BBa_M36135
1
BBa_M36135
Transcription terminator (apFAB388)
2012-05-31T11:00:00Z
2015-05-08T01:14:03Z
BIOFAB: part apFAB388, construct pFAB822
Released HQ 2013
Strong terminator from BIOFAB's terminator project
false
false
_848_
0
13700
9
In stock
false
Length similar to terminators used in Delebecque et al., Science 2011
false
Vir Choksi
BBa_M36128
1
BBa_M36128
d2' (RNA scaffold)
2012-05-31T11:00:00Z
2015-05-08T01:14:03Z
Delebecque et al, Science 2011.
Encodes for the first part of a 2-dimensional self-assembling RNA scaffold.
d2' is a sequence followed by the PP7 binding domain. The 2D RNA assembly D2 forms from d2' and d2'', each followed by a distinct PP7 and MS2 aptamer. The dormant tile d2' spontaneously generates the pro-tile d2-1, which interacts with d2'' to generate tile d2-2. d2-2 then self-assembles into the 2D RNA scaffold D2 with PP7 and MS2 binding domains.
false
false
_848_
0
13700
9
Not in stock
false
This part is only functional in the context of the other parts required for the 2D RNA scaffold.
false
Vir Choksi
BBa_M36132
1
BBa_M36132
2D inducible RNA scaffold
2012-05-31T11:00:00Z
2015-05-08T01:14:03Z
RNA scaffold comes from Delebecque et al., Science 2011
Ribozyme switch comes from Win & Smolke, PNAS 2007
Self-assembles into a two-dimensional RNA scaffold with binding domains for MS2 and PP7 proteins. When presented with theophylline, the ribozyme should cleave the scaffold sequences, releasing the aptamers from the existing scaffold and preventing other scaffolds from forming.
false
false
_848_
0
13700
9
Not in stock
false
The riboswitch was inserted into the scaffold sequence directly upstream of the aptamer. Spacers were used to prevent folding issues with the scaffold and ribozyme components of the transcripts.
false
Vir Choksi, Daniel McHugh
component2176095
1
BBa_M36126
component2176088
1
BBa_M36129
component2176092
1
BBa_M36136
component2176089
1
BBa_M36135
component2176094
1
BBa_M36127
component2176093
1
BBa_M36130
component2176087
1
BBa_M36128
component2176096
1
BBa_M36135
component2176091
1
BBa_B0040
annotation2176092
1
BBa_M36136
range2176092
1
240
390
annotation2176088
1
BBa_M36129
range2176088
1
71
106
annotation2176096
1
BBa_M36135
range2176096
1
583
621
annotation2176089
1
BBa_M36135
range2176089
1
115
153
annotation2176095
1
BBa_M36126
range2176095
1
455
574
annotation2176094
1
BBa_M36127
range2176094
1
433
446
annotation2176093
1
BBa_M36130
range2176093
1
399
424
annotation2176091
1
BBa_B0040
range2176091
1
162
231
annotation2176087
1
BBa_M36128
range2176087
1
1
62
BBa_M36136
1
BBa_M36136
Rhamnose-inducible promoter
2012-05-31T11:00:00Z
2015-05-08T01:14:03Z
The rhamnose-inducible promoter is described in Giacolone et al., Biotechniques 2006. We used bases
1951-2101 from BBa_K564001.
This is a rhamnose-inducible promoter. We used bases 1951-2101 from BBa_K564001. It is induced by 1000 micromolar rhamnose.
false
false
_848_
0
13700
9
Not in stock
false
We used bases 1951-2101 from BBa_K564001.
false
Vir Choksi
BBa_M36130
1
BBa_M36130
d2'' (RNA scaffold)
2012-05-31T11:00:00Z
2015-05-08T01:14:03Z
Delebecque et al, Science 2011
d2'' is the second part required for formation of the 2-dimensional RNA scaffold.
The 2D RNA assembly D2 forms from d2' and d2'', each followed by a distinct PP7 and MS2 aptamer. The dormant tile d2' spontaneously generates the pro-tile d2-1, which interacts with d2'' to generate tile d2-2. d2-2 then self-assembles into the 2D RNA scaffold D2 with PP7 and MS2 binding domains.
false
false
_848_
0
13700
9
Not in stock
false
d2'' is only functional when used along with other parts required for the 2D RNA scaffold.
false
Vir Choksi
BBa_M36126
1
BBa_M36126
Theophylline responsive ribozyme
2012-05-31T11:00:00Z
2015-05-08T01:14:03Z
M. N. Win, C. D. Smolke, ???A modular and extensible RNA-based gene-regulatory platform for engineering cellular function??? PNAS 36, 14283-14288 (2007).
Ribozyme that self-cleaves in the presence of theophylline.
false
false
_848_
0
13699
9
Not in stock
false
The part includes two brief spacer sequences to ensure functionality over a range of transcript contexts.
false
Daniel McHugh
BBa_M36127
1
BBa_M36127
MS2 aptamer
2012-05-31T11:00:00Z
2015-05-08T01:14:03Z
C. J. Delebecque, A. B. Lindner, P. A. Silver, F. A. Aldaye, ???Organization of intracellular reactions with rationally designed RNA assemblies??? Science 333, 470-474 (2011).
Encodes for an RNA sequence which functions as the binding domain for the MS2 bacteriophage coat protein.
false
false
_848_
0
13699
9
Not in stock
false
Can be used in the context of the one- and two- dimensional RNA scaffolds described in the Delebecque paper.
false
Daniel McHugh
BBa_B0040
1
spacer
Spacer.1 (generic)
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
Randomly generated and optimized for several parameters (see Design notes).
Released HQ 2013
Generic spacer for ensuring a 70 bp distance between the end of the suffix of the BioBrick part containing the double terminator and the prefix of the BioBrick part containing the promoter of the new gene. Please, use the AlignX function of Vector NT to check for homology with the components in your plasmid before using this spacer.</P>
false
false
_1_
0
24
7
In stock
false
<P> <P><p>The size of the spacer was choosed to meet the minimum length of a sequence that can be queried using the BLAST search engine. However, subsequences of it can be used to design shorter spacers. The sequence was selected from many more sequences randomly generated using the <a href="http://www.lifesci.ucsb.edu/~maduro/random.htm">Random DNA Generator </a>engine; the GC% parameter used as input was 50%. The sequences were selected based on the following constraints listed in their order of importance: the absence of any putative promoter regions, a low degree of homology with the Elowitz plasmid (whose components are widely used in our designs), no homology with other <em>E.coli</em> sequences as shown by BLASTN search results and the presence of a number of TAA stop codons. The second constraint was the most stringent leading to the elimination of most sequences. </p> <p> DE made the following changes to the original sequence in order to add stop codons in the -3 frame and more in the +2 frame (note, not all of these stop codons are UAA. Thus, if used in an organism that inserts an amino acid @ UGA or UAG the obvious will occur):<br> T->A @ 85<br> T->A @ 42<br> C->T @ 79<br> A->T @ 64<br> A->T @ 31<br> T->A @ 34<br> C->A @ 37<br> Also, note that the above changes further reduce (the already very weak) homology to current NCBI-stored sequences.<br> </p> <P>In the process of selecting the best sequence it appeared that a good alternative sequence for a spacer would be: AGGTTCTGATATGTAACTGTGCCCAATGTCGTTAGTGACGCATACCTCTTAAGAGGCCACTGTCCTAACA. The sequence contains no putative promoters and shows moderate homology with the 5' end of the Ampicillin resistance gene. However a strong promoter sequence starts 12 bp downstream of this sequence, and therefore the sequence presented above was preferred. </p><P> The sequence is compatible (does not show significant homology) with the components in the Elowitz repressilator plasmid.
true
Vinay S. Mahajan, Brian Chow, Peter Carr
annotation7030
1
BBa_B0040
range7030
1
1
70
annotation1721
1
Spacer-1
range1721
1
1
70
BBa_M36129
1
BBa_M36129
PP7 aptamer
2012-05-31T11:00:00Z
2015-05-08T01:14:03Z
C. J. Delebecque, A. B. Lindner, P. A. Silver, F. A. Aldaye, ???Organization of intracellular reactions with rationally designed RNA assemblies??? Science 333, 470-474 (2011).
Encodes for an RNA sequence which functions as the binding domain for the PP7 bacteriophage coat protein.
false
false
_848_
0
13699
9
Not in stock
false
Can be used in the context of the one- and two-dimensional RNA scaffolds described in the Delebecque paper.
false
Daniel McHugh
BBa_M36126_sequence
1
aaacaaacaaagctgtcaccggatgtgctttccggtctgatgagtccgtgataccagcatcgtcttgatgcccttggcagcagtggacgaggacgaaatgtcgaaaaagaaaaataaaaa
BBa_B0040_sequence
1
aggttctgttaagtaactgaacccaatgtcgttagtgacgcttacctcttaagaggtcactgacctaaca
BBa_M36136_sequence
1
gggaaaaagcgggaaatgcggacgacatcacaccggcctattagtagaaactgtgaacgctatcacgttcatctttgccttgttgccagcggctcattttcctgtcagtaacgagaaggtaggtctttgagggcttttttagactgtgcgc
BBa_M36128_sequence
1
tcaggaatcctggtgatagctatttggacaattacgtacgtagttgatgacaactacatgaa
BBa_M36129_sequence
1
gaattccgaccagaagatatggcttcggttgggttc
BBa_M36130_sequence
1
tagttgttatggattcctgatttatg
BBa_M36132_sequence
1
tcaggaatcctggtgatagctatttggacaattacgtacgtagttgatgacaactacatgaatactagaggaattccgaccagaagatatggcttcggttgggttctactagagaaaaaaaaaccccgcccctgacagggcggggtttttttttactagagaggttctgttaagtaactgaacccaatgtcgttagtgacgcttacctcttaagaggtcactgacctaacatactagaggggaaaaagcgggaaatgcggacgacatcacaccggcctattagtagaaactgtgaacgctatcacgttcatctttgccttgttgccagcggctcattttcctgtcagtaacgagaaggtaggtctttgagggcttttttagactgtgcgctactagagtagttgttatggattcctgatttatgtactagagccacagtcactgggtactagagaaacaaacaaagctgtcaccggatgtgctttccggtctgatgagtccgtgataccagcatcgtcttgatgcccttggcagcagtggacgaggacgaaatgtcgaaaaagaaaaataaaaatactagagaaaaaaaaaccccgcccctgacagggcggggtttttttt
BBa_M36127_sequence
1
ccacagtcactggg
BBa_M36135_sequence
1
aaaaaaaaaccccgcccctgacagggcggggtttttttt
igem2sbol
1
iGEM to SBOL conversion
Conversion of the iGEM parts registry to SBOL2.1
James Alastair McLaughlin
Chris J. Myers
2017-03-06T15:00:00.000Z