| 1. Plasmid DNA Purification Using the QIAprep: Use 2mL LB cultures of ligation products from 07-11-2008. Procedure:
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| a. Resuspend bacterial cells in 250uL Buffer P1 and transfer to microcentrifuge tube
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| b. Add 250 uL Buffer P2 and invert 4-6 times
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| c. Add 350uL Buffer N3 and mix immediately by inverting 4-6 times
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| d. Centrifuge for 10 minutes @ 13,000 rpm in a table-top centrifuge. White pellet will form (made up of cell debris).
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| e. Apply supernatants from step D to the QIA prep spin columns. Centrifuge for 30-60 seconds --> discard the flow through.
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| f. Wash the QIA prep spin column by adding 0.5mL (500uL) Buffer PB. Centrifuge for 30-60 seconds. Discard the flow through.
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| g. Wash QIA prep spin column by adding 0.75mL (750uL) Buffer PE. Centrifuge for 30-60 seconds. Discard the flow through.
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| h. Centrifuge for additional 1 minute to remove residual buffer.
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| i. Place the QIA prep spin column in a clean 1.5mL centrifuge tube. To elute DNA, add 50uL of Buffer EB (10mM Tris-Cl, pH 8.5) to center of spin column and centrifuge.
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| NOTE: Used Buffers to purify or washout any cell debris so only has DNA. Used spin column b/c the column binds to DNA (has DNA affinity) and all other solution will drain through.
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| 2. Spectrophotometry: 'Spec' purified preps to check concentration of DNA in the ligated products. Refer Spectrophotometry Results link on Notebook page.
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| 3. Double Digest: Perform double digest. Incubate @ 37C for 2-20hrs. Heat inactivate enzyme @ 65C for 15 mins.
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| GFP + Terminator => GFP:Term.
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| Pro/LAMBDAcI + Terminator => Pro:LAMBDAcI:Term.
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| Pro + LAMBDAcI/Terminator => Pro:LAMBDAcI:Term.
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| Refer to Double Digest table below.
| Parts | 10x Buffer | BSA | H20 | DNA | RE 1 | RE 2
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| GFP (1250 ng/uL) | 5.0uL | 0.5uL | 41.5uL | 1.0uL | 1.0uL, EcoRI | 1.0uL, Spe1
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| Terminator | 5.0uL | 0.5uL | 17.5uL | 25.0uL | 1.0uL, Xba1 | 1.0uL, Pst1
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| Promoter/LAMBDAcI | 5.0uL | 0.5uL | 40.5uL | 2.0uL (L3b) | 1.0uL, Pst1 | 1.0uL, Spe1
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| Promoter/LAMBDAcI | 5.0uL | 0.5uL | 32.5uL | 10.0uL (L3c) | 1.0uL, Pst1 | 1.0uL, Spe1
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| LAMBDAcI/Terminator | 5.0uL | 0.5uL | 27.1uL | 15.4uL (L4b) | 1.0uL, EcoRI | 1.0uL, Xba1
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| LAMBDAcI/Terminator | 5.0uL | 0.5uL | 20.3uL | 22.2uL (L4c) | 1.0uL, EcoRI | 1.0uL, Xba1
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| BaseVector (35 ng/uL) | 5.0uL | 0.5uL | 13.5uL | 29.0uL | 1.0uL, EcoRI | 1.0uL, Pst1
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| TetR Promoter | 5.0uL | 0.5uL | 8.5uL | 34.0uL | 1.0, EcoRI | 1.0uL, Spe1
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| 4. Vector Dephosphorylation next; Base Vector only. Refer to Dephosphorylation performed on 07-11-2008 for details.
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| 5. Meeting with Yiannis: Yiannis states that need to: (1) Start preparing for presentation due last Wednesday of internship, (2) Use Emma's old report/paper as a guide or starter on writing own paper that is due at end of internship, (3) submit parts to iGEM, look @ Yiannis' email and start to work on what iGEM requires and what would iGEM want for medals, (4) slightly change model or change reactions to get RFP or GFP since it is slightly mixed up, (5) PUT LINK ON WIKI FOR SYNBIOSS.
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6. Ligation: Ligating parts will allow them to rejoin ends. After ligation is finished, leave @ room temperature to ligate for 1 hour. Refer to table below:
| Part(s) | 10x Buffer | H20 | BV | Insert DNA 1 | Insert DNA 2 | T4 Ligase | #
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| BV/GFP/Term | 3.0uL | 8.0uL | 2.0uL | 4.0uL GFP | 12.0uL Term | 1.0uL | L5
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| 2x Pro:LAMBDAcI/Term | 3.0uL | 8.5uL | 0 | 2.5uL Pro:LAMBDAcI | 15.0uL Term | 1.0uL | L6, L7
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| 2x Pro/LAMBDAcI:Term | 3.0uL | 8.5uL | 0 | 15.0uL Pro | 2.5uL LAMBDAcI:Term | 15.0uL Term | 1.0uL | L8, L9
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| NOTE: 2x refers to 2 samples being used. BV refers to Base Vector.
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| 7. Transformations:
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