BBa_K1791001 1 BBa_K1791001 Standard RBS expressing MS2 Coat protein ribozyme affinity purification (RAP) 2015-09-16T11:00:00Z 2015-09-23T01:30:44Z This is an amalgamation of several biobricks an MS2 coat protein and the theophylline ribozyme (BBa_K1791000) Standard RBS expressing MS2 Coat protein ribozyme affinity purification (RAP). This part utilizes the expression of C-terminal 6X His tagged fusion MS2 coat protein under a T7 promoter and a standard shine dalgarno sequence for expression of MS2. Downstream there is a T7 promoter followed by a theophylline ribozyme and a MS2 apatamer at the 3' end. Co-expression of the two modules results in MS2 binding to the 3' end of the theophylline ribozyme transcript allowing for the MS2-RNA purification by nickel affinity chromatography. The RNA can be eluted from the complex by the addition of theophylline. false false _2216_ 17031 17031 9 true We had to consider MS2 expression levels relative to the theophylline ribozyme transcript and assessed how this affects total RNA yield. In order to test this we developed a second part with depressed MS2 expression (BBa_K1791002) false Graeme Glaister component2476614 1 BBa_K1791006 component2476613 1 BBa_K1791008 component2476612 1 BBa_K1791005 component2476610 1 BBa_B0015 component2476600 1 BBa_I719005 component2476611 1 BBa_K1791007 component2476602 1 BBa_B0034 component2476603 1 BBa_K1791003 annotation2476612 1 BBa_K1791005 range2476612 1 617 765 annotation2476614 1 BBa_K1791006 range2476614 1 788 824 annotation2476611 1 BBa_K1791007 range2476611 1 603 608 annotation2476603 1 BBa_K1791003 range2476603 1 50 457 annotation2476610 1 BBa_B0015 range2476610 1 466 594 annotation2476600 1 BBa_I719005 range2476600 1 1 23 annotation2476602 1 BBa_B0034 range2476602 1 32 43 annotation2476613 1 BBa_K1791008 range2476613 1 774 779 BBa_I719005 1 pT7 T7 Promoter 2007-10-23T11:00:00Z 2015-08-31T04:07:53Z --- Released HQ 2013 Just a T7 Promoter false false _128_ 0 2097 9 In stock true None true Imperial 2007 BBa_K1791007 1 BBa_K1791007 BamHI cut site 2015-09-22T11:00:00Z 2015-09-23T01:21:53Z https://www.neb.com/products/r0136-bamhi This site will be utilized in the composite part BBa_K1791001 and BBa_K1791002 in order to allow for insertion of new RNA strands to be generated in these constructs. false false _2216_ 17031 17031 9 false no addtional design features were considered false Graeme Glaister BBa_K1791006 1 BBa_K1791006 MS2 binding domain 2015-09-22T11:00:00Z 2015-09-22T11:21:29Z genomic sequence in E.coli This is an aptamer designed to bind MS2 coat protein upon transcription. false false _2216_ 17031 17031 9 false Had to test that it optimally binds to MS2 coat protein in vivo false Graeme Glaister BBa_K1791005 1 BBa_K1791005 T7 promoter fused with a theophylline inducible ribozyme (aptazyme) 2015-09-22T11:00:00Z 2015-09-22T11:17:58Z Win, M.N., Smolke C.D. 2007 and BBa_I719005 This part was developed in order to increase the sequence space flexibility in dsRNA generated using BBa_K1791001 and BBa_K1791002 false false _2216_ 17031 17031 9 false by changing the T7 promoter sequence (BBa_I719005) slightly after the GGG trinulceotide we get an increase in the potential for generating RNA with our composite parts BBa_K1791001 and BBa_K1791002. false Graeme Glaister BBa_B0010 1 BBa_B0010 T1 from E. coli rrnB 2003-11-19T12:00:00Z 2015-08-31T04:07:20Z Transcriptional terminator consisting of a 64 bp stem-loop. false false _1_ 0 24 7 In stock false true Randy Rettberg annotation7018 1 BBa_B0010 range7018 1 1 80 annotation4184 1 stem_loop range4184 1 12 55 BBa_K1791008 1 BBa_K1791008 KpnI cut site 2015-09-22T11:00:00Z 2015-09-23T01:29:59Z https://www.neb.com/products/r0142-kpni This site will be utilized in the composite part BBa_K1791001 and BBa_K1791002 in order to allow for insertion of new RNA strands to be generated in these constructs. false false _2216_ 17031 17031 9 false no additional design considerations were neccessary false Graeme Glaister BBa_B0034 1 BBa_B0034 RBS (Elowitz 1999) -- defines RBS efficiency 2003-01-31T12:00:00Z 2015-08-31T04:07:20Z Released HQ 2013 RBS based on Elowitz repressilator. false true _1_ 0 24 7 In stock false Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix. <p>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: <a href="mailto:(bchow@media.mit.edu)">Brian Chow</a> true Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003. annotation23325 1 conserved range23325 1 5 8 BBa_K1791003 1 BBa_K1791003 6X end terminally His tagged MS2 coat protein 2015-09-22T11:00:00Z 2015-09-22T11:10:08Z RefSeq NP_040648.1. NC_001417.2. MS2 coat protein can be easily purified via a nickel sepharose purification if this part is used downstream of a promoter and RBS. false false _2216_ 17031 17031 9 false optimized for expression in E.coli false Graeme Glaister BBa_B0012 1 BBa_B0012 TE from coliphageT7 2003-01-31T12:00:00Z 2015-08-31T04:07:20Z Derived from the TE terminator of T7 bacteriophage between Genes 1.3 and 1.4 <genbank>V01146</genbank>. Released HQ 2013 Transcription terminator for the <i>E.coli</i> RNA polymerase. false false _1_ 0 24 7 In stock false <P> <P>Suggested by Sri Kosuri and Drew Endy as a high efficiency terminator. The 5' end cutoff was placed immediately after the TAA stop codon and the 3' end cutoff was placed just prior to the RBS of Gene 1.4 (before AAGGAG).<P> Use anywhere transcription should be stopped when the gene of interest is upstream of this terminator. false Reshma Shetty annotation1686 1 T7 TE range1686 1 8 27 annotation7020 1 BBa_B0012 range7020 1 1 41 annotation1690 1 polya range1690 1 28 41 annotation1687 1 stop range1687 1 34 34 BBa_B0015 1 BBa_B0015 double terminator (B0010-B0012) 2003-07-16T11:00:00Z 2015-08-31T04:07:20Z Released HQ 2013 Double terminator consisting of BBa_B0010 and BBa_B0012 false true _1_ 0 24 7 In stock false true Reshma Shetty component1916610 1 BBa_B0010 component1916612 1 BBa_B0012 annotation1916610 1 BBa_B0010 range1916610 1 1 80 annotation1916612 1 BBa_B0012 range1916612 1 89 129 BBa_K1791001_sequence 1 taatacgactcactatagggagatactagagaaagaggagaaatactagatggcaagcaacttcacgcagtttgtgctggtcgacaatggcggtaccggtgacgttacggttgccccaagcaacttcgccaacggtgtcgccgagtggatttccagcaactctcgctcccaggcatataaagtaacatgtagcgtgcgccagtcaagtgcacagaatcgcaagtacaccatcaaagtggaggtgccgaaagtcgcaacccagacggtgggcggtgttgaacttccggttgccgcgtggcgctcctatctgaatatggaactgaccatcccgatctttgctaccaattccgattgcgaattgattgtcaaagcgatgcaggggttactgaaggacggaaatccgattccaagtgcaattgctgctaacagcggaatctatcaccaccaccatcatcattactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttatatactagagggatcctactagagtaatacgactcactatagggagaaaacaaacaaagctgtcaccggatgtgctttccggtctgatgagtccgtgttgctgataccagcatcgtcttgatgcccttggcagcagtggacgaggacgaaacagcaaaaagaaaaataaaaaatactagagggtacctactagaggaaaagaaaacatgaggatcacccatgtcaaaagaaa BBa_B0010_sequence 1 ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc BBa_I719005_sequence 1 taatacgactcactatagggaga BBa_B0034_sequence 1 aaagaggagaaa BBa_K1791008_sequence 1 ggtacc BBa_K1791003_sequence 1 atggcaagcaacttcacgcagtttgtgctggtcgacaatggcggtaccggtgacgttacggttgccccaagcaacttcgccaacggtgtcgccgagtggatttccagcaactctcgctcccaggcatataaagtaacatgtagcgtgcgccagtcaagtgcacagaatcgcaagtacaccatcaaagtggaggtgccgaaagtcgcaacccagacggtgggcggtgttgaacttccggttgccgcgtggcgctcctatctgaatatggaactgaccatcccgatctttgctaccaattccgattgcgaattgattgtcaaagcgatgcaggggttactgaaggacggaaatccgattccaagtgcaattgctgctaacagcggaatctatcaccaccaccatcatcat BBa_K1791006_sequence 1 gaaaagaaaacatgaggatcacccatgtcaaaagaaa BBa_B0012_sequence 1 tcacactggctcaccttcgggtgggcctttctgcgtttata BBa_K1791007_sequence 1 ggatcc BBa_B0015_sequence 1 ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata BBa_K1791005_sequence 1 taatacgactcactatagggagaaaacaaacaaagctgtcaccggatgtgctttccggtctgatgagtccgtgttgctgataccagcatcgtcttgatgcccttggcagcagtggacgaggacgaaacagcaaaaagaaaaataaaaaa 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