Team:Harvard/Lambda Red

From 2011.igem.org

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[[Team:Harvard/MAGE | MAGE]] | [[Team:Harvard/Lambda_Red | Lambda Red]]| [[Team:Harvard/Chip_Based_Library | Chip-Based Library]]
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__NOTOC__
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To see how we used lambda red to build our selection system, go to our [https://2011.igem.org/Team:Harvard/Project/Test#Building_the_selection_strain:_Lambda_Red_Recombineering Test] page.
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For a step-by-step procedure, see our [https://2011.igem.org/Team:Harvard/Protocols#Lambda_Red Lambda Red Protocols].
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= Lambda Red=
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[[File:Lambda_Red,_Tech.gif]] low resolution
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==Summary (adapted from Mosberg and Lajoie et al)[[#References|[1]]]==
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To make targeted genetic changes in E.Coli with larger constructs of tens to thousands of base pairs, unlike the smaller changes made in [https://2011.igem.org/Team:Harvard/Technology/MAGE MAGE], we can use lambda red recombineering to create insertions, deletions and replacements in chromosomal DNA.
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==How lambda red works (adapted from Yu et al)[[#References|[2]]]==
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Even though homologous recombination can occur naturally, its efficiency can be greatly enhanced through the presence of the phage λ-based recombination system, Red.  While it is very efficient, the exact mechanism is not known.
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For efficient genome editing using lambda red, you can use [https://2011.igem.org/Team:Harvard/Results/Biobricks#EcNR2_strain_.28BBa_K615002.29 the ECNR2 strain] with your own insertion construct and overhangs (i.e. 30-50bp homology to the locus in which the gene is being inserted). The ECNR2 strain is especially suited for lambda red recombineering, because in addition to having the lambda-phage based recombination system, it also has the mutS gene knocked out to reduce DNA mismatch repair activity, so that the insert (which will not match the original genomic code) is less likely to be excised. To obtain this strain, you can make a request at [http://partsregistry.org/Part:BBa_K615002 the Registry of Standard Biological Parts.]
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Figure 1. How to perform lambda red. First, we run a PCR to get the required insertion product i.e. construct A with an antibiotic resistance marker, and then use lambda red recombination to insert the desired product into the genome.
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[[File:Lambda_Red,_Tech_generic.gif |frameless|center|915px]]
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'''== Procedure=='''
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==References:==
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Lambda-Red Recombination
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'''1.''' Mosberg JA, Lajoie MJ, Church GM. Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. ''Genetics'' 2010;186:791-799.[http://www.genetics.org/content/186/3/791]
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===Part A) PCR to get the required product.===
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'''2.''' Yu, D., H. M. Ellis, et al. (2000). "An efficient recombination system for chromosome engineering in Escherichia coli." Proceedings of the National Academy of Sciences of the United States of America 97(11): 5978-5983.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165854/]
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*We designed primers flanking the region of interest (the zeocin cassette), and added 30 to 50 base pairs of homology matching the ECNR2 genome flanking the rpoZ gene. The lengths of the annealing regions of the primers are chosen so that they have a similar (within 1°C ) melting temperature for the PCR reaction.
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*The PCR reaction is done with the above primers, and a template of a small amount of liquid culture (diluted 30 times) of the omega knockout bacteria hybrid selection strain.
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*The product is run on a gel, and then either gel extracted (if there are side products) or PCR purified (if the reaction ran clear) and eluted in molecular grade water, not EB, since the ions and salts would otherwise cause electrical arcing during electroporation
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== Part B) Lambda-red recombination ==
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'''3.''' (Supporting material for) Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. (2011). Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. ''Science'', 333(6040):348-53.[http://www.sciencemag.org/content/suppl/2011/07/13/333.6040.348.DC1/Isaacs.SOM.pdf]
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*1 Activate lambda red through temperature sensitive activation. For the ECNR2 strain, this involved taking the culture that’s grown in LB, at 30C at around midlog, and placing it in a water bath at 42C for 15 min to activate the lambda red machinery.
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*2 Add 1-1.5 mL of mid-log cells in culture to 1.5 mL eppendorf tube. Spin in the centrifuge for 1 minute at 15000rpm (max speed)
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*3 (All steps need to be done on ice and the pipette tips, the cuvettes, and the molecular grade water must be kept cold at all times.)
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*4 Decant the liquid at the top, and use a pipette to remove as much of the liquid as possible without disturbing the pellet. Change tips. Wash cells with 1 mL of cold H2O, and spin in centrifuge for 1 minute at max speed
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5. Repeat the wash step.
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6. Tip: When you are removing the liquid after spinning down, it helps to hold tube so that the bacterial pellet is at the top and then use the pipette to draw out the liquid right below it
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7. Resuspend cells with 50 μL of cold H2O
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8. Add 50-200 ng of insertion construct to eppendorf tube. It also could be accomplished by taking a separate eppendorf, and adding enough of the insertion construct to almost 50 μL of cold H2O in an earlier step, so that these steps can be accomplished more quickly. It helps to reduce the amount of time the bacteria are suspended in water since it can lyse the cells because the surrounding solution is hypotonic to the bacterial cytoplasm.
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9. Add the 50 μL solution to the cells, pipette up and down to mix them well, and then place in chilled cuvette.
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10. Set electroporation machine to Eco1, 1.8 volts. A time constant of 4.8ms is a good number. You can do a blank with a cuvette filled with 50 μL of water to check its time constant. We want a time constant as close to that for molecular grade water as possible.
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11. Before placing the cuvette in the electroporator, make sure that all water is wiped off of cuvette, so that it is dry, or it can interfere with electrical contact.
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12. After electroporation immediately place 1 mL of LB in cuvette, pipette up and down to mix the cells in the LB and resuspend them.
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13. Then place that 1mL of bacteria in LB into  2 mL of LB in a culture tube and allow them to grow for 2 to 3 hours in correct temperature (30C for ECNR2).
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14. After three hours, plate out culture in different concentrations of bacteria on specific plates (in this case, of zeocin).
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15. Grow up the cultures  on the plates overnight, and use a colony to do PCR or sequencing to check for the insert via its sequence, or the band size on the gel.
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Latest revision as of 03:54, 29 October 2011

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Overview | MAGE | Chip-Based Synthesis | Lambda Red | Protocols

To see how we used lambda red to build our selection system, go to our Test page.

For a step-by-step procedure, see our Lambda Red Protocols.

Lambda Red

Summary (adapted from Mosberg and Lajoie et al)[1]

To make targeted genetic changes in E.Coli with larger constructs of tens to thousands of base pairs, unlike the smaller changes made in MAGE, we can use lambda red recombineering to create insertions, deletions and replacements in chromosomal DNA.

How lambda red works (adapted from Yu et al)[2]

Even though homologous recombination can occur naturally, its efficiency can be greatly enhanced through the presence of the phage λ-based recombination system, Red. While it is very efficient, the exact mechanism is not known. For efficient genome editing using lambda red, you can use the ECNR2 strain with your own insertion construct and overhangs (i.e. 30-50bp homology to the locus in which the gene is being inserted). The ECNR2 strain is especially suited for lambda red recombineering, because in addition to having the lambda-phage based recombination system, it also has the mutS gene knocked out to reduce DNA mismatch repair activity, so that the insert (which will not match the original genomic code) is less likely to be excised. To obtain this strain, you can make a request at [http://partsregistry.org/Part:BBa_K615002 the Registry of Standard Biological Parts.]

Figure 1. How to perform lambda red. First, we run a PCR to get the required insertion product i.e. construct A with an antibiotic resistance marker, and then use lambda red recombination to insert the desired product into the genome.

915px

References:

1. Mosberg JA, Lajoie MJ, Church GM. Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. Genetics 2010;186:791-799.[http://www.genetics.org/content/186/3/791]

2. Yu, D., H. M. Ellis, et al. (2000). "An efficient recombination system for chromosome engineering in Escherichia coli." Proceedings of the National Academy of Sciences of the United States of America 97(11): 5978-5983.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165854/]

3. (Supporting material for) Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. (2011). Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science, 333(6040):348-53.[http://www.sciencemag.org/content/suppl/2011/07/13/333.6040.348.DC1/Isaacs.SOM.pdf]

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