Southern_Blot_Protocol

SOUTHERN BLOT PROTOCOL

Uniformed Services University Department of Microbiology and Immunology 4301 Jones Bridge Road Bethesda, MD 20814

Used by the Laboratory of William C. Gause, Ph.D.

BUFFERS
10X TBE: (1 Liter) TRIS Base 108.0 g Boric Acid 55.0 g 0.5 M EDTA 40.0 mL 20X SSPE: (4 Liters) NaCl 701.2 g NaH2PO4 H2O 110.4 g EDTA 29.6 g *NaOH 34.0 g

*Dissolve reagents in 3200mL dH2O; adjust pH to 7.4; bring volume to 4 L.

1X Denaturing Solution: (2 Liters) NaCl 175.32 g NaOH 40.0 g pH should be ~13.0.

1X Neutralizing Solution: (2Liters) NaCl 175.32 g TRIS HCl 315.02 g Adjust pH to 7.5. 1X Hybridization Solution: 100mL (without 32P-labeled probe) 20X SSPE 30mL (final = 6X) 10% SDS 10mL (final=1X) dH2O 60mL Need 10mL/blot; used at 49°C; should be kept frozen between assays.

1X Prehybridization Solution: 100mL (without salmon sperm DNA) 20X SSPE 30mL (final = 6X) 100X Denhardt’s Soln 10mL (final = 10X) 10% SDS 10mL (final = 1X) dH2O 50mL Need 10mL/blot; used at 42°C; should be kept frozen at –20°C between assays. 1X Probe Buffer: 100?L (make fresh each time) 1.0M TRIS, pH 7.6 50?L 2.0M MgCl2 5?L 0.5M Dithiothreitol (DTT)10?L dH2O 35?L 6X Wash Solution: 600mL 20X SSPE 180mL (final = 6X) 10%SDS 12mL (final = 0.2%) dH2O 408mL

1X Probe Mix: (27?L) Probe Buffer Oligonucleotide Probe (0.2 ?g/?L) T4 Phosphonucleotide Kinase(PNK) dH2O 32P-ATP High-Stringency Wash: 600mL 20X SSPE 30mL (final = 1X) 10%SDS 12mL (final = 0.2%) dH2O 558mL

2.7?L 2.0?L 1.0?L 11.3?L 10.0?L ?

Southern Blot Protocol – Gause Laboratory

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RUNNING THE GEL
1. Make 350 mL of a 1% agarose gel as follows: 3.5 g agarose in 300mL ddH2O, stir briefly, cover beaker with plastic wrap, and microwave on high for 5 min. If agarose has not dissolve completely, microwave an additional 1-2 min. 2. Transfer the beaker to a stirplate, remove plastic wrap, add 30mL 10X TBE (final = 1X TBE) and 20mL+ ddH2O (total volume of 300mL), and allow to cool while stirring. 3. Add 3 ?L ethidium bromide solution while stirring, when agarose is <65°C. 4. Pour 50°C agarose into gel tray that has been wrapped and sealed with tape on both ends, and set up with combs on a level surface. Allow to cool to room temperature for a minimum of ? hour, before attempting to remove combs. 5. Remove combs and tape from gel. Place gel in gel box and cover with 1X TBE (~2L). 6. Remove 9 ?L of cDNA from PCR tubes by carefully pepetting through the mineral oil layer, mix sample gently by pipetting up and down, wipe sides of pipet tip with a Kimwipe to remove excess oil, and dispense to a clean tube. (NOTE: Mineral oil does not need to be used with the 9600 PCR machine.) 7. Add 1?L loading buffer, mix by pipetting, and heat samples at 65°C for 6 minutes and 30 seconds. After heating, chill samples on ice (~2 min.), then microfuge briefly. 8. Load samples onto gel. Run samples at ~120 V. Run time varies. Usually, a 2-comb, 40-sample gel can be run in ~1-1? hours. 9. After running the gel, nick a corner to define orientation of the gel.

GEL TRANSFER
1. Transfer gel to a tray containing ~250 mL of denaturing solution. Gel needs to be covered by the solution. Shake gently for 25 minutes. 2. Decant denaturing solution and replace with fresh denaturing solution. Shake again for 25 minutes. 3. Decant denaturing solution; rinse gel with ddH2O, slosh gently, rinse again with ddH2O, decant, and add ~250 mL of neutralizing solution. Shake for 15 minutes. 4. Decant neutralizing solution; replace with fresh neutralizing solution; shake again for 15 minutes. 5. Decant neutralizing solution; rinse gel with ddH2O, slosh gently, rinse again with ddH2O, decant, and add ~250 mL of 20X SSPE; shake again for 30 min. 6. Soak the following while gel is shaking in SSPE: 1 transfer membrane in ddH2O 2 thin blotting papers in 10X SSPE 1 thick blotting paper in 5X SSPE 7. Remove and invert the gel on saran wrap so that the bottom of the gel is facing up. 8. Remove the bubbles between the gel and saran wrap. 9. Cover the gel with the transfer membrane that was soaked in ddH2O. Remove ALL of the bubbles between the gel and membrane. 10. Cover with the 2 thin blotting papers soaked in 10X SSPE. 11. Cover with thick blotting paper soaked in 5X SSPE. 12. Cover with a stack of dry blotting paper, tray, and bottles to provide weight. Let stand overnight.

Southern Blot Protocol – Gause Laboratory

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PREHYBRIDIZATION/HYBRIDIZATION
NOTE: The following protocol assumes that the individual performing the procedure has been appropriately trained in the proper handling of radioactive isotopes and will therefore observe the necessary precautions and regulations regarding personal/lab safety. 1. After Southern transfer is complete, place the blot in the UV Crosslinker and crosslink on the automatic setting. 2. Prepare prehybridization solution. a. Warm 10mL/blot of prehybridization solution to 42°C. b. Denature salmon sperm by heating sample to 95°C for 5 minutes, chilling sample quickly on ice, and microcentrifuging the sample. (Stock solution is 20mg/mL; 50?g/mL is needed; so add 25-30?L/10mL prehybridization solution.) c. Add denatured salmon sperm to warmed prehybridization solution. 3. Carefully roll blot and place in hybridization tube. Add prehybridization solution to the tube. 4. Place tube in 42°C hybridization oven for 5 hours. 5. Make probe buffer, and then probe mix. After adding the isotope to the probe “mix”, incubate the sample in a 37°C water bath for 40 minutes. 6. Separate the nonincorporated label with a G-25 Sephadex spin column. Determine the specific activity of the probe by liquid scintillation. Add 1 ?L of the probe to 5 mL of scintillation fluid. 7. Warm the hybridization solution to 49°C. Add 10-15 x 106 cpm of the probe to 10mL of the hybridization solution. Mix the solution. 8. Pour off the prehybridization solution from the blot and add the hybridization solution. 9. Incubate the container at 49°C overnight. 10. Remove the hybridization solution and discard properly. Preheat the 6X wash solution to 49°C. 11. Cover the blot with wash solution. Shake the blot covered with 6X wash solution for 15 minutes at 49°C. Remove the membrane and blot dry with absorbent paper. 12. Preheat the 2X wash solution to 49°C. Wash the blot as described above for only ~30 sec. 13. Check the blot with a radiation detection device. The background on blank areas of the membrane should be 200 cpm or less. If the background is too high, repeat wash with 2X wash solution. 14. Quantify the blot by the method of your choice.

Southern Blot Protocol – Gause Laboratory

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