DNA Ligation & Colony Transformation
Carolina Kit
Isabelle Muschamp

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The plasmid vector must be cut with a restriction endonuclease (aka: restriction enzyme)
DNA ligase joins the DNA fragment & vector
DNA
Host cell is made competent so can plasmid can enter
Transformed cells are grown on selection media

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Extrachromosomal
DNA molecules
Small; varies from 1 to over 1,000 kilobase pairs
Circular
Usually carry one or a few genes
Replicate separately from the chromosome
A type of cloning vector used to carry a gene not found in the bacterial host’s chromosome
Treatment of plasmids pAMP and pKAN with a mixture of BamHI and
HindIII are given for the Easy Gene Splicer lab

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4539 base pairs a single replication origin a gene (amp r )conferring resistance to the antibiotic ampicillin (a relative of penicillin) a single occurrence of the sequence
5' GGATCC 3'
3' CCTAGG 5‘ that, as we saw above, is cut by the restriction enzyme BamHI a single occurrence of the sequence
5' AAGCTT 3'
3' TTCGAA 5‘ that is cut by the restriction enzyme HindIII
Treatment of pAMP with a mixture of BamHI and HindIII produces:
-a fragment of 3755 base pairs carrying both the amp r gene and the replication origin
-a fragment of 784 base pairs
-both fragments have sticky ends

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4207 base pairs a single replication origin a gene (kan r ) conferring resistance to the antibiotic kanamycin a single site cut by BamHI a single site cut by HindIII
Treatment of pKAN with a mixture of BamHI and
HindIII produces:
-a fragment of 2332 base pairs
-a fragment of 1875 base pairs with the kan r gene
(but no origin of replication)
-both fragments have sticky ends

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Both the DNA that will be inserted and the plasmid DNA are ligated together
Sticky ends help this process by stabilizing the pieces together with base-pairing, but the enzyme DNA ligase is added to the reaction to cause the DNAs to become covalently linked together

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After ligation of the insert DNA and your plasmid, the new chimeric (an organism that is composed of genetically different tissues, either naturally or as a result of a laboratory procedure) of DNA into bacteria
Transformation of the bacteria with recombinant DNA is easily performed by shocking the cells

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The process of transferring foreign DNA fragments into a recipient (host) cell for growth and replication
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Scientists begin this process by fusing two different sets of
DNA together creating a molecule of recombinant DNA or rDNA. This particular molecule is the product of the gene of interest (the desired gene) and another source of plasmid DNA coming together through the use of a restriction enzyme, which cuts the DNA at a specific nucleotide sequence, and a ligase which binds the separate strands of DNA into one form.
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After the rDNA is made, the cells which are going to be used as a vehicle for transformation are made
“competent” or prepared to receive foreign DNA.

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The cells are concentrated into a pellet through the use of a centrifuge, and their membranes are made porous so that the rDNA has a route to enter the cell.
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The rDNA is added to the cell culture and some of the rDNA plasmids are absorbed, but to increase their absorption numbers the culture undergoes a heat/cold shock. The hot water bath enlarges the cell’s pores and more plasmids are “sucked” in. The culture is then quickly transferred to the ice which traps the plasmids within the cell’s membrane.
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Cells containing the foreign DNA grow and multiply within the tube, but to ensure that transformation was successful and purification of the gene of interest to proceed, the culture is grown on mediums so visual confirmation can be made.

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Endonucleases:
◦ in nature, they protect bacteria from intruding DNA
◦ cut up (restrict) the viral DNA
◦ cut only at very specific nucleotide sequences
Restriction site: recognition sequence for a particular restriction enzyme
Restriction fragments: segments of DNA cut by restriction enzymes in a reproducible way
DNA ligase: joins the sticky ends of DNA fragments

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 rDNA (recombinant DNA)—the produced piece of DNA from inserted another piece of DNA
Recognize specific sites to cut the DNA
Blunt ends—straight across
Sticky ends—one side of DNA is longer than the other, these overhangs allow for complementary matches between two DNA pieces cut by the same enzyme, the sticky ends match and pasting may occur to produce an rDNA molecule
More than 1200 restriction enzymes discovered & isolated from bacteria
Read 5  3
Palindromic (example radar or

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Transformation – the uptake and expression of foreign DNA by a cell
Transduction – the use of viruses to transform or genetically engineer cells
Competent/competency – the ability of cells to take up DNA
Selection – the process of screening potential clones for the expression of a particular gene, for example, the expression of a resistance gene (such as resistance to ampicillin) in transformed cells
Transformation efficiency – a measure of how well cells are transformed to a new phenotype
Recovery period – the period following transformation where cells are given nutrients and allowed to repair their membranes and express the
“selection gene(s)”
Beta-galactosidase gene – a gene that produces beta-galactosidase, an enzyme that converts the carbohydrate X-gal into a blue product
Green fluorescent protein – a protein found in certain species of jellyfish that glows green when excited by certain wavelengths of light
(fluorescence)
Scale-up – the process of increasing the size or volume of the production of a particular product

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Week Before: read lab & Flowchart, only 6 groups
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Thursday—Lecture, pre-quiz
Monday—part A
Tuesday—part B
Thursday--part C
Friday FIRE—come view results

Prepare
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LB agar plates (<1 month before)
2 LB agar plates for streaking to use in part B
16 (gives 4 extra) LB agar plates for part C
12 (gives 4 extra) LB agar plates with ampicillin and kanamycin coming with kit—check for 2 LB/amp and 2 LB/kan for control group
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Aliquot for 6 groups
Part A
--20uL Ligation Buffer/ATP/ligase (6)
--10uL pAMP (5 tubes—pKAN control does not get one)
--10uL pKAN (5 tubes—pAMP control does not get one)
Part B
--500uL Calcium Chloride (6)
--500uL LB (6)
Locate Supplies:
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Spreaders
 loops set up for part A
 ice set up for part B
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Streak starter plates (12-20 hours before part B) (start after school)
42C water bath
37C incubator put calcium chloride on ice
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When finish store at 0C (beaker of ice in fridge) set up for part C
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37C incubator

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2 lab station groups will be control groups:
1. -–pAMP + ligase (use 10uL water)
2. --pKAN + ligase (use 10uL water)
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Follow same directions, but run these instead of pAMP/KAN
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Only plate on LB/amp and LB/kan plate (do not spread on LB plates)

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Group 1—pAMP control
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Group 2—pKAN control
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Group 3
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Group 4
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Group 5
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Group 6

 http://bioinformatics.dnalc.org/gmo/animation/g mo.html
 http://www.carolina.com/text/teacherresourc es/instructions/biotech/ez_gene_splicer_kit.p
df

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Endonucleases – enzymes that cut RNA or
DNA at specific sites; restriction enzymes are endonucleases that cut DNA
Sticky cells – restriction fragments in which one end of the double stranded DNA is longer than the other; necessary for the formation of recombinant DNA
Restriction enzyme mapping – determining the order of restriction sites of enzymes in relation to each other

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Samples of the plasmid fragments are mixed with DNA ligase and incubated at room temperature for 2-24 hours.
Complementary Bam HI and Hind III “sticky ends” hydrogen-bond to align restriction fragments. Ligase catalyzes the formation of phosphodiester bonds that covalently link the DNA fragments to form stable recombinant DNA molecules.
Use micropipets (instead of transfer)
After 2-24hours, will store in fridge at 4C

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Transform E.coli with the ligated plasmid
DNA. E. coli cells are scraped off an LB agar plate and suspended in two tubes containing solution of calcium chloride.
The ligated pAMP/KAN plasmid is added to one cell suspension, and both tubes are incubated at 0C, then heat shocked at 42C, cooling and addition of LB broth, cells then recover.
I will store cells at 0C (beaker of ice in fridge) after 5-6 hours of incubation

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Samples of the cells are plated on two types of growth media: plain LB agar and LB agar with ampicillin and kanamycin. Incubate to grow cells. Only cells with both ampicillin and kanaycin will be expressed on the 2 nd plate
Come in at FIRE to see
You are receiving 2 LB plates—so you can do both plates in PART C step 1.C and 2
Use spreaders at Part C 3