Difference between revisions of "Part:BBa K837000:Design"

 
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===References===
 
===References===
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(1). Jens Kortmann and Franz Narberhaus. Bacterial RNA thermometers: molecular zippers and switches. NATURE REVIEWS MICROBIOLOGY, VOLUME 10, 265, APRIL 2012 (2). Birgit Klinkert and Franz Narberhaus. Microbial thermosensors. Cell. Mol. Life Sci. (2009) 66:2661–2676 (3). Miyo Terao Morita, Yoshiyuki Tanaka, Takashi S. Kodama, Yoshimasa Kyogoku, Hideki Yanagi and Takashi Yura. Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor.. Genes Dev. 1999 13: 655-665 (4). David H. Mathews. Revolutions in RNA Secondary Structure Prediction. J. Mol. Biol. (2006) 359, 526–532 (5). David H Mathews and Douglas H Turner. Prediction of RNA secondary structure by free energy minimization. Current Opinion in Structural Biology 2006, 16:270–278 (6). J. S. McCASKlLL. The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure. Biopolymers, Vol. 29,1105-1119 (1990) (7). http://www.tbi.univie.ac.at/~ivo/RNA/ (8). http://www.tbi.univie.ac.at/~ivo/RNA/man/RNAfold.html (9). L. Hofacker, W. Fontan. Fast folding and comparison of RNA secondary structures. Monatshefte fur Chemie , 125, 167-188. (10). In-Line Probing Analysis of Riboswitches.Elizabeth E. Regulski and Ronald R. Breaker. NATURE PROTOCOL EXCHANGE http://www.nature.com/protocolexchange/protocols/1889

Latest revision as of 17:08, 26 September 2012

RNAT.1-eGFP-pSB1C3


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal prefix found in sequence at 1
    Illegal suffix found in sequence at 790
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 1
    Illegal SpeI site found at 791
    Illegal PstI site found at 805
    Illegal NotI site found at 7
    Illegal NotI site found at 798
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 1
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal prefix found in sequence at 1
    Illegal suffix found in sequence at 791
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal prefix found in sequence at 1
    Illegal XbaI site found at 16
    Illegal SpeI site found at 791
    Illegal PstI site found at 805
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The SD sequence that benefits the bond between the RNA and the ribosome is designed in front of the eGFP sequence.


Source

The RNAT sequence is designed by us, using computational method. The eGFP gene is from the iGEM part,BBa_I714891.

References

(1). Jens Kortmann and Franz Narberhaus. Bacterial RNA thermometers: molecular zippers and switches. NATURE REVIEWS MICROBIOLOGY, VOLUME 10, 265, APRIL 2012 (2). Birgit Klinkert and Franz Narberhaus. Microbial thermosensors. Cell. Mol. Life Sci. (2009) 66:2661–2676 (3). Miyo Terao Morita, Yoshiyuki Tanaka, Takashi S. Kodama, Yoshimasa Kyogoku, Hideki Yanagi and Takashi Yura. Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor.. Genes Dev. 1999 13: 655-665 (4). David H. Mathews. Revolutions in RNA Secondary Structure Prediction. J. Mol. Biol. (2006) 359, 526–532 (5). David H Mathews and Douglas H Turner. Prediction of RNA secondary structure by free energy minimization. Current Opinion in Structural Biology 2006, 16:270–278 (6). J. S. McCASKlLL. The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure. Biopolymers, Vol. 29,1105-1119 (1990) (7). http://www.tbi.univie.ac.at/~ivo/RNA/ (8). http://www.tbi.univie.ac.at/~ivo/RNA/man/RNAfold.html (9). L. Hofacker, W. Fontan. Fast folding and comparison of RNA secondary structures. Monatshefte fur Chemie , 125, 167-188. (10). In-Line Probing Analysis of Riboswitches.Elizabeth E. Regulski and Ronald R. Breaker. NATURE PROTOCOL EXCHANGE http://www.nature.com/protocolexchange/protocols/1889