Difference between revisions of "Team:iTesla-SoundBio/Parts"
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<p>This part contains a coding site for the PCBA5 gene, extracted from the organism d.mycarti. The resultant enzyme is a reductive dehalogenase and is able to degrade PCB toxins by stripping away chlorine groups from the overall structure. Three gene strains of this nature were identified by in 2014 by Dr. Shanquan Wang et. all, CG1, CG4, and CG5 (renamed PCBA1, PCBA4, and PCBA5). We used NCBI to acquire the sequences of each gene (accession number CP006951.1), then codon optimized and synthesized each one. This is the coding region only (1442 base pairs) and does not contain any promoter or RBS regions. We did, however, add a start and stop codon. We found a high confidence interval between the PCBA sequences and pceA (a well-characterized reductive dehalogenase), leading us to believe that they have the same interaction with the cofactor norpseudo B12 (Krautler 2003).<p> | <p>This part contains a coding site for the PCBA5 gene, extracted from the organism d.mycarti. The resultant enzyme is a reductive dehalogenase and is able to degrade PCB toxins by stripping away chlorine groups from the overall structure. Three gene strains of this nature were identified by in 2014 by Dr. Shanquan Wang et. all, CG1, CG4, and CG5 (renamed PCBA1, PCBA4, and PCBA5). We used NCBI to acquire the sequences of each gene (accession number CP006951.1), then codon optimized and synthesized each one. This is the coding region only (1442 base pairs) and does not contain any promoter or RBS regions. We did, however, add a start and stop codon. We found a high confidence interval between the PCBA sequences and pceA (a well-characterized reductive dehalogenase), leading us to believe that they have the same interaction with the cofactor norpseudo B12 (Krautler 2003).<p> | ||
Revision as of 07:14, 1 November 2017
BBa_K2363000
This part contains a coding site for the PCBA5 gene, extracted from the organism d.mycarti. The resultant enzyme is a reductive dehalogenase and is able to degrade PCB toxins by stripping away chlorine groups from the overall structure. Three gene strains of this nature were identified by in 2014 by Dr. Shanquan Wang et. all, CG1, CG4, and CG5 (renamed PCBA1, PCBA4, and PCBA5). We used NCBI to acquire the sequences of each gene (accession number CP006951.1), then codon optimized and synthesized each one. This is the coding region only (1442 base pairs) and does not contain any promoter or RBS regions. We did, however, add a start and stop codon. We found a high confidence interval between the PCBA sequences and pceA (a well-characterized reductive dehalogenase), leading us to believe that they have the same interaction with the cofactor norpseudo B12 (Krautler 2003).
Wang S, Chng KR, Wilm A, et al. Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(33):12103-12108. doi:10.1073/pnas.1404845111.
Krautler, Bernhard. The Cofactor of Tetrachloroethene Reductive Dehalogenase of Dehalospirillim multivorans Is Norpseudo-B12, a New Type of a Natural Corrinoid. Helvetica Chimica Acta. 2003;vol86:3698. 10/31/17
(sequence accesible via link below)
BBa_K2363001
This part contains the upstream region (160 base pairs) of the PCBA4/5 gene, found originally in d.mycarti (Wang et all. 2014). The sequence contains the promoter region, which we plan to manipulate in the future for further characterization. We originally planned to extract the upstream regions from all four of the PCBA1, 4, 5, but discovered that the upstream region of 4 and 5 were nearly identical in sequence. To pick an adequate number of base pairs upstream from the coding region to form our geneblock, we used the Neural Network Promoter Prediction software with BDGP with all three sequences, locating the base pair position of all predicted promoters, and designing our upstream-region geneblock around the average distance the predicted promoters were from the start codon.
Wang S, Chng KR, Wilm A, et al. Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(33):12103-12108. doi:10.1073/pnas.1404845111.
(sequence accesible via link below)
