Daniel’s Part Design

This design is pretty much plagiarized off of Part: BBa1731009, designed by Stephanie 
Lo (Harvard 2007).

##NOTE: THIS IS NOT TO BE SYNTHESIZED!!

Parts Used:

-BBa_R0040: TetR repressible promoter

#TetR is a repressor that regulates “biosynthesis of antibiotics, efflux pumps, osmotic 
stress, etc.” (Microbiol. Mol. Biol. Rev. 2005 69(2)).
#This may help with secretion systems on a biomechanical level (cf. efflux pumps).
#Repression can be inhibited by the addition of tetracycline.

Sequence from registry:

tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac

-BBa_B0034: RBS based on Elowitz repressilator

#Wonder if necessary, considering repressilators are oscillators and I’m not too sure if we 
necessarily need them, but apparently it is useful in regulating GFP expression in cells.

Sequence from registry:

aaagaggagaaa

-Unnamed: Mefp-5

#I will need help in cutting this sequence short.

Sequence from Genbank:

atgaagctta gttgtatagt cttggtgctc tttcttgtga ccttagcagc ttatagcgat
gtaggctcat cgagttctga agaatacaag ggggggtatt acccaggcaa tgcgtaccac
tatcattcag gtggtagtta tcacggatcc ggctatcatg gaggatataa aggaaagtat
tacggaaaag caaagaaata ctattataaa tataaaaaca gcggaaaata caagtatctg
aagaaggcta gaaaatacca tagaaagggt tacaagtatt atggaggtag cagttagaca
ctcttgatag aatgaccact acatgaagat gaattctaaa gagtacaatg gtattgttca
gcaactattc caaatatggt catctttaat cgacaggttg tcataaaaat acaaataaac
aaatatatgt ataaaaaaaa aaaaaaaaaa aaaaaaa

Sequence to optimize:

atgaagctta gttgtatagt cttggtgctc tttcttgtga ccttagcagc ttatagcgat
gtaggctcat cgagttctga agaatacaag ggggggtatt acccaggcaa tgcgtaccac
tatcattcag gtggtagtta tcacggatcc ggctatcatg gaggatataa aggaaagtat
tacggaaaag caaagaaata ctattataaa tataaaaaca gcggaaaata caagtatctg
aagaaggcta gaaaatacca tagaaagggt tacaagtatt atggaggtag cagttagaca
ctcttgatag aatgaccact acatgaagat gaattctaaa gagtacaatg gtattgttca
gcaactattc caaatatggt catctttaat cgacaggttg tcataaaaat acaaataaac
aaatatatgt ataaaaaa

#Inclusive to bp438

-BBa_B0032: RBS.3 (medium)—derivative of BBa_0030

#Weak1 RBS based on “Ron Weiss thesis.” (Google search shows “Auto-repression can 
reduce noise”)
#Once again, more of an oscillatory system, so wonder if we need it.  It’ll help 
characterize the way the genes are expressed in the cells, hopefully.

Sequence from registry:

tcacacaggaaag

-BBa_E0040: GFP

#Excitation max – 501nm, Emission max – 511nm.

Sequence from registry:

atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgg
gcacaaattttctgtcagtggagagggtg
aaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatgg
ccaacacttgtcactactttcggttatgg
tgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaag
gttatgtacaggaaagaactatatttttc
aaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcga
gttaaaaggtattgattttaaagaagatg
gaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaa
aagaatggaatcaaagttaacttcaaaat
tagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatg
gccctgtccttttaccagacaaccattac
ctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgt
aacagctgctgggattacacatggcatgg
atgaactatacaaataataa

-BBa_B0010: T1 from E. coli rrnB

Sequence from registry:

ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtg
aacgctctc

-BBa_B0012: TE from coliphageT7

Sequence from registry:

tcacactggctcaccttcgggtgggcctttctgcgtttata

#I don’t know why they used two different stop sequences; if anyone can explain to me, 
please do!