Difference between revisions of "Part:BBa K1041000:Experience"

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Parts BBa_K1041000 and BBa_J04450 were transformed into Alpha-Select competent ''E.Coli'' cells and plated onto LB Agar plates which contained the antibiotic ampicillin. Both plates have colonies that appear red under natural light ''Fig.1''. Therefore the addition of a NdeI site has not effected the ability for the RFP gene to be transcribed.
 
Parts BBa_K1041000 and BBa_J04450 were transformed into Alpha-Select competent ''E.Coli'' cells and plated onto LB Agar plates which contained the antibiotic ampicillin. Both plates have colonies that appear red under natural light ''Fig.1''. Therefore the addition of a NdeI site has not effected the ability for the RFP gene to be transcribed.
  
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[[Image:WP 000051.jpg|thumb|Fig 1: Plates containing (left) BBa_K1041000 and (right) BBa_J04450 visualized under non-UV lightbox]]
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[[Image:WP 000051.jpg|thumb|centre|Fig 1: Plates containing (left) BBa_K1041000 and (right) BBa_J04450 visualized under non-UV lightbox]]
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===Restriction Digests===
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Parts Bba_K1041000 and Bba_J04450 were analysed by restriction digests and run on agarose gels. Both biobricks were cut with NdeI, ''Fig 2'' and PvuII ''Fig 3.''
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[[image:K1041000 digest 2.JPG|thumb|left|Fig 2:Analysis of Restriction enzyme digest with NdeI. Lanes 1 and 2 contain uncut Bba_K1041000 and Bba_K1041000 digested with NdeI. Lanes 3 and 4 contain uncut Bba_J04450 and Bba_J04450 digested with NdeI respectively.]]
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[[image:K1041000 digest.JPG|thumb|centre|Fig 3:Analysis of Restriction enzyme digest with PvuII. Lanes 2 and 3 contain uncut BBa_J04450 and BBa_J04450 digested with PvuII respectively. Lane 5 contains Bba_K1041000 with PvuII.]]
  
 
===Sequencing===
 
===Sequencing===
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The biobrick was sent off to a company for sequencing, ''Fig 2,3,4.''The data we recieved back showed the DNA is of good quality.
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The biobrick was sent off to a company for sequencing, ''Fig 3,4,5.''The data we recieved back showed the DNA is of good quality.
  
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[[image:3a vf2 0-540.JPG|thumb|left|Fig. 2:K1041000 sequencing data part 1]]
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[[image:3a vf2 0-540.JPG|thumb|left|Fig. 3:K1041000 sequencing data part 1]]
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[[image:3a vf2 440-860.JPG|thumb|left|Fig. 3:K1041000 sequencing data part 2 ]]
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[[image:3a vf2 440-860.JPG|thumb|left|Fig. 4:K1041000 sequencing data part 2 ]]
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[[image:3a vf2 860-.JPG|thumb|left|Fig. 4:K1041000 sequencing data part 3]]
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[[image:3a vf2 860-.JPG|thumb|left|Fig. 5:K1041000 sequencing data part 3]]
  
 
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===BLAST Analysis===
 
===BLAST Analysis===
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The data we recieved back from the sequencing company was aligned using BLAST with the expected DNA sequence ''Fig 5,6''
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The data we recieved back from the sequencing company was aligned using BLAST with the expected DNA sequence ''Fig 6,7''
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[[image:3a Forward.JPG|thumb|left|Fig. 5: Forward primer K1041000 sequencing data aligned with the expected DNA sequence]]
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[[image:3a Forward.JPG|thumb|left|Fig. 6: Forward primer K1041000 sequencing data aligned with the expected DNA sequence]]
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[[image:3a Reverse.JPG|thumb|left|Fig. 6: Reverse primer K1041000 sequencing data aligned with expected DNA sequence]]
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[[image:3a Reverse.JPG|thumb|left|Fig. 7: Reverse primer K1041000 sequencing data aligned with expected DNA sequence]]
  
 
===User Reviews===
 
===User Reviews===

Revision as of 13:49, 18 September 2013

This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Team NRP-UEA_Norwich 2013

Team NRP-UEA_Norwich 2013 added an NdeI restriction site at the start of the RFP coding region of BBa_J04450 using mutagenesis. This was to allow either the promoter region or RFP gene to be excised and exchanged for a different promoter or gene and provide restriction sites for further cloning such as part Bba_K1041002.

Characterisation of this biobrick involved comparisons with the original Bba_J04450 biobrick by performing transformations, restriction digests and BLAST analysis. We also had our biobrick sequenced.

Transformation

Parts BBa_K1041000 and BBa_J04450 were transformed into Alpha-Select competent E.Coli cells and plated onto LB Agar plates which contained the antibiotic ampicillin. Both plates have colonies that appear red under natural light Fig.1. Therefore the addition of a NdeI site has not effected the ability for the RFP gene to be transcribed.

Fig 1: Plates containing (left) BBa_K1041000 and (right) BBa_J04450 visualized under non-UV lightbox

Restriction Digests

Parts Bba_K1041000 and Bba_J04450 were analysed by restriction digests and run on agarose gels. Both biobricks were cut with NdeI, Fig 2 and PvuII Fig 3.

Fig 2:Analysis of Restriction enzyme digest with NdeI. Lanes 1 and 2 contain uncut Bba_K1041000 and Bba_K1041000 digested with NdeI. Lanes 3 and 4 contain uncut Bba_J04450 and Bba_J04450 digested with NdeI respectively.
Fig 3:Analysis of Restriction enzyme digest with PvuII. Lanes 2 and 3 contain uncut BBa_J04450 and BBa_J04450 digested with PvuII respectively. Lane 5 contains Bba_K1041000 with PvuII.

Sequencing

The biobrick was sent off to a company for sequencing, Fig 3,4,5.The data we recieved back showed the DNA is of good quality.

Fig. 3:K1041000 sequencing data part 1
Fig. 4:K1041000 sequencing data part 2
Fig. 5:K1041000 sequencing data part 3










BLAST Analysis

The data we recieved back from the sequencing company was aligned using BLAST with the expected DNA sequence Fig 6,7

Fig. 6: Forward primer K1041000 sequencing data aligned with the expected DNA sequence
Fig. 7: Reverse primer K1041000 sequencing data aligned with expected DNA sequence

User Reviews

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