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Laboratory 1. Plant Genomic DNA Extraction and Gel Electrophoresis Exercise 1. Lab safety and sterile techniques: Exercise 2. Pipetting exercise: Exercise 3. DNA Extraction using CTAB: Materials: CTAB solution Liquid nitrogen Phenol/EB pH 8.0 96:4 (chloroform: Isoamyl) Elution Buffer (EB)

β-mercaptoethanol 3M NaOAc 100% isopropanol 70% EtOH

1. Pre heat 500 μl CTAB in 65ºC water bath. 2. Place 0.2 to 0.5g plant material into the mortar and add liquid nitrogen, grind to a powder. 3. Add plant material to the pre-heated CTAB and add1%β-mercaptoethanol (5μl) to the centrifuge tube and incubate at 65˚C for 0.5 hr. Vortex well at least every 10min. 4. Centrifuge for 8min. at 13,000rpm, transfer top layer to new microcentrifuge tube. 5. Add 500ul 96:4 chlorofor:isoamyl alcohol, vortex well, centrifuge for 3min., transfer top layer to a new microcentrifuge tube. 6. Repeat step 5. 7. Add 0.1 volume 3M NaOAc and 0.7 volumes 100% isopropanol, vortex, incubate in ice bath for 10min. Centrifuge for 10min. at 13,000 rpm and discard the supernatant. Be careful not to disturb the pellet. 8. Wash pellet in 500μl cold 70% EtOH, invert 5X; incubate 10min. in an ice bath. 9. Centrifuge for 2min. add maximum speed to secure the pellet, discard the supernatant. 10. Dry the pellet by placing inverted, cap open, in the 37o incubator for 10 min. 11. Add 50μl EB Buffer, store in 4˚C overnight before quantifying. CTAB Solution: 2g CTAB 2g PVP 28ml 5M NaCl (29.22g/100ml) 4ml EDTA pH 8.0 10ml 100mM TrisHCl pH8.0 1% β-mercaptoethanol (just before use) ·Prepare the solution without CTAB, PVP, β-mercaptoethanol and autoclave for 20 min. ·After autoclave add CTAB and PVP; heat to dissolve CTAB and PVP on the hot tray. Add the 1% β-mercaptoethanol directly to the extraction vial (5μl/500μl of CTAB solution). Pre-heat the solution in a 65˚C water bath before use. Modified from Dr. Sarah Wyatt’s handout

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General Considerations and Rationale Three components are necessary for successful nucleic acid extraction: 1) inhibition of nucleases, 2) removal of proteins, and 3) physical separation of the nucleic acid from other cellular components. Nuclease inhibition and removal of proteins are not mutually exclusive and often are accomplished in a single step (such as phenol extraction). Inhibition of Nucleases Detergents inhibit nucleases and help separate the proteins from the nucleic acids. A common detergent is sodium dodecylsulfate (SDS). Avoid the use of potassium salts or temperatures below 10 °C with SDS since this may cause precipitation of the detergent. One of the most widely used detergents for plant DNA extraction buffers is CTAB (cetyltrimethyl-ammonium bromide). CTAB is most often used in a 2% (w/v) solution (Rogers & Bendich 1985, Doyle & Doyle 1987, Nickrent 1994). Removal of Proteins Phenol is a strong denaturing agent for proteins. In phenol extractions, proteins partition into the organic phase (and interface) whereas nucleic acids partition in the aqueous phase. Usually phenol is used in a 1: 1 mixture with chloroform since deproteinization is more effective when two different organic solvents are used simultaneously. In addition to denaturing proteins, chloroform is useful in removing lipids and a final chloroform extraction helps to remove the last traces of phenol. The isoamyl alcohol helps with the phase separation, decreases the amount of material found at the aqueous and organic interface, and helps reduce foaming. Antioxidants such as 8-hydroxyquinoline or ß-mercaptoethanol are often added to phenol. During phenol extractions, the pH of the buffer is important in determining whether DNA and/or RNA are recovered. At pH 5-6, DNA is selectively retained in the organic phase leaving RNA in the aqueous phase (hence water saturated phenol is useful for RNA extractions). At pH 8.0 or higher, both DNA and RNA are retained in the aqueous phase. Phenol can be stored under buffer for up to one month. Protease The most common proteolytic enzyme used in nucleic acid extractions is protease K (e.g. Sigma P4755) which is generally made up in 50 units/ml aliquots and stored frozen for immediate use during extractions. Solutions are generally incubated with this enzyme at 37 °C for at least one hour. Other Extraction Buffer Components Two common reducing agents found in extraction buffers are ß-mercaptoethanol or dithiothreitol (DTT). EDTA is also present to chelate Mg+2 ions thus mediating aggregation of nucleic acids to each other and to proteins. Modified from Dr. Sarah Wyatt’s handout

3 Ethanol and/or Isopropanol Precipitation The most common method of concentrating nucleic acids is with alcohol precipitation. This occurs in the presence of a salt (see below) at low temperatures (-20 °C or less). Either 2.0 volumes of ethanol can be used to precipitate DNA or 0.6 volumes of isopropanol. Isopropanol is often used for the first precipitation, but not for final ones because it tends to bring down salts more readily than ethanol. Isopropanol can also be used when the volume of the tube will not allow the addition of 2 volumes of ethanol. The nucleic acid is collected by centrifugation at 10,000 rpm for ca. 20 - 30 minutes. The most common monovalent cations used in nucleic acid precipitations are shown in the following table:

Sodium acetate

Stock Solution 2.5 M (pH 5.2 - 5.5)

Sodium chloride

5.0 M

Ammonium acetate*

4.0 M

Final Concentration 0.25 M to 0.3 M 0.10 M (optimal < 0. 15 M = 1/50 vol.) 1.3 M

* Filter sterilize, do not autoclave The choice of salt is determined by the nature of the sample and the intended use of the nucleic acid. Samples with phosphate or greater than 10 mM EDTA should not be ethanol precipitated because the salts will come down with the nucleic acid. Butanol Extractions DNA is recovered from dilute solutions by extracting with 2-butanol. The water from the sample moves into the butanol which is discarded, thus leaving a higher DNA concentration in the aqueous phase. Water saturated butanol is also used to remove residual ethidium bromide from samples obtained via CsCl centrifugation or agarose gel purification. Reagents: • 2X CTAB buffer: 100 mM Tris-HCI, 1.4 M NaCl, 30 mM EDTA, and 2 % (w/v) CTAB. The buffer is usually ca. pH 8.0 without adjustment. • protease K (Sigma Type H, ca. 0. 13 units/mg, P-4755). I store the enzyme in 50 units/1 ml aliquots in the freezer. • Dithiothreitol (DTT) 0.5 M. Stored as 0.5 ml aliquots - added to buffer just before use. • 1X TE buffer • Ammonium acetate, 4.0 M. • Organics: chloroform:isoamyl alcohol (24: 1), Tris buffered phenol, cold isopropanol, cold 100% ethanol, and 70% ethanol. Modified from Dr. Sarah Wyatt’s handout

4 The best DNA extracts come from young plant material. Attempt to conduct the extraction soon after collection if refrigeration is not possible. Day 2 Exercise 4. Gel Electrophoresis The standard method for separating DNA fragments is electrophoresis through agarose gels. DNA is applied to a slab of gelled agarose and then an electric current is applied across the gel. Because DNA is negatively charged (phosphate groups in the backbone), it migrates through the gel towards the positive electrode. The rate of migration depends on: 1) the size of the fragment; the smaller the DNA, the faster it "runs" through the gel; 2) the concentration of agarose; the higher the concentration, the more the agarose retards the movement of the DNA fragments; and 3) the voltage applied to the gel; the higher the voltage the quicker the DNA "runs" (but at a trade-off--the DNA fragments do not separate as efficiently).

a. Pouring the gel A demonstration on preparing and running an agarose gel will be given. Each group should have a gel apparatus and cover, two end walls, two combs and a plastic gel tray. The gel tray should be placed in the chamber and the two end walls inserted. A comb should be placed near one of the end walls. Make 100 ml of a 1.0% agarose in 1X TBE for your gel in a 250 ml flask. Minigels require ~30 ml agarose. Use the microwave to melt the agarose. Be sure the solution is completely melted and homogenous. Warning!! Never leave the agarose solution unattended when using the microwave. The solution must be frequently swirled during the heating process to prevent superheating of local areas. Always use "hot hands" or autoclave gloves when heating the agarose.

You will be provided Ethidium Bromide (EtBr) at a concentration of 1 mg/ml in a 1.5 microfuge tube. This tube should be saved and stored at 4ºC. Warning!! Ethidium bromide is a mutagen. Remember to wear gloves when working with EtBr and to dispose of contaminated tips in specially marked containers. Gels should be placed in a plastic bag for disposal. Microwaving EtBr produces harmful volatiles. Modified from Dr. Sarah Wyatt’s handout

5 Add EtBr to a final concentration of 0.1 to 0.5 µg/ml to agarose immediately before you pour the gel. To do this, label a 50 ml conical tube EtBr/agarose. Add the EtBr to the tube and then pour about 30 mls of the agarose into the tube. Cap and invert a few times. The agarose solution should be cooled to about 50ºC (a temperature at which one can hold the flask, but it is uncomfortable) before pouring the gel. Pouring the gel when the agarose is too hot may damage the gel apparatus. Pour the 1.0% agarose minigel with 0.1 µg/ml EtBr and allow it to solidify. Practice loading a few lanes with loading dye if you've never loaded a gel before. This can be run into the gel without affecting the migration of DNA added to the well at a later time. At first it will be easier to load the wells dry. Add 1X TBE buffer to submerge the gel prior to electrophoresis. Later, you should become adept at loading wells submerged in buffer.

b. Loading the Samples and Running the Gel: To a new eppendorf or on parafilm, add 5 µl loading dye to 15 µl of your sample and finger flick. Load 20 µl total volume of your samples per well for minigels with 8-well combs. Load 10 µl of the molecular weight markers provided. Your gel should contain: 1. molecular weight marker 2. gDNA group 1 3. Positive control - PCR product-1 4. Empty lane 5. Empty lane 6. molecular weight marker 7. gDNA group 2 8. Positive control - PCR product-2 Run the gel at 100 V until the bromophenol blue is about 3/4 through the gel (approx. 1 h). Using gloves, carefully remove the tray with the agarose gel. Take it to the UV transilluminator and slide the gel off the tray onto the lamp. Wearing UV-protective goggles (NOT YOUR SAFETY GLASSES), examine the gel. The cover of the transilluminator may also be used to protect your eyes. Photograph your gel with a ruler (optional) for your notebook. You will use this gel for Southern blotting procedure.

Modified from Dr. Sarah Wyatt’s handout