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Team:Washington/Protocols/pGA
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After performing PCR as outlined above, each fragment was run on a 1% agarose gel and gel-extracted using a Qiagen QIAquick gel extraction kit. 20 ng of gel-extracted insert and 20 ng of gel-extracted backbone were added to a 20 μL Gibson reaction which was set up on ice and incubated at 50°C for one hour. | After performing PCR as outlined above, each fragment was run on a 1% agarose gel and gel-extracted using a Qiagen QIAquick gel extraction kit. 20 ng of gel-extracted insert and 20 ng of gel-extracted backbone were added to a 20 μL Gibson reaction which was set up on ice and incubated at 50°C for one hour. | ||
| - | + | ===pGA transformations=== | |
[[File:Washington_iGEM2011_pGAprotocol.png|thumb|right|175px| pGA vector Assembly ]] | [[File:Washington_iGEM2011_pGAprotocol.png|thumb|right|175px| pGA vector Assembly ]] | ||
'''Note: Prepare these mixtures on ice''' | '''Note: Prepare these mixtures on ice''' | ||
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6. * BCKctrl | 6. * BCKctrl | ||
* add 100 pg of 1A3 gel extract | * add 100 pg of 1A3 gel extract | ||
| - | + | ===pSB transformations=== | |
Repeat the process for the comparison pSB vector as follows: | Repeat the process for the comparison pSB vector as follows: | ||
[[File:Washington_iGEM2011_pSBprotocol.png|thumb|right|175px| pSB vector Assembly ]] | [[File:Washington_iGEM2011_pSBprotocol.png|thumb|right|175px| pSB vector Assembly ]] | ||
Revision as of 21:00, 28 September 2011
Contents |
Gibson assembly efficiency assay
PCR
The PCR reactions were conducted at 20 μL volumes with 2x Phusion Flash polymerase master mix, 1 ng plasmid template, and 0.5 μM of each primer.
For the pGA assay, the insert came from a pGA1C3 vector and the insert came from a pGA1A3 vector expressing GFP. We used primers pGAprefix_fwd and pGAsuffix_rev to amplify the insert, and pGAsuffix_fwd and pGAprefix_rev to amplify the backbone.
For the pSB assay, the insert came from a pSB3K3 vector and the insert came from a pSB1A3 vector expressing low GFP levels that are not strong enough to see visually. We used pre-existing Biobrick primers [http://partsregistry.org/wiki/index.php?title=Part:BBa_G1004 BioBrick_f] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_G1005 BioBrick_r] to amplify the insert and [http://partsregistry.org/wiki/index.php?title=Part:BBa_G1000 Suffix_f] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_G1001 Prefix_r] to amplify the backbone.
Gibson reactions
After performing PCR as outlined above, each fragment was run on a 1% agarose gel and gel-extracted using a Qiagen QIAquick gel extraction kit. 20 ng of gel-extracted insert and 20 ng of gel-extracted backbone were added to a 20 μL Gibson reaction which was set up on ice and incubated at 50°C for one hour.
pGA transformations
Note: Prepare these mixtures on ice
- . Obtain a 40 uL aliquot of BL21 cells.
- . Add 120 uL of ice water to the aliquot.
- . The total volume is now 160 uL; split evenly among four labeled tubes: INS + BCK, INS + BCK, INSctrl, BCKctrl.
- . * INS + BCK tubes (x 2)
- add 1 uL of 10X-diluted pGA Gibson product (1A3 BCK/INS pLacGFP)
- . * INSctrl tube
* add 100 pg of pLacGFP gel extract
6. * BCKctrl
* add 100 pg of 1A3 gel extract
pSB transformations
Repeat the process for the comparison pSB vector as follows:
- 1 uL of pSB Gibson product (T19-1A3/pLacGFP)
- 1 ng INS (pLacGFP- gel extract)
- 1 ng BCK (T19-1A3- gel extract)
- Once all the samples are ready, begin the transformation.
- Rescue each sample in 500 mLs of LB
- Incubate all samples @ 37oC for ~45 min.
- Plate 50 uL on each sample onto a LB + Chlor + Amp + IPTG plate.
- 1 plate for each control in each vector set.
- 3 plates for each Gibson product tube in each set. ( 6 plates for each vector set + 2 control plates)
