BISC 219/F10: RNAi Lab 7

Lab 7: Series 3- Reverse Genetics: Picking Your Transformant

Colony PCR
In theory, any colony of bacteria growing on your LB+amp plate should contain a vector plasmid because the gene for antibiotic resistance is not chromosomal, but expressed from your plasmid. Because only transformed bacteria are resistant to ampicillin, if we grow the bacteria on or in a medium containing ampicillin, those bacteria that did not take up plasmid DNA will die while those that express plasmid gene products and transfer the plasmid to their progeny will grow just fine. This process of using a marker (usually antibiotic resistance) to differentiate transformed cells from those not transformed is called selection. Because bacteria reproduce asexually and are immobile on solid media, if you have an isolated colony on a plate, it is likely that the hundreds of thousands of bacteria making up that colony are daughters of a single cell (genetically identical). This allows us to take bacteria from a colony and sub-culture them in liquid media to make millions of identical copies. However, knowing that the bacteria growing in your broth or on your plate with ampicillin all have the vector plasmid responsible for amp resistance, that does not mean that these bacteria also have our gene of interest insert. There are a small proportion of bacteria on your selection plates that have a plasmid without the gene of interest. That can happen when, during ligation, the plasmid DNA annealed back on itself. We need a way to find the colonies that are expressing our gene of interest off the vector plasmid.

To achieve this goal we are going to do a "colony PCR". Instead of adding purified bli-1 or rol-5 gene fragments as template DNA in a pcr reaction with primers specific for your gene (as we did in LAB5), you will add a TINY little part of a colony as the template for your PCR reaction. During the first heat cycle the cells will burst open and release their DNA into the reaction. We will test 8 colonies per group to be sure we continue with bacteria that have the bli-1 or rol-5 gene.

1. Obtain a strip of PCR tubes and lids from your instructor. DO NOT separate the tubes!
2. Label the side of each tube 1-7
3. Find 7 medium to large size, well isolated colonies and circle them and number them 1-7.
4. Add 30 ul of master mix to each tube. Your master mix will include: 1X PCR buffer, 10 mM dNTPs, 0.4 uM forward primer, 0.4 uM reverse primer and 2 units/ul Taq.
5. After each tube has master mix use a sterile toothpick and gently touch your colony of interest - starting with #1 - and pick up a small, barely visible amount of the bacteria NOT THE ENTIRE COLONY!!!
6. Gently twirl the toothpick in the tube then discard the toothpick
7. Repeat until all 7 colonies are picked.
8. Snap the lid on the tubes, pulse them in the microcentrifuge with the appropriate rotor and adapters and bring them to the thermal cycler for pcr initiation.

PCR Conditions:

Step	Temperature	Time	Repeat
1	94°C	2 minutes	1 time
2	94°C	30 seconds
3	54°C	30 seconds
4	72°C	1 minutes	Steps 2-4 30 times total
5	72°C	10 minutes	1 time
6	4°C	forever	end program

Agarose Gel Electrophoresis
After the PCR reactions are completed you will run a gel to analyze the results of the amplification (the search for your gene).
Add 5 μL of loading dye to each pcr tube.
You will find a precast 1% agarose gel with Sybr-Green in 1x TAE buffer that is just for your group's use. Make sure that the wells of the gel are closest to the black (negative) electrode and that the gel apparatus has plenty of buffer. Draw a template in your lab notebook so you know which colony is to be put in each lane (1-7 left to right) and which lane contains your DNA ladder. Make sure you get a copy of the DNA ladder key.
Load 15μL of each pcr product into separate wells in the gel. Make sure they are loaded in numerical order 1-7 left to right.
Load 5 μL of the 100base pair DNA ladder in the well on the far right.

Run the gel for ~ 20min. at ~120 volts.
Directions for using the Kodak imager to photograph your gel can be downloaded at: Media: How_to_take_gel_photos.doc

To do on the day before the next lab:

You and your partner will return to the lab to make an overnight broth culture of one of the colonies that you are sure contains the gene of interest (determined from your visualization of successfully amplified, appropriately sized DNA seen on your gel photo). The sub-culture you will set up tonight will create many identical copies of bacteria that carry the vector plasmid containing your gene of interest.

1. Find your transformation plate in the glass front refrigerator in a rack labeled with your lab day. Make sure there is some bacteria remaining on the plate of a colony (1-7) that you saw successful gene amplification in the pcr product.
   
2. Begin by pouring (DO NOT PUT A PIPET INTO THE STOCK LB!!) 10 ml of sterile LB + tetracycline (12.5 μg/ml) broth from one of the stock containers in the refrigerator into a sterile orange-capped 15ml conical tube. You will use the volumetric marks on the tube for measuring the media rather than using a pipet. Make sure the LB stock does not look cloudy (indicating contamination by a previous user) and take care not to contaminate it yourself.
   
3. Add 10 microliters of the 50mg/ml ampicillin stock (also found in the refrigerator). Calculate the effective concentration of ampicillin that you will have in your LB tube (remember V1 x C1= V2 x C2) and record that information in your lab notebook.
   
4. Replace the cap of your LB +amp broth and invert the tube several times to mix the contents.
   
5. Label two sterile glass culture tubes (found in a rack in the lab) with tape in your team color. Label one with "pL4440 and the gene name" and your initials. Label the other with your initials only.
   
6. Using a 5 or 10 ml sterile disposable pipet, pipet 4 ml of your working solution of LB+ampicillin broth into each of the 2 tubes. Be careful not to touch the tip to anything non-sterile.
   
7. Inoculate the broth with your bacteria by using a sterile toothpick to scrape your candidate colony off the plate. Be sure not to touch the plate with the toothpick except on the desired colony and don’t pick up any satellite colonies. Make sure the toothpick falls into the sterile broth. The second tube of broth labeled with just your initials is a control and should not be inoculated with bacteria as it is your control for contamination.
   
8. Balance the 2 tubes across from each other on the rotating wheel in the incubator at the front of the room when you come in the door and incubate them at 37°C overnight. Do not forget to make sure the wheel is rotating when you leave!
   

Outline of Experimental Design for REVERSE Genetics Project

Where are you now in this process?(What have you done so far; What's next?)
Make the feeder strain of bacteria

1. Amplify gene of interest by pcr ;
   
2. Restriction Enzyme digestion of amplified DNA to create "sticky ends" for ligation;
   
3. Clean up DNA (remove enzymes);
   
4. Cloning: ligate gene into vector plasmid with amp resistance gene ;
   
5. Transform competent bacterial cells of a strain genetically modified to be tetracycline resistant;
6. Select for transformants on media with tetracycline and ampicillin;
   
7. Perform colony pcr on several transformants to be sure to find one colony containing a vector plasmid with the gene of interst
8. Culture the selected colony from colony pcr to create a lot of copies of these bacteria
9. Isolate the cloned plasmid DNA from that cultured colony by miniprep;
   
10. Retransform isolated plasmids (with gene interest) into HT115 (DE3)cells genetically modified to have impaired ability to degrade RNA;
    
11. Select for transformants on media with tetracycline and ampicillin
12. Choose an isolated colony to culture and make lots of feeder strain bacteria;
    
13. Induce expression of C. elegans gene dsRNA from the pL4440 vector in the bacteria by IPTG induction.
    
14. Seed NM lite worm growth media plates with feeder strain produced as described
    

Plate wild type C. elegans worms (N2 and rrf-3 strains) on feeder plates made as described (containing bacteria expressing dsRNA of our gene of interest).

Observe phenotype change in progeny caused by RNAi silencing or knockdown of the gene of interest compared to control worms of same strains that we NOT fed feeder strain bacteria.

Isolate RNA from RNAi worms and control worms of same strains.

Perform RT-PCR (Reverse Transcriptase) using the mRNA of the gene of interest as template, isolated from the RNAi worms.

Visualize cDNA in the pcr product by agarose gel electrophoresis and compare size of amplified fragment to known size of coding regions of gene of interest.

Assignment

Remember to check the Assignment section of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Calendar for other work to accomplish before the next lab.

Links to Labs& Project Info

Series1:
Worm Info
Lab 1: Worm Boot Camp & Sex-Linked or Autosomal Start
Lab 2: Sex-Linked or Autosomal Finale
Series2:
Background: Classical Forward Genetics and Gene Mapping
Lab 2: Mutant Hunt
Lab 3: Linkage Test Part 1
Lab 4: Linkage Test Part 2, Mapping and Complementation
Lab 5: Finish Complementation; Mapping Con't
Lab 6: DNA sequence analysis; Mapping Con't
Lab 7: Complete Mapping: Score
Series3:
Schedule of Reverse Genetics Project
RNAi General Information
Media Recipes
Lab 5: Picking your gene to RNAi
Lab 6: Cloning your gene of interest
Lab 7: Picking your transformant
Lab 8: Plasmid purification and transformation
Lab 9: Induction of bacteria for RNAi
Lab 10: Scoring your worms and RNA purification
Lab 11: RT PCR reactions