Difference between revisions of "Part:BBa K3408005"

Revision as of 09:11, 22 October 2020

Optimized DpnI

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.

Bacillus subminis 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 Bacillus subtilis in the way of synthetic biology to control the environment by taking advantage of its DNA eradication.

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 (see also Sharp, P.M., Li, W.H., Nucleic Acids Res. 15 (3),1987).

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.

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]

@@ Line 11: / Line 11: @@
 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
+&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 (see also Sharp, P.M., Li, W.H., Nucleic Acids Res. 15 (3),1987).
@@ Line 16: / Line 18: @@
 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
+&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.
@@ Line 21: / Line 25: @@
 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
+&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.