Endy:Northern Blot, 32P End-Labeled Probes

Adapted from: Parker Lab Protocols, Sauer Lab, Heather Keller, Molecular Cloning, Current Protocols in Molecular Biology, Schleicher & Schuell Bioscience Turboblotter, Millipore Immobilon-Ny+ Transfer Membrane.

Contact: Caitlin Conboy

Samples to be probed

Experimental Samples

Total cellular RNA RNA Extraction ~10 µg of total cellular RNA, would contain 10 fg -1 pg of rare RNA, ~300 pg of moderately abundant RNA. (Molecular Cloning)

In Vitro Standard Curve Samples

RNA In Vitro Standards 1 fg - 100 pg range suggested. (Molecular Cloning) 3 - 50 ng for high copy/plasmid-based (cmc, 04-20-05)

Workflow outline

Probe Preparation

1. For DNA probes: Design and order synthetic oligos (https://catalog.invitrogen.com/)
2. End-Label Probe Prep, 32P End-Labeled Probes

Northern

1. Gel
2. Transfer
3. UV Cross-linking
4. Overnight Probe Hybridization
5. Stringency Washes
6. Incubation
7. Phosphoimaging
8. Strip/re-probe (optional)

**Radiation Use and Safety Reminders**

1. Always record amount of radiation used per experiment in Radiation Log Book.
2. Scan work area with Geiger counter before and after work.
3. Always wear Radiation Badge when handling radioactivity.
4. Use shields and radiation warning signs as necessary.
5. Record activity of waste on waste container log sheets.

Protocol

Process the Gel (3-4 hours)

For RNase free electrophoresis apparatus: Clean electrophoresis tanks and combs used for electrophoresis of RNA with detergent solution, rinse in H20, dry with ethanol, and then fill with a solution of 3% H2O2. After 10 minutes at room temperature, rinse the electrophoresis tanks and combs thoroughly with H2O2 treated with 0.1% DEPC

1. Set up the glyoxal denaturation reaction by combining 1-2 ul of RNA (up to 10 ug) with 10 ul of glyoxal reaction mixture. Run molecular weight markers for staining with sybrGold.
2. Incubate the RNA solutions for 60 minutes at 55°C. Chill the samples for 10 minutes in ice water and then centrifuge them for 5 seconds to deposit all of the fluid in the bottom of the microfuge tubes.
3. While the samples are incubating, clean electrophoresis tank if necessary, and pour a 1.5% agarose gel in 1X BPTE (1.05 g agarose in 70 mL buffer). When set, cover the gel with sufficient buffer.
4. Add 2.5 ul of 6X gel loading buffer to the glyoxylated RNA samples, and without delay, load the glyoxylated RNA samples into the wells of the gel.
5. Carry out electrophoresis at 70 Volts.
6. Trim away areas of the gel to be stained with sybrGold. (Membrane should be cut to match the size of the gel.) Wrap gel to be stained in saran wrap and store at 4°C until post-transfer gel is ready to be stained.
7. Soak gel 30 min in 0.05 M NaOH/1.5 M NaCl (~400 mL) without agitation.
8. Soak gel 20 min in 0.5 M Tris (pH 7.4)/ 1.5 M NaCl (~400 mL)

7 and 8 are optional steps for improving the transfer of long RNAs, esp from >1% gels.

Prepare the Membrane (5-15 minutes)

NOTE: Be gentle with the membrane. The number of times a membrane can be stripped and re-probed is usually limited by physical damage to the blot.

1. Cut a piece of membrane to the dimensions of the agarose gel. Max dimensions for hybridization in 50mL tubes: 8 x 9 cm (circumference x diameter). If membrane is larger, sandwich between sheets of nylon mesh to allow buffer to penetrate overlap.
2. Wet the membrane by carefully laying it on top of Milli-Q water in a shallow tray. (Do not immerse the Immobilon-Ny+ membrane in liquid on the first liquid exposure. If you wet both sides, air can become trapped in the pores and form bubbles.)
3. Agitate the tray gently once the membrane is wet to completely immerse the membrane.
4. Transfer the membrane to a second tray containing transfer buffer (20 x SSC).
5. Equilibrate the membrane at least 5 minutes.

Transfer of RNA onto Membrane by Turboblotter Capillary Transfer (3-4 hours)

NOTE: Refer to Fig. 1 when setting up the TurboBlotter System.

1. Place stack tray of transfer device on bench, making sure it is level.
2. Place 20 sheets of dry GB004 blotting paper (thick) in stack tray.
3. Place 4 sheets of dry GB002 blotting paper (thin) on top of stack.
4. Place one sheet of GB002 blotting paper, prewet in transfer buffer on stack.
5. Place transfer membrane on stack.Smooth bubbles by rolling a clean glass pipette over the surface. Do not touch with gloves.
6. Cover the membrane with agarose gel, cut the gel to the size of the membrane, making sure there are no air bubbles between the gel and the membrane.
7. Wet the top surface of the gel with transfer buffer and place 3 sheets of GB002 Blotting Paper, presoaked in transfer buffer on top of the gel.
8. Attach the buffer tray of the transfer device to the bottom tray using the circular alignment buttons to align both trays.
9. Fill the buffer tray with 125 ml transfer buffer for 7 x 8 cm to 11 x 14 cm transfers; (200 ml for 12 x 21 cm to 20 x 25 cm transfers).
10. Start the transfer by connecting the gel stack with the buffer tray using the precut buffer wick (included in each blotter stack), presoaked in transfer buffer. Place the wick cover on top of the stack to prevent evaporation. Make sure the edges of the wick are immersed in the transfer buffer.
11. Continue the transfer for 3 hr. Additional transfer time may be required for gels thicker than 4 mm or larger-size nucleic acids. (Try 4 hr, since gel is 1.5%, cmc 3.25.05)
12. Disassembly: mark edges of gel and lane borders onto blot with pencil.

NOTE: Do not place any other weight on top of the wick cover during transfer. This is unnecessary and may inhibit transfer by crushing the pore structure of the agarose gel.

RNA Fixation with UV Cross-Linking (5 minutes)

1. It is not necessary to allow the blot to dry completely prior to UV cross-linking.
2. Place the blot on a sheet of clean filter paper to prevent contamination if you plan to place the UV light source above the blotted RNA. (If you plan to place the membrane on a UV transilluminator, clean the surface with Milli-Q water and a Kimwipe.)
3. Expose the side of the blot with the bound RNA to a UV light source (254 nm). Using Pabo Lab UV lamp, above blot, ~5 min. This lamp has not been calibrated, but multiple users have had success with 2-5 minutes exposure.

Hybridization (2 hours + overnight + >1 hour)

1. If blot dimensions are less than 8 x 9 cm, place blot in a 50 mL conical tube, RNA facing in. Make sure the blot doesn't overlap itself. 50 mL conical tubes fit in the Sauer Lab "Bambino" mini-hybridization oven. If blot is too large for a 50 mL conical tube, use large glass tubes and Baker Lab hybridization oven.
2. Prewash Blot in 0.1x SSC/ 0.1% SDS for 1 hour at 65°C in hybridization oven. 10 - 15 mL of solution is required to cover the blot in a 50 mL tube, and sufficient for all steps. This incubation can be cut to 30 min if pressed (says Sean.)
3. Remove Prewash
4. Prehybridize blot for > 1 hour in 10 - 15 mL of pre-hybridization solution at hybridization temp. Hybridization temp ~15°C below estimated Tm of probe. If reusing probe in hybridization solution, thaw probe as balance. NOTE: It is possible to store blots in prehybridization solution sort-term to indefinitely at 4°C or -20°C (Sean)
5. Remove prehybridization buffer if reusing probe, otherwise retain same buffer.
6. Add hybridization buffer with old probe to blot or add new probe to pre-hybridization buffer. Hybridize >6 hrs at hybridization temp.
7. Pour off probe either into 32P liquid waste (remember to record waste) or into tube for storage at -20°C for later reuse. NOTE: if storing probe in 13 mL conical tube, remember not to fill tube completely.
8. Wash blot in 10 - 15 mL of 6x SSC/ 0.1% SDS for 5 min at room temp in the hybridization oven (Leave door open to change temp quickly. Put shield up.)
9. Repeat wash twice for a total of three room temp washes. Dispose of the first wash in the 32P liquid waste. For subsequent washes pour off buffer in the sink. (Record waste.)
10. During washes, pre-erase PhosphorImager screen 20 min on light table.
11. Repeat wash a forth time for 20 min at 10°C below estimated Tm in hybridization oven.
12. Pour off final wash. Remove damp blot from tube and lay on clean saran wrap. Fold saran wrap to seal blot.
13. Expose wrapped blot to PhosphorImager screen in casette.
14. Image screen after 1 hour.
15. Erase screen.
16. Expose screen overnight if original image is faint.
17. Erase screen before returning casette.

Northern Blot Solutions

Prewash Solution (0.1x SSC/ 0.1% SDS)

50 mL Total Volume

1. • 250 µL of 20x SSC
   • 500 µL of 10% SDS
   • 49.25 mL of nuclease-free H2O

100x Denhardt Solution

1. • 5 g of Ficoll 400
   • 5 g of polyvinylpyrrolidone (Not polyvinylpolypyrrolidone!)
   • 5 g of BSA Fraction V (stored at 4°C)
2. dissolve to 250 mL in nuclease-free H2O
3. Sterile filter and freeze in 5 mL aliquots

Pre-hybridization Buffer

50 mL Total Volume

1. • 5 mL of 100x Denhart's Solution
   • 15 mL of 20x SSC
   • 0.5 mL of 10% SDS
   • 29.5 mL of Nuclease-free H2O

Stringency Wash (6x SSC/ 0.1% SDS)

200 mL Total Volume

1. • 2 mL of 10% SDS
   • 60 mL of 20X SSC
   • 138 mL of nuclease-free H2O