Team:Washington/Gram Positive/Build

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=Generating Mutant CapD=
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=Building Mutant CapD_CP=
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To build the mutant proteins, we follow the path of the central dogma. First, we created DNA that contains our mutations. Second, we induced our transformed cells containing the desired DNA to express the mutant proteins. Lastly, we harvested the proteins by lysing open the cells and filtering out non-desired cell components.
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==Mutate DNA==
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==Generating Mutant DNA==
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[[Image:Washington_Kunkel_summary.jpg|center|thumb|800px| Kunkel Mutagenesis Protocol: Generate ssDNA, Anneal Oligos, Synthesize Mutant Plasmids]]
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[[Image:Washington_Kunkel_summary_revised2.jpg|center|thumb| 760px| Kunkel Mutagenesis Protocol: Generate single stranded dU-DNA, Anneal primers, polymerization, Synthesize Mutant Plasmids and replace uracil with thymine to complete]]
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After we came up with the desired mutant protein designs, we employed the [[Team:Washington/Protocols/KunkelCapD|Kunkel Mutagenesis]] method to generate the desired mutant DNA. Kunkel mutagenesis is a three step process. First, we obtained ssDNA of wild-type CapD_CP gene from transformed cells that contain the CapD_CP gene and lack the enzyme to destroy uracil. The presence of uracil is used later to obtain the correct DNA strand. The second step involved annealing our mutation-containing primers to the ssDNA and polymerizing the strand that contains our desired mutations. The result is a double-stranded DNA, consisting of a wild-type CapD_CP strand and a mutations-containing (desired) strand. Lastly, to obtain a dsDNA that consists of only the desired strands, we transformed it into another type of cell that contains enzymes to destroy the uracil-containing strand. Once the uracil-containing wild-type strand is destroyed, the complementary strand is synthesized, resulting in a dsDNA that contains only our desired mutations.[[#References | [1]]]
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==='''Order Oligonucleotides'''===
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After we come up with the desired mutant proteins designs, we employ the method Kunkle Mutagenesis to generate our mutant proteins. ([https://2010.igem.org/Team:Washington/Protocols/Kunkel Kunkel Mutagenesis protocol]) Kunkel is a site-directed mutagenesis, requiring knowledge of wild-type sequences. After the desired mutation is modeled using [https://2010.igem.org/Team:Washington/Project/Tools/FoldIt Foldit], we order a mutation's antisense oligonucleotides from [http://www.idtdna.com/ Integrated DNA Technologies].
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==='''Generate ssDNA'''===
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In order to anneal oligos, CapD expression gene ssDNA must be obtained by transforming CJ236 cells with a plasmid containing the CapD gene. These cells use Uracil instead of Thymine, and are unable to destroy Uracil containing DNA.
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==='''Annealing to ssDNA'''===
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Received oligonucleotides lack activity-inducing phosphates. Adding phosphates by kinasing readies them for annealing to ssDNA. The oligonucleotide binds to a specified location on the ssDNA except where the mutation is. This creates an area where the oligonucleotide will not bond to the template ssDNA.
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[[Image:Washington_Kunkel_pt_2.jpg|center|thumb|800px| After transformation, DNA polymerase completes the mutant plasmid through error correction mechanism, replacing uracils with thymines.]]
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==='''Synthesize the Plasmid'''===
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Using DNA polymerase, the rest of the missing strand is synthesized. Finally the area in the plasmid where the mutation is fixed because the former ssDNA strand that contains uracil is destroyed by the cell we transform our mutant plasmid into. Since the cell uses the other strand (the strand with the Oligonucleotides) to fix the DNA, the result is a complete mutant plasmid. Plasmids are then sent for sequencing by [http://www.genewiz.com/ GENEWIZ] to confirm mutations.
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==Grow Protein==
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To grow and harvest our protein, we used two different protocols: [https://2010.igem.org/Team:Washington/Protocols/50mLPurificationCapD small scale] and [https://2010.igem.org/Team:Washington/Protocols/1LPurificationCapD large scale]. The concepts described below are the same for both protocols.
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==='''Protein Production'''===
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By introducing Isopropyl β-D-1-thiogalactopyranoside (IPTG), an allolactose mimic, we induce E. Coli to produce our protein. IPTG binds with the lac inhibitor protein and activates the lac operon, turning on the CapD gene and causing production of our mutant protein.
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==Harvest Protein==
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[[Image:Washington_lyse.png|thumbnail|500px|Protein Purification Process]]
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==='''Lyse cells'''===
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The supernatant (media) from spinning down the cells is emptied and the cells at the bottom are lysed open. The result is a slurry containing all the cell’s proteins and DNA. Lysis is then spun down and the supernatant, containing all the proteins, is collected. Among the proteins is CapD.
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==='''Purify proteins'''===
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To purify the protein, we run the supernatant collected from lysis through a column containing TALON resin cobalt beads. CapD's designed histidine tags bind to the beads, whilst everything else flows through. Finally, the CapD is eluted with imidazole, a histidine without a backbone, which outcompetes the affinity to bind. The result is our purified mutant CapD.
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[[Image:Washington_TALON_2Bonding.png|thumbnail|750px|CapD's Histidine tags bond to Cobalt bead (Photo credit:[http://bioenergy.asu.edu/photosyn/courses/bio_343/lab/experiment-i.html])]]
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==Protein Expression and Purification==
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[[Image:Washington_lyse_revised4.png|thumbnail|700px|left|Protein Purification Process]]
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Once we obtained cells transformed with our desired mutant DNA, we induced the cells to express the mutant protein. By introducing Isopropyl β-D-1-thiogalactopyranoside (IPTG), an allolactose mimic, we induce E. Coli to produce our protein. IPTG binds with the lac inhibitor protein and activates the lac operon, turning on the CapD_CP gene and causing production of our mutant protein. For this step, we used two different protocols: [https://2010.igem.org/Team:Washington/Protocols/50mLPurificationCapD small scale] and [https://2010.igem.org/Team:Washington/Protocols/1LPurificationCapD large scale]. The concepts described below are the same for both protocols. To harvest our mutant proteins, we needed to first lyse open the induced cells and then purified out our proteins (refer to small/large scale protocol). For the purification procedure, we employed Talon beads. CapD_CP's designed histidine tags bind to the beads, whilst everything else flows through. The result of this process is our purified mutated CapD_CP proteins.
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==References==
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1. T.A. KUNKEL, P NATL ACAD SCI USA 82, 488 (JANUARY 1985, 1985)
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'''&larr; [[Team:Washington/Project/Baker/Design|Designing the Gram(+) Therapeutic]]'''
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'''&larr; [[Team:Washington/Gram Positive/Design|Designing the Gram(+) Therapeutic]]'''
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'''[[Team:Washington/Project/Baker/Test|Testing the Gram(+) Therapeutic]] &rarr;'''
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'''[[Team:Washington/Gram Positive/Test|Testing the Gram(+) Therapeutic]] &rarr;'''
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Latest revision as of 20:37, 27 October 2010

Building Mutant CapD_CP

To build the mutant proteins, we follow the path of the central dogma. First, we created DNA that contains our mutations. Second, we induced our transformed cells containing the desired DNA to express the mutant proteins. Lastly, we harvested the proteins by lysing open the cells and filtering out non-desired cell components.

Generating Mutant DNA

Kunkel Mutagenesis Protocol: Generate single stranded dU-DNA, Anneal primers, polymerization, Synthesize Mutant Plasmids and replace uracil with thymine to complete

After we came up with the desired mutant protein designs, we employed the Kunkel Mutagenesis method to generate the desired mutant DNA. Kunkel mutagenesis is a three step process. First, we obtained ssDNA of wild-type CapD_CP gene from transformed cells that contain the CapD_CP gene and lack the enzyme to destroy uracil. The presence of uracil is used later to obtain the correct DNA strand. The second step involved annealing our mutation-containing primers to the ssDNA and polymerizing the strand that contains our desired mutations. The result is a double-stranded DNA, consisting of a wild-type CapD_CP strand and a mutations-containing (desired) strand. Lastly, to obtain a dsDNA that consists of only the desired strands, we transformed it into another type of cell that contains enzymes to destroy the uracil-containing strand. Once the uracil-containing wild-type strand is destroyed, the complementary strand is synthesized, resulting in a dsDNA that contains only our desired mutations. [1]

Protein Expression and Purification

Protein Purification Process


















Once we obtained cells transformed with our desired mutant DNA, we induced the cells to express the mutant protein. By introducing Isopropyl β-D-1-thiogalactopyranoside (IPTG), an allolactose mimic, we induce E. Coli to produce our protein. IPTG binds with the lac inhibitor protein and activates the lac operon, turning on the CapD_CP gene and causing production of our mutant protein. For this step, we used two different protocols: small scale and large scale. The concepts described below are the same for both protocols. To harvest our mutant proteins, we needed to first lyse open the induced cells and then purified out our proteins (refer to small/large scale protocol). For the purification procedure, we employed Talon beads. CapD_CP's designed histidine tags bind to the beads, whilst everything else flows through. The result of this process is our purified mutated CapD_CP proteins.

References

1. T.A. KUNKEL, P NATL ACAD SCI USA 82, 488 (JANUARY 1985, 1985)

Designing the Gram(+) Therapeutic       Testing the Gram(+) Therapeutic