Difference between revisions of "Part:BBa K3408005"
 
(7 intermediate revisions by 2 users not shown)
Line 3: Line 3:
 
<partinfo>BBa_K3408005 short</partinfo>
 
<partinfo>BBa_K3408005 short</partinfo>
  
−
It is an enzyme which could cut all methylated DNA so that engineering 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.
−
<b><i>Bacillus subminis<i/></b> has been increasingly applied in genetic engineered due to its powerful secretion capacity.  
+
 
−
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.
+
<b><i>Bacillus subtilis</i></b> 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 <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
 
https://static.igem.org/mediawiki/parts/a/a2/T--NAU-CHINA--DPNI2cp.png
 
https://static.igem.org/mediawiki/parts/a/a2/T--NAU-CHINA--DPNI2cp.png
  
−
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., Nucleic Acids Res. 15 (3),1987).
+
&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
 +
 
 +
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
 
https://static.igem.org/mediawiki/parts/5/58/T--NAU-CHINA--DPNI4cp.png
 
https://static.igem.org/mediawiki/parts/5/58/T--NAU-CHINA--DPNI4cp.png
 +
 +
&nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Fig.3. Codon quality plot              &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &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.4. Optimized codon quality plot
  
 
The plots show the quality of the used codon at the indicated codon position.
 
The plots show the quality of the used codon at the indicated codon position.
Line 19: Line 25:
 
https://static.igem.org/mediawiki/parts/d/dd/T--NAU-CHINA--DPNI5cp.png
 
https://static.igem.org/mediawiki/parts/d/dd/T--NAU-CHINA--DPNI5cp.png
 
https://static.igem.org/mediawiki/parts/b/bd/T--NAU-CHINA--DPNI6cp.png
 
https://static.igem.org/mediawiki/parts/b/bd/T--NAU-CHINA--DPNI6cp.png
 +
 +
&nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Fig.5. GC content              &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &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.6. Optimized GC content
  
 
The plots show the GC content in a 40 bp window centered at the indicated nucleotide position.
 
The plots show the GC content in a 40 bp window centered at the indicated nucleotide position.

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
    COMPATIBLE WITH RFC[1000]