Getting Started
You have bacterial cultures and you want to extract something inside of them (e.g., overexpressed protein, plasmid DNA, tRNAs, total lysate, etc.). You’re going to need to lyse this culture. You can use an sonicator to do so, disrupting bacterial walls and membranes using ultrasonic frequencies pumped into the bacterial culture. This protocol shows you how to use a sonicator to mechanically lyse cells.
Materials and Equipment
Name | Product | Manufacturer | Part # | Price | Storage Conditions | Link |
Sonicator | ||||||
Sonicator | Q700 Sonicator | QSonica | Q700A-110 | $5500 | 4C to 30C | [link] |
Sonicator Probe | Standard Probe, Replaceable Tip, 1/2” (12.7mm) diameter | QSonica | 4220 | $670 | 4C to 30C | [link] |
Sound Enclosure | Sound Enclosure | QSonica | 432B2 | $995 | 4C to 30C | [link] |
Lab Jack | Fisherbrand™ Lab Jacks (15cmx15cm) | Fisher Scientific | 14-673-51 | $484 | 4C to 30C | [link] |
Consumables | ||||||
15 mL centrifuge tubes | Corning® 15 mL PP Centrifuge Tubes, Rack Packed with CentriStar™ Cap, Sterile, 50/Rack, 500/Case | Corning | 430790 | $230.44 | 4C to 30C | [link] |
10 mL Luer Lock Syringes | Syringes with BD Luer-Lok® Tip, BD Medical, Syringe with Luer-Lok® Tip, Volume=10 mL | BD Industrial/Difco | 550-80620-PK | $102.40 | 4C to 30C | [link] |
0.45 um syringe filters | PES Syringe Filter, 0.45μm, 30mm, Sterile | CELLTREAT Scientific Products | 229749 | $84 | 4C to 30C | [link] |
Salts (for Buffers) | ||||||
Potassium Hydroxide | Potassium hydroxide - ACS reagent, ≥85%, pellets | Sigma-Aldrich | 221473-1KG | $99.90 | 4C to 30C | [link] |
HEPES | HEPES, Crystalline Powder, ≥99.5% (titration), Poly bottle | Sigma-Aldrich | H3375-500G | $431 | 4C to 30C | [link] |
Ammonium Chloride | Ammonium chloride,ACS reagent, ≥99.5% | Sigma-Aldrich | 213330-500G | $73.50 | 4C to 30C | [link] |
Sodium Chloride | Sodium Chloride, Redi-Dri™, anhydrous, free-flowing, ACS, ≥99% | Sigma-Aldrich | 746398-1KG | $133.00 | 4C to 30C | [link] |
Magnesium Chloride hexahydrate | BioXtra Magnesium chloride, Hexahydrate, Powder or Crystals, ≥99.0% | Sigma-Aldrich | M2670-100G | $50.50 | 4C to 30C | [link] |
Supplements (for Buffers) | ||||||
Lysozyme | Lysozyme from chicken egg white, protein ≥90%, ≥40,000 units/mg protein, lyophilized powder | Sigma-Aldrich | L6876-1G | $76.90 | -25C to -15C | [link] |
TCEP-HCl (0.5M; presuspended) | Thermo Scientific, Bond-Breaker® Tris[2-Carboxyethyl]phosphine Neutral Solution (TCEP), Application=Water-Soluble Reducing Agent, Molecular Weight=286.65, Size=5 mL | Thermo Scientific | 77720 | $175.65 | 4C to 30C | [link] |
cOmplete Protease Inhibitor | cOmplete™ Protease Inhibitor Cocktail, EDTA-Free, Tablets | Roche | 11873580001 | $472 | 1C to 4C | [link] |
Prerequisite Protocols
Prepare lysis buffer: Make Protein Purification Buffers and Media.
Prepare pellets of bacteria expression proteins: Grow and Induce Expression Strains.
Protocol
Prepare Stock Solutions.
Reagent | MW [g/mol] | Amount [g] | Final Volume [mL] | Storage | Needs pH adjustment? | Needs Sterilization? |
Stock Solutions | ||||||
Potassium Hydroxide (1M) | 56.11 | 14.0 | 250 | 4C to 30C | no | no |
HEPES-KOH (pH=7.6; 1M) | 238.3 | 59.5 | 250 | 4C to 30C; dark | yes | no |
Ammonium Chloride (1M) | 53.49 | 13.4 | 250 | 4C to 30C | no | no |
Sodium Chloride (5M) | 58.44 | 73.1 | 250 | 4C to 30C | no | no |
Magnesium Chloride (1M) | 203.3 | 20.3 | 100 | 4C to 30C | no | no |
Lysozyme (30 mg/mL) | 14320 | 1 | 33 | -25C to -15C | no | no |
Prepare Lysis Buffer - used to resuspend bacterial pellets for mechanical lysis by sonication. Also chemically lyses cells with lysozyme (G. gallus). Contains protease inhibitor (cOmplete) to slow proteolysis. Make fresh and use the same day!
Reagent | Final Concentration [mM] | Stock Concentration [mM] | Volume to Add [mL] |
HEPES-KOH | 50 | 1000 | 5 |
Ammonium Chloride | 100 | 1000 | 10 |
Sodium Chloride | 500 | 5000 | 10 |
Magnesium Chloride | 10 | 1000 | 1 |
Lysozyme | 0.3 mg/mL | 30 mg/mL | 1 |
TCEP | 1 | 500 | 0.2 |
cOmplete Protease Inhibitor | 1 tablet / 50 mL | n/a | 2 tablets |
water (milliQ) | 72.8 | ||
Total | 100 |
Prepare centrifuge and lysis buffer.
Prechill centrifuge and lysis buffer to 4C.
Finish lysis buffer with TCEP (500x, or 1 mL TCEP per 2 L buffer).
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Resuspend pellets in cold lysis buffer.
Thaw bacterial pellets on ice.
Add 10 mL lysis buffer to each pellet. Resuspend pellets completely by vortexing.
Transfer resuspended pellets to 15 mL centrifuge tubes.
Lyse cells by sonication.
Set sonicator to appropriate setting. We lysed cells to a final energy of 12 000J / 40 mL total lysate (50% amplitude, 20s on / 20s s off).
Put resuspended pellets in an ice bucket. Place samples on a lab jack beneath the sonicator tip(s).
Adjust sample height using the lab jack such that the sonicator tip(s) are submerged about one quarter (1/4) of the way into the sample (e.g., 2.5 mL into a 10 mL sample).
Lyse cells by sonication.
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Clarify lysates by centrifugation and filtration.
Centrifuge lysates at 4 krcf / 4C / 45 min.
(Meanwhile) for each lysate, assemble 10 mL Luer lock syringes and filters (we used 0.45 um for lysates). Pull the plunger out of the syringe, screw on the filter, and leave the plunger outside of the syringe.
For each lysate, decant the supernatant into syringe and put in the plunger. Plunge lysate through filter into a collection tube (we used 15 mL centrifuge tubes).
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Resources and References
- Papers
- Original PURE paper
- OnePot PURE
Credits
Yan Zhang, Zoila Jurado, and Miki Yun (Richard Murray Lab, Caltech)
- Developers