Please refer to individual parts. They are all more or less modified versions of E. coli K12 loci and its phage lambda.
This device gives PoPS-output on cell division. The DNA flanked by the opposing repeats of the dif-site is inverted and allows transcription of both any downstream element and a repressor which, upon sufficient build-up, switches off the promoter which controls downstream transcription. Inversion only occurs when the XerCD complex is activated, and this only occurs at cell division. Therefore this device produces a short burst of PoPS as a function of cell division. Any added downstream elements will likewise be activated, briefly, as a function of cell division.
Again, please refer to to part in question. However, as a general rule, all parts in 'non-default', bottom DNA strand need be synthesised in reverse complementary fashion. You will encounter parts that are called 'upside-down' or 'reverse complementary' for this reason.
RBS (Elowitz 1999) -- defines RBS efficiency
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix. No secondary structures are formed in the given RBS region. Users should check for secondary structures induced in the RBS by upstream and downstream elements in the +50 to -50 region, as such structures will greatly affect the strength of the RBS. Contact info for this part: Brian Chow
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
Lutz, R., Bujard, H., Nucleic Acids Research (1997) 25, 1203-1210.
Sequence for pTet inverting regulator driven by the TetR protein.
BBa_R0040 TetR-Regulated Promoter is based on a cI promoter. It has been modified to include two TetR binding sites and the BioBrick standard assembly head and tail restriction sites.
June Rhee, Connie Tao, Ty Thomson, Louis Waldman
Constitutive Promoter, High Transcription
Vikram Vijayan, Allen Hsu, Lawrence Fomundam
tetracycline repressor from transposon Tn10 (+LVA)
Elowitz, M. B. Transport, Assembly, and Dynamics in Systems of Interacting Proteins. Thesis, Princeton Univ., Princeton (1999)
Coding region for the TetR protein without the Ribosome Binding Site. Modified with an LVA tail for rapid degradation of the protein and faster fall time for the emission. TetR binds to the pTet regulator (BBa_R0040). aTc (anhydrotetracycline) binds to TetR and inhibits its operation.
References (unparsed) here: Elowitz, M. B. Transport, Assembly, and Dynamics in Systems of Interacting Proteins. Thesis, Princeton Univ., Princeton (1999). Lutz R, Bujard H., Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 1997 Mar 15;25(6):1203-10. PMID: 9092630 References (unparsed) here: Elowitz, M. B. Transport, Assembly, and Dynamics in Systems of Interacting Proteins. Thesis, Princeton Univ., Princeton (1999). Lutz R, Bujard H., Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 1997 Mar 15;25(6):1203-10. PMID: 9092630 BBa_C0040 TetR Protein is based on the TetR sequence from Elowitz's repressilator. It has been modified to include a rapid degradation LVA tail, and includes the BioBrick standard assembly head and tail restriction sites. The RBS has been removed. The stop codon has been changed from TAA to a double stop codon TAATAA.
June Rhee, Connie Tao, Ty Thomson, Louis Waldman.
This is an exact 'upside down' version of BBa_R0051. The promoter has two DNA binding sites for lambda cI repressor BBa_C0051. By adding this part, we wish to emphasise the possibility of engineering both DNA strands, and the additional regulatory potential that it gives.
Any 'upside down' (reverse complementary) sequences made by PCR amplification need be made with suffix and prefix is opposite order with respect to the original default sequence.
'dif' (division induced filamentation) is the recombination site for XerC and XerD recombinases. Once replicated, aligned direct repeats of the dif site are vital to DNA monomerisation during bacterial septation. As with other recombinase sites, inverted repeats cause inversion of the DNA in between. However, XerCD requires activation by FtsK and thus two dif-sites (see also part BBa_I742102) enables recombination that is temporally isolated to septation.
Constructed as two complimentary oligonucleotides.
Reverse terminator BBa_B0011 LuxICDABEG (+/-)
LuxICDABEG (+/-) forms a stem-loop which cancels transcription on both strands, whichever you choose to place it in. Please see BBa_B0011 for details about the terminator.
Please refer to the original (BB_B0034).
DNA is double-stranded. To translate genes of both strands, you need RBSs in both strands.
Please refer to the original, BBa_C0051.
This sequence encodes the cl repressor, only it encodes it in the 'non-default', bottom strand, rather than the straight-forward top one. When combined with the cl-responsive promoter, it enables regulatory control of both strands.
'dif' (division induced filamentation) is the recombination site for XerC and XerD recombinases. Once replicated, aligned direct dif repeats are vital to DNA monomerisation during bacterial septation. As with other recombination sites, inverted repeats cause inversion of the DNA in between. However, XerCD requires activation by FtsK and thus two dif-sites (see also part BBa_I742102) enable recombination that is temporally isolated to division.
Conversion of the iGEM parts registry to SBOL2.1