Difference between revisions of "Part:BBa K1041002:Experience"

Revision as of 11:18, 4 October 2013

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Please enter how you used this part and how it worked out.

Team NRP-UEA_Norwich 2013

Team NRP-UEA_Norwich 2013 created this part using biobricks BBa_K1041000 and BBa_K1041001. These biobricks both contain a Nde1 site after their promoter sequence, enabling a restriction digest to be performed. The RFP coding gene was excised from BBa_K1041000 and ligated in front of the AntG promoter of BBa_K1041001 to create a new biobrick.

Due to the major research side of our project involving actinomycetes not E.coli this part was cloned into an appropriate actinomycete-specific intergrative plasmid PMS82. This was to allow the reporter to be utilised in screening for antimycin producing actinomycetes. The plasmid containing the reporter sequence (Bba_K1041002)was transformed into specialised E.colistrains: ET12567 and pUZ8002. These cells were then conjugated with spore stocks of actinomycetes cultivated from soil samples to transfer the active biosensor in the plasmid.

Characterisation

This involved sequencing, restriction digests and BLAST analysis.

Restriction Digest

Part Bba_K1041002 was digested with enzymes XbaI and NdeI and compared to uncut DNA Fig 1.The enzyme digest shows the NdeI restriction has been conserved after ligation of fragments from parts Bba_J04450 and Bba_K1041001.

Fig 1:Lane 1 contains and Bba_K1041002 cut with XbaI and NdeI and lane 2 uncut Bba_K1041002.

Sequencing

The biobrick was sent off to a company for sequencing and the data we received back Fig 2,3,4 showed the DNA is good quality as strong peaks were produced throughout analysis of the sample.

Fig 2:K1041002 sequencing data part 1

Fig 3:K1041002 sequencing data part 2

Fig 4:K1041002 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 5,6The sequencing with both the forward and reverse primers had over 96% matches.

Fig 5: Forward primer K1041002 sequencing data aligned with the expected DNA sequence

Fig 6: Reverse primer K1041002 sequencing data aligned with the expected DNA sequence

User Reviews

UNIQf9680cf3fb2eb992-partinfo-00000000-QINU UNIQf9680cf3fb2eb992-partinfo-00000001-QINU

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 Team NRP-UEA_Norwich 2013 created this part using biobricks [[BBa_K1041000]] and [[BBa_K1041001]]. These biobricks both contain a Nde1 site after their promoter sequence, enabling a restriction digest to be performed. The RFP coding gene was excised from BBa_K1041000 and ligated in front of the AntG promoter of BBa_K1041001 to create a new biobrick.
-Due to the major research side of our project involving ''actinomycetes'' not ''E.coli'' this part was cloned into an appropriate ''actinomycete''-specific intergrative plasmid PMS82. This was to allow the reporter to be utilised in screening for antimycin producing ''actinomycetes.''
+Due to the major research side of our project involving actinomycetes not ''E.coli'' this part was cloned into an appropriate actinomycete-specific intergrative plasmid PMS82. This was to allow the reporter to be utilised in screening for antimycin producing actinomycetes.
-The plasmid containing the reporter sequence (Bba_K1041002)was transformed into specialised ''E.coli''strains: ET12567 and pUZ8002. These cells were then conjugated with spore stocks of ''actinomycetes'' cultivated from soil samples to transfer the active biosensor in the plasmid.
+The plasmid containing the reporter sequence (Bba_K1041002)was transformed into specialised ''E.coli''strains: ET12567 and pUZ8002. These cells were then conjugated with spore stocks of actinomycetes cultivated from soil samples to transfer the active biosensor in the plasmid.
 ====Characterisation====