Difference between revisions of "Part:BBa K2012001:Design"

 
 
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<partinfo>BBa_K2012001 short</partinfo>
 
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<p>The bc3 riboswitch is apart of the tandem riboswitch bc3-5. We analysed the sequence of bc3-5 and its scendary structure, found linkers between three complete riboswitches. Using PCR amplify the bc3 sequence which is similar with bc4 and bc5 with prefix and suffix, whereas the secondary structure of bc3 is different from other riboswitches</p>
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<img src="https://static.igem.org/mediawiki/parts/4/49/Illustration_of_riboswitch_mechanism.png" width="600px"/>
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<h1>Illustration of riboswitch mechanism</h1>
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<p>As show in the illustration, transcript of riboswitches region would form a hairpin and terminate transcription under low concentration of c-di-GMP. </p>
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<img src="https://static.igem.org/mediawiki/parts/6/66/Schematic_of_riboswitches.png"  width="800px"/>
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<h1>Schematic of riboswitches</h1>
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<p>(a)Comparison of Bc3, Bc4, Bc5 terminators. Red rectangle shows the GC rich region of three terminators, respectively. (b) Secondary structure comparisons of Bc3, Bc4 and Bc5 aptamers with Vc2 aptamer. Conserved motifs such as tetra-loop (blue motif in stem P2), tetra-loop receptor (green motif in stem P3) and G·C base pair (C base in stem P2 and G base in stem P3 were drawn in magenta) connecting P2 with P3 were all colored to facilitate comparison. c-di-GMP was drawn in cyan and its interacting bases drawn in red.(Zhou et al., 2016) (c) Multiply local sequence blast of riboswitches’ terminators. Blue rectangle shows U region of riboswitches.</p>
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<h1>Reference:</h1>
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<p>Zhou, H., Zheng, C., Su, J., Chen, B., Fu, Y., Xie, Y., . . . He, J. (2016). Characterization of a natural triple-tandem c-di-GMP riboswitch and application of the riboswitch-based dual-fluorescence reporter. Sci Rep, 6, 20871. doi:10.1038/srep20871</p>
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===Design Notes===
 
===Design Notes===
 
The bc3 riboswitch is apart of the tandem riboswitch bc3-5. We analysed the sequence of bc3-5 and its scendary structure, found linkers between three complete riboswitches. Using PCR amplify the bc3 sequence which is similar with bc4 and bc5 with prefix and suffix, whereas the secondary structure of bc3 is different from other riboswitches'.  
 
The bc3 riboswitch is apart of the tandem riboswitch bc3-5. We analysed the sequence of bc3-5 and its scendary structure, found linkers between three complete riboswitches. Using PCR amplify the bc3 sequence which is similar with bc4 and bc5 with prefix and suffix, whereas the secondary structure of bc3 is different from other riboswitches'.  
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<partinfo>BBa_K2012001 SequenceAndFeatures</partinfo>
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Latest revision as of 16:00, 4 October 2016


c-di-GMP tandem riboswitche bc3


The bc3 riboswitch is apart of the tandem riboswitch bc3-5. We analysed the sequence of bc3-5 and its scendary structure, found linkers between three complete riboswitches. Using PCR amplify the bc3 sequence which is similar with bc4 and bc5 with prefix and suffix, whereas the secondary structure of bc3 is different from other riboswitches

Illustration of riboswitch mechanism

As show in the illustration, transcript of riboswitches region would form a hairpin and terminate transcription under low concentration of c-di-GMP.




Schematic of riboswitches

(a)Comparison of Bc3, Bc4, Bc5 terminators. Red rectangle shows the GC rich region of three terminators, respectively. (b) Secondary structure comparisons of Bc3, Bc4 and Bc5 aptamers with Vc2 aptamer. Conserved motifs such as tetra-loop (blue motif in stem P2), tetra-loop receptor (green motif in stem P3) and G·C base pair (C base in stem P2 and G base in stem P3 were drawn in magenta) connecting P2 with P3 were all colored to facilitate comparison. c-di-GMP was drawn in cyan and its interacting bases drawn in red.(Zhou et al., 2016) (c) Multiply local sequence blast of riboswitches’ terminators. Blue rectangle shows U region of riboswitches.




Reference:

Zhou, H., Zheng, C., Su, J., Chen, B., Fu, Y., Xie, Y., . . . He, J. (2016). Characterization of a natural triple-tandem c-di-GMP riboswitch and application of the riboswitch-based dual-fluorescence reporter. Sci Rep, 6, 20871. doi:10.1038/srep20871


Design Notes

The bc3 riboswitch is apart of the tandem riboswitch bc3-5. We analysed the sequence of bc3-5 and its scendary structure, found linkers between three complete riboswitches. Using PCR amplify the bc3 sequence which is similar with bc4 and bc5 with prefix and suffix, whereas the secondary structure of bc3 is different from other riboswitches'.


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]



Source

In the CT-43 genome(GenBank accession: NC_017208.1), five type I c-di-GMP riboswitches named Bc1, Bc2, Bc3, Bc4 and Bc5 RNAwere annotated in the Rfam database (http://rfam.sanger.ac.uk/search)42. While Bc1 and Bc2 are widely distributed in the B. cereus group4, Bc3, Bc4, and Bc5are connected in triple-tandem and only located in the 5′ -UTR of the cspABCDE mRNA in some B. cereus and B. thuringiensis

References