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Team:Washington/Alkanes/Future/LuxCDE
From 2011.igem.org
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==Methods== | ==Methods== | ||
| - | + | ===PCR and Standard Biobrick Assembly=== | |
This method revolved around designing oligos to PCR amplify LuxCD and LuxE off of the LuxBrick; LuxE was not directly adjacent to LuxCD in the Luxbrick, and therefore had to be obtained separately. Sticky ends on the oligos would then allow us to obtain a LuxCDE using stitching PCR. We would then digest and cut the resulting fragment, ligate it into a similarly-cut vector, and use transformation to obtain the desired plasmid with LuxCDE embedded into it. | This method revolved around designing oligos to PCR amplify LuxCD and LuxE off of the LuxBrick; LuxE was not directly adjacent to LuxCD in the Luxbrick, and therefore had to be obtained separately. Sticky ends on the oligos would then allow us to obtain a LuxCDE using stitching PCR. We would then digest and cut the resulting fragment, ligate it into a similarly-cut vector, and use transformation to obtain the desired plasmid with LuxCDE embedded into it. | ||
| - | + | ===Gibson Assembly=== | |
We would design oligos to amplify C, D, and E off of the LuxBrick. Unlike the previous method, the oligos would have sticky ends of [ ] base pairs to prevent misannealing, and the fragment containing C would also contain the vector for ligation. A 3-piece Gibson assembly was then done on C, D, and E, and the product was then transformed into cells. | We would design oligos to amplify C, D, and E off of the LuxBrick. Unlike the previous method, the oligos would have sticky ends of [ ] base pairs to prevent misannealing, and the fragment containing C would also contain the vector for ligation. A 3-piece Gibson assembly was then done on C, D, and E, and the product was then transformed into cells. | ||
| - | + | ===Gene Synthesis=== | |
Instead of using the LuxBrick to obtain C, D, and E, we would optimize C, D, and E, then assemble them ourselves. PCR was then used to amplify the respective pieces, and each of the three pieces was then digested and transformed into cells. | Instead of using the LuxBrick to obtain C, D, and E, we would optimize C, D, and E, then assemble them ourselves. PCR was then used to amplify the respective pieces, and each of the three pieces was then digested and transformed into cells. | ||
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==Results== | ==Results== | ||
Revision as of 23:04, 15 September 2011
Contents |
Alternative Routes for Fatty Aldehyde Production
Background
LuxCDE is an enzyme complex that produces a tetradecanal (14 carbon aldehyde) substrate by drawing from the fatty acid biosynthesis pathway. This tetradecanal substrate is to be catalyzed by the luxAB luciferase complex to produce light. The waste from the lucerferase is then sent back to luxCDE to be recycled. Since the aldehyde decarbonalse (ADC) uses aldehyde substrate to make alkane, we plan to use the luxCDE complex and ADC to synthesize alkane. The entire lux operon was submitted to the registry last year by Cambridge 2010.
Methods
PCR and Standard Biobrick Assembly
This method revolved around designing oligos to PCR amplify LuxCD and LuxE off of the LuxBrick; LuxE was not directly adjacent to LuxCD in the Luxbrick, and therefore had to be obtained separately. Sticky ends on the oligos would then allow us to obtain a LuxCDE using stitching PCR. We would then digest and cut the resulting fragment, ligate it into a similarly-cut vector, and use transformation to obtain the desired plasmid with LuxCDE embedded into it.
Gibson Assembly
We would design oligos to amplify C, D, and E off of the LuxBrick. Unlike the previous method, the oligos would have sticky ends of [ ] base pairs to prevent misannealing, and the fragment containing C would also contain the vector for ligation. A 3-piece Gibson assembly was then done on C, D, and E, and the product was then transformed into cells.
Gene Synthesis
Instead of using the LuxBrick to obtain C, D, and E, we would optimize C, D, and E, then assemble them ourselves. PCR was then used to amplify the respective pieces, and each of the three pieces was then digested and transformed into cells.
Results
The PCR and Gibson methods failed at multiple steps for uncertain reasons. Since we do not have our LuxCDE construct, no method or assay for testing the hypothetical construct was developed as of this time. We hypothesize that LuxCD's abnormally high AT concentration may have caused misannealing for primers, causing primer-dimer errors and other problems, but no concrete evidence exists for this as of yet. For gene assembly, we have lowered the AT concentration of C, D, and E to more optimal levels for PCR.
[Still working on this, will be expanded once all experiments are complete]
Current Status
Attempts to clone LuxCDE using the PCR and Gibson method have been abandoned. Gene assembly is still a work in progress; sequencing was being done at the time of writing.
Parts Submitted
This is also a work in progress, seeing we haven't completed our experiments yet.
Image(s)
Subsection will be deleted and intergrated into article once images are found.
