BBa_I1010 1 cI-ptetR cI(1) fused to tetR promoter 2003-01-31T12:00:00Z 2015-08-31T04:07:29Z Lutz, R., Bujard, H., <em>Nucleic Acids Research</em> (1997) 25, 1203-1210<BR> <a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/abs/403335a0_fs.html&dynoptions=doi1043774228">A synthetic oscillatory network of transcriptional regulators</a> , Elowitz M.B. , Leibler S., Nature(403),335-38: 2000 This part has been optimized for anti-sense inhibition. It is inhibited by anti-sense parts <bb_part>BBa_I1011</bb_part>, <bb_part>BBa_I1012</bb_part>, and <bb_part>BBa_I1013</bb_part>. It contains the following regions: tetR promoter, anti-sense binding region, RBS, and cI protein with modified initial codons. false false _1_ 0 24 7 It's complicated false References (unparsed) here: <p><a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/abs/403335a0_fs.html&dynoptions=doi1043774228">A synthetic oscillatory network of transcriptional regulators</a> , Elowitz M.B. , Leibler S., Nature(403),335-38: 2000<P> Coleman, J., et al. <em>Nature</em>. (1985) 315, 601-3.<P> Coleman, J., et al. <em>Cell</em> (1984) 37, 429-36. <P> Pestka, S., et al. <em>Proc. Natl. Acad. Sci. USA</em> (1984) 81, 7525-28.<P> Jain, C. (1995). IS10 Antisense Control in Vivo is Affected by Mutations Throughout the Region of Complementarity Between the Interacting RNAs. J. Mol. Biol. 246:585-594. <P> Kittle, J.D., Simons, R.W., Lee, J., and Kleckner, N. (1989). Insertion Sequence IS10 Anti-sense Pairing Initiates by an Interaction Between the 5' End of the Target RNA and a Loop in the Anti-sense RNA. J. Mol. Biol. 210:561-572. <P>Jain, C. (1997). Models for Pairing of IS10 Encoded Antisense RNAs in vivo. J. theor. Biol. 186: 431-439. <P>E. coli codon usage table at http://bioinfo.weizmann.ac.il:3456/kegg/codon_table/codon_eco.html. <P>Lutz, R., Bujard, H., <em>Nucleic Acids Research</em> (1997) 25, 1203-1210 <P>Mizuno, T., et al. <em>Proc. Natl. Acad. Sci. USA</em> (1984) 81, 1966-1970. <P> <P> References (unparsed) here: <p><a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v403/n6767/abs/403335a0_fs.html&dynoptions=doi1043774228">A synthetic oscillatory network of transcriptional regulators</a> , Elowitz M.B. , Leibler S., Nature(403),335-38: 2000<P> Coleman, J., et al. <em>Nature</em>. (1985) 315, 601-3.<P> Coleman, J., et al. <em>Cell</em> (1984) 37, 429-36. <P> Pestka, S., et al. <em>Proc. Natl. Acad. Sci. USA</em> (1984) 81, 7525-28.<P> Jain, C. (1995). IS10 Antisense Control in Vivo is Affected by Mutations Throughout the Region of Complementarity Between the Interacting RNAs. J. Mol. Biol. 246:585-594. <P> Kittle, J.D., Simons, R.W., Lee, J., and Kleckner, N. (1989). Insertion Sequence IS10 Anti-sense Pairing Initiates by an Interaction Between the 5' End of the Target RNA and a Loop in the Anti-sense RNA. J. Mol. Biol. 210:561-572. <P>Jain, C. (1997). Models for Pairing of IS10 Encoded Antisense RNAs in vivo. J. theor. Biol. 186: 431-439. <P>E. coli codon usage table at http://bioinfo.weizmann.ac.il:3456/kegg/codon_table/codon_eco.html. <P>Lutz, R., Bujard, H., <em>Nucleic Acids Research</em> (1997) 25, 1203-1210 <P>Mizuno, T., et al. <em>Proc. Natl. Acad. Sci. USA</em> (1984) 81, 1966-1970. <P> <P>This protein is built from several parts: <BR> - tetR promoter <bb_part> BBa_R0040</bb_part> <BR> - anti-sense binding region, as optimized from references above. <BR> - RBS from references above. <BR> - cI <bb_part>BBa_C0051</bb_part>) with slightly altered codons in the first 73 bases of the coding region (see codon usage table in references). <blockquote> <B>Anti-sense</B></P> <P>The success of this system clearly rests on the ability to effectively and specifically target mRNA transcripts for degradation using anti-sense RNA. While many papers, articles, and books have been written on the subject, there are no consensus anti-sense building strategies presented. We thus chose to implement three different types of antisense inhibition: KISS, micRNA, and IS10. In the description that follows, the following nomenclature will be used:</P> <P><em>target</em>- the mRNA transcript that we wish to inhibit.</P> <P><em>anti-sense</em>- the anti-sense molecule which will bind and inhibit <em>target</em>. </P> <blockquote> <P><em><strong>KISS (Keep it SImple, Silly)</strong></em></P> <img src="http://biobricks.ai.mit.edu/IAP_Projects/YoungPower/as_KISS.gif"> <P>The simplest of the three methods, this type relies on a single-stranded linear 103 bp anti-sense that is specific to the target of interest. In addition, the first 76 base pairs of the cI region of BBa_I1010 have been codon-modified to give a different sequence that codes for the same cI protein (See BBa_I1030 and I1040). </P> <P>BBa_I1011 contains the reverse complement of the RBS, start codon, and 76 bp region for BBa_I1010. Thus, if both BBa_I1010 and BBa_I1011 are transcribed, the transcripts will bind to each other and BBa_I1010 will not be translated. </P> <P>Note that BBa_I1010 already contains a regulatory region, RBS, and coding region (a terminator must be added), while BBa_I1011 does not - thus, when using this component, the appropriate regulatory region, RBS, and terminator must be added to this part.</P> <P><em><strong>micRNA</strong></em></P> <img src="http://biobricks.ai.mit.edu/IAP_Projects/YoungPower/as_micRNA.gif"> <P>This anti-sense mechanism relies on two stem loops flanking an anti-sense sequence that is specific for the target. The function of the stem loops is to maintain the anti-sense region in a quasi-linear state. BBa_I1012 is built in this manner, with a linear region that will bind over the RBS, start codon, and 76 bp of BBa_I1010.</P> <P><strong><em>IS10</em></strong> </P> <img src="http://biobricks.ai.mit.edu/IAP_Projects/YoungPower/as_IS10.gif"> <P>This method is modeled after the mechanism by which IS10 inhibits production of IS10 transposase. The anti-sense strand is transcribed from the complementary strand of the target (see below), resulting in an anti-sense strand that is 115 bp long, of which 35 bp are complementary to the target. In the absense of a target, these 35 bp form a weak stem loop with the rest of the anti-sense molecule (see below). The key element of the system is the loop at the tip of this stem loop (C-G-G-C-U-U...), which is held in a linear state by the rest of the loop. Upon exposure to the target, the linear loop is able to bind to the 5' end of the target (G-C-C-G-T-T...), and initiate an energetically-favorable zipping/twisting-together of the target and the 5' end of the stem loop (see below). In other words, one side of the weakly stable anti-sense stem loop binds 35 bp of the target, to form a more stable duplex.</P> <P><em>I1010 and I1013</em></P> <P>Biobricks part BBa_I1013 codes for the exact anti-sense stem loop used in IS10, with two base changes. The 5'-most residues from IS10 anti-sense transcript ( U-C), which do not form part of the stem loop, were changed to G-A. These two bases are reverse-complementary to the first two base pairs of the wildtype cI coding region of BBa_I1010, and thus can bind this region. The rest of the stem loop is wild-type. </P> <P>The BBa_1010 transcript is targeted by BBa_I1013. The first 35 bases at the 5' end of BBa_I1010 are identical to the first 35 bases at the 5' end of the wild type target, with two differences. Note that three bases T-G-C (which code for cysteine) have been inserted at the 5' end of the cI coding region immediately after the start codon. This allows us to use a wild-type binding pattern at the base of the stem. Since this cysteine is added to the N-terminus of cI, it is not expected to alter the repression ability of cI.</P> </blockquote> </blockquote><P> Incompatible with systems containing cI (wild type). <br>Compatible with systems containing <bb_part>BBa_I1020</bb_part>, <bb_part>BBa_I1021</bb_part>, <bb_part>BBa_I1022</bb_part>, <bb_part>BBa_I1023</bb_part>. false June Rhee, Connie Tao, Ty Thomson, Louis Waldman annotation1785 1 -35 range1785 1 20 25 annotation1794 1 added codon (Cys) range1794 1 85 87 annotation1787 1 -10 range1787 1 43 48 annotation1788 1 start range1788 1 55 55 annotation1784 1 TetR 1 range1784 1 1 19 annotation1781 1 start range1781 1 82 84 annotation1780 1 cI range1780 1 82 834 annotation1789 1 tetR range1789 1 1 54 annotation7042 1 BBa_I1010 range7042 1 1 834 annotation1786 1 TetR 2 range1786 1 26 44 annotation1782 1 rbs range1782 1 72 77 annotation1791 1 2 range1791 1 829 834 annotation1793 1 Complementary to Antisense mRNA range1793 1 55 157 annotation1783 1 Modified cI cds range1783 1 85 157 annotation1790 1 SsrA range1790 1 796 834 BBa_I1010_sequence 1 tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcacgcgaaaaatcaataatcagacaacaagatgtgctcgacaaaaaagaaaccattaacacaagagcagcttgaggacgcacgtcgccttaaagcaatttatgaaaaaaagaaaaatgaacttggcttatcccaggaatctgtcgcagacaagatggggatggggcagtcaggcgttggtgctttatttaatggcatcaatgcattaaatgcttataacgccgcattgcttgcaaaaattctcaaagttagcgttgaagaatttagcccttcaatcgccagagaaatctacgagatgtatgaagcggttagtatgcagccgtcacttagaagtgagtatgagtaccctgttttttctcatgttcaggcagggatgttctcacctgagcttagaacctttaccaaaggtgatgcggagagatgggtaagcacaaccaaaaaagccagtgattctgcattctggcttgaggttgaaggtaattccatgaccgcaccaacaggctccaagccaagctttcctgacggaatgttaattctcgttgaccctgagcaggctgttgagccaggtgatttctgcatagccagacttgggggtgatgagtttaccttcaagaaactgatcagggatagcggtcaggtgtttttacaaccactaaacccacagtacccaatgatcccatgcaatgagagttgttccgttgtggggaaagttatcgctagtcagtggcctgaagagacgtttggcgctgcaaacgacgaaaactacgctttagtagcttaataa 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