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Single-stranded M13 DNA isolation using phenol

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Single-stranded M13 DNA isolation using phenol

This isolation procedure (23) is the method of choice for preparation of M13-based templates to be used in Sequenase[TM] catalyzed dye-terminator reactions. A pre-incubated early log phase JM101 culture is prepared by transferring a thawed glycerol stock into 50 ml of liquid media and incubating for 1 hour at 37degC with no shaking. M13 plaques are picked with a sterile toothpick and placed into 1.5 ml aliquots of the early log phase JM101 culture, which are incubated in a 37deg C shaker for 4-6 hours. After incubation, the bacterial cells are pelleted by centrifugation and the viral containing supernatant is transferred to a clean tube. The phage particle are precipitated with PEG, collected by centrifugation, and the pellet is resuspended in buffer. The phage protein coat is denatured and removed by one phenol and two ether extractions. After ethanol precipitation, the dried DNA pellet is resuspended in buffer, and the concentration and purity crudely are assessed by agarose gel electrophoresis against known standards.

Protocol

1. Prepare an early log phase culture of JM101, as above, and pick M13-based plaques with sterile toothpicks into 12 X 75 mm Falcon tubes containing 1.5 ml aliquots of the cells. Incubate for 4-6 hours at 37degC with shaking at 250 rpm.

2. Transfer the culture to 1.5 ml microcentrifuge tubes and centrifuge for 15 minutes at 12,000 rpm at 4degC.

3. Pipette the top 1 ml of supernatant to a fresh 1.5 ml microcentrifuge tube containing 0.2 ml 20% PEG/2.5 M NaCl to precipitate the phage particles. Mix by inverting several times and incubate for 15-30 minutes at room temperature.

4. Centrifuge for 15 minutes at 12,000 rpm at 4degC to collect the precipitated phage. Decant the supernatant and remove residual PEG supernatant by suctioning twice.

5. Resuspend the pellet in 100 ul of 10 mM Tris-HCl, pH 7.6 by vortexing, and add 50 ul of TE-saturated phenol.

6. Extract the DNA with phenol and twice with ether, as discussed above, and then ethanol precipitate.

7. Resuspend the dried DNA in 6 ul of 10:0.1 TE for use in single-stranded Sequenase[TM] catalyzed dye-terminator sequencing reactions.

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