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 annotation1721 1 Spacer-1 range1721 1 1 70 annotation7030 1 BBa_B0040 range7030 1 1 70 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_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_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 component2176087 1 BBa_M36128 component2176093 1 BBa_M36130 component2176096 1 BBa_M36135 component2176091 1 BBa_B0040 annotation2176095 1 BBa_M36126 range2176095 1 455 574 annotation2176096 1 BBa_M36135 range2176096 1 583 621 annotation2176088 1 BBa_M36129 range2176088 1 71 106 annotation2176093 1 BBa_M36130 range2176093 1 399 424 annotation2176094 1 BBa_M36127 range2176094 1 433 446 annotation2176089 1 BBa_M36135 range2176089 1 115 153 annotation2176092 1 BBa_M36136 range2176092 1 240 390 annotation2176091 1 BBa_B0040 range2176091 1 162 231 annotation2176087 1 BBa_M36128 range2176087 1 1 62 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