.

References

[1] Edelmann, G.M. et al. Synthetic promoter elements obtained by nucleotide sequence variation and selection for activity. PNAS 97, 3038-43 (2000).
[2] Ogawa, R. Construction of strong mammalian promoters by random cis-acting element elongation. Biotechniques 42, 628-632 (2007).
[3] Tornoe, J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 297, 21-32 (2002).
[4] Rattner, A. NF-kappa B activates the HIV promoter in neurons. EMBO 12, 4261–4267 (1993).