Difference between revisions of "Part:BBa K313018"
m (→‎verification experiments)
 
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This is a device that aims to measure the leakiness of a terminator BBa_B1006.
 
This is a device that aims to measure the leakiness of a terminator BBa_B1006.
 
If RNA polymerase transcribes the coding region of Cre regardless of the terminator, Cre is expressed from this part.
 
If RNA polymerase transcribes the coding region of Cre regardless of the terminator, Cre is expressed from this part.
−
With our cre recombinase assay device such as BBa_K313016 or BBa_K313009, we can detect the quantity of Cre and can assess the leakiness of the terminator.
+
With our cre recombinase assay device such as BBa_K313016 or BBa_K313009, you would be able to detect the quantity of Cre and assess the leakiness of the terminator.
 
The difference between this part and BBa K313017 is the number of the terminator.
 
The difference between this part and BBa K313017 is the number of the terminator.
 +
 +
===verification experiments===
 +
 +
We tested the function of this Cre recombianse generator.
 +
 +
 +
This part is ligated with double loxP unit (Fig.1A) and transformed into E.coli, JM109 strain.
 +
 +
[[Image:ROKUJYO.png|800px|]]
 +
 +
Please note that double loxP unit is inserted between the SpeI site and PstI site of the plasmid containing this part (Double loxP unit was inserted as SpeI and PstI fragment, so SpeI site remains).
 +
Originally the length between SpeI site and PstI site is 1778bp. So, if Cre is not expressed, SP digestion will make 1778bp fragment(Fig.1A). On the other hand, if Cre is expressed, SP digestion will make 726bp fragment(Fig.1B).
 +
 +
We incubated the E.coli for about 20 hours in LB, and then extracted plasmids.
 +
Sequencing was performed on these samples(Fig.2) and the results proved that the excision occurred between loxP sites. Thus, we confirmed proper generation of Cre recombinase from this parts, and its correct operation.
 +
 +
[[Image:Fig2.jpg]]
 +
 +
The result of sequence alignment.
 +
The upper one is the predicted sequence resulting from the excision by Cre recombinase, and the lower one is the result of sequencing.
 +
 +
These two sequences completely match.
 +
 +
 +
Although two terminator exists upstream of Cre generator and the strain used in this experiment doesn't have T7 RNA polymerase, the excision did occur. This result indicates the possibility that transcription occurred from unpredicted region and terminator did not stop this transcription and Cre was expressed.
 +
 +
 +
The same experiments was done for BBa_K313017.
 +
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Latest revision as of 21:49, 7 November 2010

terminator leakiness assay device

This is a device that aims to measure the leakiness of a terminator BBa_B1006. If RNA polymerase transcribes the coding region of Cre regardless of the terminator, Cre is expressed from this part. With our cre recombinase assay device such as BBa_K313016 or BBa_K313009, you would be able to detect the quantity of Cre and assess the leakiness of the terminator. The difference between this part and BBa K313017 is the number of the terminator.

verification experiments

We tested the function of this Cre recombianse generator.


This part is ligated with double loxP unit (Fig.1A) and transformed into E.coli, JM109 strain.

ROKUJYO.png

Please note that double loxP unit is inserted between the SpeI site and PstI site of the plasmid containing this part (Double loxP unit was inserted as SpeI and PstI fragment, so SpeI site remains). Originally the length between SpeI site and PstI site is 1778bp. So, if Cre is not expressed, SP digestion will make 1778bp fragment(Fig.1A). On the other hand, if Cre is expressed, SP digestion will make 726bp fragment(Fig.1B).

We incubated the E.coli for about 20 hours in LB, and then extracted plasmids. Sequencing was performed on these samples(Fig.2) and the results proved that the excision occurred between loxP sites. Thus, we confirmed proper generation of Cre recombinase from this parts, and its correct operation.

Fig2.jpg

The result of sequence alignment. The upper one is the predicted sequence resulting from the excision by Cre recombinase, and the lower one is the result of sequencing.

These two sequences completely match.


Although two terminator exists upstream of Cre generator and the strain used in this experiment doesn't have T7 RNA polymerase, the excision did occur. This result indicates the possibility that transcription occurred from unpredicted region and terminator did not stop this transcription and Cre was expressed.


The same experiments was done for BBa_K313017.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 525
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 211
  • 1000
    COMPATIBLE WITH RFC[1000]