Difference between revisions of "Part:BBa K3408005"
 
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It is an enzyme which could cut all methylated DNA so that engineered bacteria may die in a certain situation. It could be used to ensure bio-safety.
 
It is an enzyme which could cut all methylated DNA so that engineered bacteria may die in a certain situation. It could be used to ensure bio-safety.
  
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<b><i>Bacillus subminis</i></b> has been increasingly applied in genetic engineered due to its powerful secretion capacity.  
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<b><i>Bacillus subtilis</i></b> has been increasingly applied in genetic engineering due to its powerful secretion capacity.  
  
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As a restriction enzyme which is capable of cutting all methylated DNA, DPNI can be applied to <b><i>Bacillus subtilis</i></b> in the way of synthetic biology to control the environment by taking advantage of its DNA eradication.
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As a restriction enzyme which is capable of cutting all methylated DNA, optimized DpnI via codon optimization can be applied in <i>Bacillus subtilis</i> more efficiently.
  
 
https://static.igem.org/mediawiki/parts/1/13/T--NAU-CHINA--DPNI1cp.png
 
https://static.igem.org/mediawiki/parts/1/13/T--NAU-CHINA--DPNI1cp.png
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Fig.1. Codon quality distribution        &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp;        Fig.2. Optimized codon quality distribution
 
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Fig.1. Codon quality distribution        &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp;        Fig.2. Optimized codon quality distribution
  
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The histograms show the percentage of sequence codons which fall into a certain quality class. The quality value of the most frequently used codon for a given amino acid in the desired expression system is set to 100, the remaining codons are scaled accordingly (see also Sharp, P.M., Li, W.H., <i>Nucleic Acids Res</i>. 15 (3),1987).
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The histograms show the percentage of sequence codons which fall into a certain quality class. The quality value of the most frequently used codon for a given amino acid in the desired expression system is set to 100, the remaining codons are scaled accordingly (Sharp, P.M., Li, W.H., <i>Nucleic Acids Res</i>. 15 (3),1987).
  
 
https://static.igem.org/mediawiki/parts/2/20/T--NAU-CHINA--DPNI3cp.png
 
https://static.igem.org/mediawiki/parts/2/20/T--NAU-CHINA--DPNI3cp.png

Latest revision as of 02:48, 28 October 2020


Optimized DpnI

It is an enzyme which could cut all methylated DNA so that engineered bacteria may die in a certain situation. It could be used to ensure bio-safety.

Bacillus subtilis has been increasingly applied in genetic engineering due to its powerful secretion capacity.

As a restriction enzyme which is capable of cutting all methylated DNA, optimized DpnI via codon optimization can be applied in Bacillus subtilis more efficiently.

T--NAU-CHINA--DPNI1cp.png T--NAU-CHINA--DPNI2cp.png

                                 Fig.1. Codon quality distribution                                              Fig.2. Optimized codon quality distribution

The histograms show the percentage of sequence codons which fall into a certain quality class. The quality value of the most frequently used codon for a given amino acid in the desired expression system is set to 100, the remaining codons are scaled accordingly (Sharp, P.M., Li, W.H., Nucleic Acids Res. 15 (3),1987).

T--NAU-CHINA--DPNI3cp.png T--NAU-CHINA--DPNI4cp.png

                                 Fig.3. Codon quality plot                                                         Fig.4. Optimized codon quality plot

The plots show the quality of the used codon at the indicated codon position.

T--NAU-CHINA--DPNI5cp.png T--NAU-CHINA--DPNI6cp.png

                                 Fig.5. GC content                                                                     Fig.6. Optimized GC content

The plots show the GC content in a 40 bp window centered at the indicated nucleotide position.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 1322
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 210
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Unknown