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Cold Spring Harbor Laboratory Press - Molecular Cloning - Table of Contents Table of Contents Chapter 1: Plasmids and Their Usefulness in Molecular Cloning Chapter 2: Bacteriophage and Its Vectors Chapter 3: Working with Bacteriophage M13 Vectors Chapter 4: Working with High-Capacity Vectors Chapter 5: Gel Electrophoresis of DNA and Pulsed-Field Agarose Chapter 6: Preparation and Analysis of Eukaryotic Genomic DNA Chapter 7: Extraction, Purification, and Analysis of mRNA from Eukaryotic Cells Chapter 8: In Vitro Amplification of DNA by the Polymerase Chain Reaction Chapter 9: Preparation of Radiolabeled DNA and RNA Probes Chapter 10: Working with Synthetic Oligonucleotide Probes Chapter 11: Preparation of cDNA Libraries and Gene Identification Chapter 12: DNA Sequencing Chapter 13: Mutagenesis Chapter 14: Screening Expression Libraries Chapter 15: Expression of Cloned Genes in Escherichia coli Chapter 16: Introducing Cloned Genes into Cultured Mammalian Cells Chapter 17: Analysis of Gene Expression in Cultured Mammalian Cells Chapter 18: Protein Interaction Technologies Protocols | Bioinformatics | Cautions | Trademarks | Forums Contact Us | Help | Logout | Members Home | My Account Buy The Book | Our Vision | Take The Tour | Newsletter | Search Copyright © 2001 by Cold Spring Harbor Laboratory Press. All rights reserved. No part of these pages, either text or image may be used for any purpose other than personal use. Therefore, reproduction modification, storage in a retrieval system or retransmission, in any form or by any means, electronic, mechanical, or otherwise, for reasons other than personal use, is strictly prohibited without prior written permission. http://www.molecularcloning.com/members/toc.jsp [2002-2-18 16:10:23] Cold Spring Harbor Laboratory Press - Molecular Cloning - Chapter 1 Chapter 1 Plasmids and Their Usefulness in Molecular Cloning Protocol 1: Preparation of Plasmid DNA by Alkaline Lysis with SDS: Minipreparation Plasmid DNA is isolated from small-scale (1-2 ml) bacterial cultures by treatment with alkali and SDS. Protocol 2: Preparation of Plasmid DNA by Alkaline Lysis with SDS: Midipreparation Plasmid DNA is isolated from intermediate-scale (20-50 ml) bacterial cultures by treatment with alkali and SDS. Protocol 3: Preparation of Plasmid DNA by Alkaline Lysis with SDS: Maxipreparation Plasmid DNA is isolated from large-scale (500 ml) bacterial cultures by treatment with alkali and SDS. Protocol 4: Preparation of Plasmid DNA by Small-scale Boiling Lysis Plasmid DNA is isolated from small-scale (1-2 ml) bacterial cultures by treatment with Triton X- 100 and lysozyme, followed by heating. This method is not recommended for preparing plasmid DNA from strains of E. coli that express endonuclease A (endA+ strains). Protocol 5: Preparation of Plasmid DNA by Large-scale Boiling Lysis Plasmid DNA is isolated from large-scale (500 ml) bacterial cultures by treatment with Triton X- 100 and lysozyme, followed by heating. This method is not recommended for preparing plasmid DNA from strains of E. coli that express endonuclease A (endA+ strains). Protocol 6: Preparation of Plasmid DNA: Toothpick Minipreparation Plasmid DNA is prepared directly from bacterial colonies plucked from the surface of agar media with toothpicks. Protocol 7: Preparation of Plasmid DNA by Lysis with SDS Large (>15 kb), closed circular plasmids are prepared (albeit inefficiently and in small yield) by lysing bacteria with SDS. Protocol 8: Purification of Plasmid DNA by Precipitation with Polyethylene Glycol Crude preparations of plasmid DNA are first treated with lithium chloride and RNase (to remove RNA). The plasmid DNA is then precipitated in a solution containing polyethylene glycol and MgCl2. Protocol 9: Purification of Plasmid DNA by Chromatography The following table summarizes the salient features of many of the commercial resins that are currently available for plasmid purification. Individual manufacturers supply detailed instructions, which should be followed to the letter. Protocol 10: Purification of Closed Circular DNA by Equilibrium Centrifugation in CsCl- Ethidium Bromide Gradients: Continuous Gradients Solutions containing plasmid DNA are adjusted to a density of 1.55 g/ml with solid CsCl. The intercalating dye, ethidium bromide, which binds differentially to closed circular and linear DNAs, is then added to a concentration of 200 µg/ml. During centrifugation to equilibrium, the closed circular DNA and linear DNAs form bands at different densities. Protocol 11: Purification of Closed Circular DNA by Equilibrium Centrifugation in CsCl- Ethidium Bromide Gradients: Discontinuous Gradients A solution containing plasmid DNA, saturating amounts of ethidium bromide, and CsCl (44% w/v) is layered between two solutions of lesser (35% w/v CsCl) and greater density (59% w/v CsCl). During centrifugation to equilibrium, the closed circular plasmid DNA and linear DNAs form bands at different densities. Protocol 12: Removal of Ethidium Bromide from DNA by Extraction with Organic Solvents Ethidium bromide is removed from DNA by phase extraction with organic solvents. Protocol 13: Removal of Ethidium Bromide from DNA by Ion-exchange Chromatography Ethidium bromide is removed from DNA by chromatography through a cation-exchange resin. Protocol 14: Removal of Small Fragments of Nucleic Acid from Preparations of Plasmid DNA by Centrifugation through NaCl Contamination of plasmid DNA by fragments of DNA and RNA is reduced to an acceptable level by centrifugation through 1 M sodium chloride. This method was devised by Brian Seed when he was a graduate student at Harvard University. Protocol 15: Removal of Small Fragments of Nucleic Acid from Preparations of Plasmid DNA by Chromatography through Sephacryl S-1000 Contamination of plasmid DNA by small fragments of nucleic acid is reduced dramatically by size-exclusion chromatography through Sephacryl S-1000. Protocol 16: Removal of Small Fragments of Nucleic Acid from Preparations of Plasmid DNA by Precipitation with Lithium Chloride High-molecular-weight RNA and proteins can be precipitated from preparations of plasmid DNA by high concentrations of LiCl and removed by low-speed centrifugation. Protocol 17: Directional Cloning into Plasmid Vectors Directional cloning requires that the plasmid vector be cleaved with two restriction enzymes that generate incompatible termini and that the fragment of DNA to be cloned carries termini that are compatible with those of the doubly cleaved vector. Protocol 18: Attaching Adaptors to Protruding Termini Adaptors are short double-stranded synthetic oligonucleotides that carry an internal restriction endonuclease recognition site and single-stranded tails at one or both ends. Adaptors are used to exchange restriction sites at the termini of linear DNA molecules. They may be purchased in phosphorylated and unphosphorylated forms. Protocol 19: Blunt-ended Cloning into Plasmid Vectors http://www.molecularcloning.com/members/chapter.jsp?chapter=112 (1 / 3) [2002-2-18 16:10:49] Cold Spring Harbor Laboratory Press - Molecular Cloning - Chapter 1 Target DNA is ligated to a blunt-ended plasmid DNA, and the products of the ligation reaction are used to transform competent E. coli. The maximum number of "correct" clones can generally be obtained from ligation reactions containing equimolar amounts of plasmid and target DNAs, with the total DNA concentration being <100 µg/ml. Blunt-end ligation catalyzed by bacteriophage T4 DNA ligase is suppressed by high concentrations (5 mM) of ATP and polyamines such as spermidine. Protocol 20: Dephosphorylation of Plasmid DNA During ligation in vitro, T4 DNA ligase will catalyze the formation of a phosphodiester bond between adjacent nucleotides only if one nucleotide carries a 5´-phosphate residue and the other carries a 3´-hydroxyl terminus. Recircularization of vector DNA can therefore be minimized by removing the 5´-phosphate residues from both termini of the linear, double- stranded plasmid DNA with alkaline phosphatase. Protocol 21: Addition of Synthetic Linkers to Blunt-ended DNA Linkers are small self-complementary pieces of synthetic DNA, usually 8-16 nucleotides in length, that anneal to form blunt-ended, double-stranded molecules containing a restriction site. Linkers are used to equip blunt-ended termini of DNA with restriction sites as an aid to cloning. Protocol 22: Ligating Plasmid and Target DNAs in Low-melting-temperature Agarose Ligation in low-melting-temperature agarose is much less efficient than ligation with purified DNA in free solution and requires a large amount of DNA ligase. The method is used chiefly for rapid subcloning of segments of DNA in dephosphorylated vectors and assembling recombinant constructs. Protocol 23: The Hanahan Method for Preparation and Transformation of Competent E. coli: High-efficiency Transformation This procedure generates competent cultures of E. coli that can be transformed at high frequencies (5 x 108 transformed colonies/mg of superhelical plasmid DNA). IMPORTANT All steps in this protocol should be carried out aseptically. Protocol 24: The Inoue Method for Preparation and Transformation of Competent E. Coli: "Ultra-Competent" Cells This protocol reproducibly generates competent cultures of E. coli that yield 1 x 108 to 3 x 108 transformed colonies/mg of plasmid DNA. The protocol works optimally when the bacterial culture is grown at 18°C. If a suitable incubator is not available, a standard bacterial shaker can be set up in a 4°C cold room and regulated to 18°C. Protocol 25: Preparation and Transformation of Competent E. coli Using Calcium Chloride This protocol, developed approx. 30 years ago, is used to prepare batches of competent bacteria that yield 5 x 106 to 2 x 107 transformed colonies/µg of supercoiled plasmid DNA. Protocol 26: Transformation of E. coli by Electroporation Electrocompetent bacteria are prepared by growing cultures to mid-log phase, washing the bacteria extensively at low temperature, and then resuspending them in a solution of low ionic strength containing glycerol. DNA is introduced during exposure of the bacteria to a short high- voltage electrical discharge. Protocol 27: Screening Bacterial Colonies Using X-gal and IPTG: -Complementation -complementation occurs when two inactive fragments of E. coli -galactosidase associate to form a functional enzyme. Many plasmid vectors carry a short segment of DNA containing the coding information for the first 146 amino acids of -galactosidase. Vectors of this type are used in host cells that express the carboxy-terminal portion of the enzyme. Although neither the host nor the plasmid-encoded fragments of -galactosidase are themselves active, they can associate to form an enzymatically active protein. Lac+ bacteria that result from - complementation are easily recognized because they form blue colonies in the presence of the chromogenic substrate X-gal. However, insertion of a fragment of foreign DNA into the polycloning site of the plasmid almost invariably results in production of an amino-terminal fragment that is no longer capable of -complementation. Bacteria carrying recombinant plasmids therefore form white colonies. The development of this simple blue-white color test has greatly simplified the identification of recombinants constructed in plasmid vectors. Protocol 28: Screening Bacterial Colonies by Hybridization: Small Numbers This procedure, a variant of the Grunstein and Hogness (1979) method, is used to screen a small number of bacterial colonies (<200) that are dispersed over several agar plates and are to be screened by hybridization to the same radiolabeled probe. The colonies are gridded onto a master plate and onto a nitrocellulose or nylon filter laid on the surface of a second agar plate. After a period of growth, the colonies on the filter are lysed and processed for hybridization. The master plate is stored until the results of the screening procedure become available. Protocol 29: Screening Bacterial Colonies by Hybridization: Intermediate Numbers Bacterial colonies growing on agar plates are transferred en masse to nitrocellulose filters. The spatial arrangement of colonies on the plates is preserved on the filters. After transfer, the filters are processed for hybridization to an appropriate radiolabeled probe while the original (master) plate is incubated for a few hours to allow the bacterial colonies to regrow in their original positions. This technique, a variant of the Grunstein and Hogness (1975) method, was developed at Cold Spring Harbor Laboratory in 1975. The procedure works best with 90-mm plates containing <2500 colonies. Protocol 30: Screening Bacterial Colonies by Hybridization: Large Numbers This procedure is used to plate, replicate, and subsequently screen large numbers of bacterial colonies (up to 2 x 104 colonies per 150-mm plate or 104 colonies per 90-mm plate). Protocol 31: Lysing Colonies and Binding of DNA to Filters In this protocol, based on the procedure of Grunstein and Hogness (1975), alkali is used to liberate DNA from bacterial colonies on nitrocellulose or nylon filters. The DNA is then fixed to the filter by UV-cross-linking or baking under vacuum. Protocol 32: Hybridization of Bacterial DNA on Filters This protocol describes procedures to hybridize DNA from transformed colonies immobilized on filters with radiolabeled probes and to recover from a master plate the corresponding colonies that hybridize specifically to the probe. The method is based on the procedure published by Grunstein and Hogness (1975). http://www.molecularcloning.com/members/chapter.jsp?chapter=112 (2 / 3) [2002-2-18 16:10:49] Chapter:1 Protocol:1 Preparation of Plasmid DNA by Alkaline Lysis with SDS: Minipreparation CHAPTER 1 > PROTOCOL 1 printer friendly version Protocol 1 Preparation of Plasmid DNA by Alkaline Lysis with SDS: Minipreparation Plasmid DNA is isolated from small-scale (1-2 ml) bacterial cultures by treatment with alkali and SDS. MATERIALS CAUTION: Please click for information about appropriate handling of materials. RECIPE: Please click for components of stock solutions, buffers, and reagents. Buffers and Solutions Alkaline lysis solution I Alkaline lysis solution II Alkaline lysis solution III Antibiotic for plasmid selection Ethanol Phenol:chloroform (1:1, v/v) STE TE (pH 8.0) containing 20 µg/ml RNase A Media Rich medium METHOD 1. Inoculate 2 ml of rich medium (LB, YT, or Terrific Broth) containing the appropriate antibiotic with a single colony of transformed bacteria. Incubate the culture overnight at 37°C with vigorous shaking. 2. Pour 1.5 ml of the culture into a microfuge tube. Centrifuge at maximum speed for 30 seconds at 4°C in a microfuge. Store the unused portion of the original culture at 4°C. 3. Remove the medium by aspiration, leaving the bacterial pellet as dry as possible. 4. Resuspend the bacterial pellet in 100 µl of ice-cold Alkaline lysis solution I by vigorous vortexing. 5. Add 200 µl of freshly prepared Alkaline lysis solution II to each bacterial suspension. Close the tube tightly, and mix the contents by inverting the tube rapidly five times. Do not vortex! Store the tube on ice. 6. Add 150 µl of ice-cold Alkaline lysis solution III. Close the tube and disperse Alkaline lysis solution III through the viscous bacterial lysate by inverting the tube several times. Store the tube on ice for 3-5 minutes. 7. Centrifuge the bacterial lysate at maximum speed for 5 minutes at 4°C in a microfuge. Transfer the supernatant to a fresh tube. 8. (Optional) Add an equal volume of phenol:chloroform. Mix the organic and aqueous phases by vortexing and then centrifuge the emulsion at maximum speed for 2 minutes at 4°C in a microfuge. Transfer the aqueous upper layer to a fresh tube. 9. Precipitate nucleic acids from the supernatant by adding 2 volumes of ethanol at room temperature. Mix the solution by vortexing and then allow the mixture to stand for 2 minutes at room temperature. 10. Collect the precipitated nucleic acids by centrifugation at maximum speed for 5 minutes at 4°C in a microfuge. 11. Remove the supernatant by gentle aspiration as described in Step 3 above. Stand the tube in an inverted position on a paper towel to allow all of the fluid to drain away. Use a Kimwipe or disposable pipette tip to remove any drops of fluid adhering to the walls of the tube. 12. Add 1 ml of 70% ethanol to the pellet and invert the closed tube several times. Recover the DNA by centrifugation at maximum speed for 2 minutes at 4°C in a microfuge. 13. Remove all of the supernatant by gentle aspiration as described in Step 3.Take care with this step, as the pellet sometimes does not adhere tightly to the tube. 14. Remove any beads of ethanol that form on the sides of the tube. Store the open tube at room temperature until the ethanol has evaporated and no fluid is visible in the tube (5-10 minutes). 15. Dissolve the nucleic acids in 50 µl of TE (pH 8.0) containing 20 µg/ml DNase-free RNase A (pancreatic RNase). Vortex the solution gently for a few seconds. Store the DNA solution at -20°C. REFERENCES 1. Birnboim H.C. and Doly J. 1979. A rapid alkaline procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7:1513-1523. 2. Ish-Horowicz D. and Burke J.F. 1981. Rapid and efficient cosmid cloning. Nucleic Acids Res. 9:2989-2998. printer friendly version Buy The Book | Our Vision | Take The Tour | Newsletter | Search CSHL Press Home | Contact | Members Home | CSHL Home Copyright © 2000. Cold Spring Harbor Laboratory Press. http://www.molecularcloning.com/members/protocol.jsp?pronumber=1&chpnumber=1 [2002-2-18 16:11:00] Chapter:1 Protocol:2 Preparation of Plasmid DNA by Alkaline Lysis with SDS: Midipreparation CHAPTER 1 > PROTOCOL 2 printer friendly version Protocol 2 Preparation of Plasmid DNA by Alkaline Lysis with SDS: Midipreparation Plasmid DNA is isolated from intermediate-scale (20-50 ml) bacterial cultures by treatment with alkali and SDS. MATERIALS CAUTION: Please click for information about appropriate handling of materials. RECIPE: Please click for components of stock solutions, buffers, and reagents. Buffers and Solutions Alkaline lysis solution I For preparations of plasmid DNA that are to be subjected to further purification by chromatography (please see Chapter 1, Protocol 9 ), sterile Alkaline lysis solution I may be supplemented just before use with the appropriate volume of 20 mg/ml DNase-free RNase A (pancreatic RNase) to give a final concentration of 100 µg/ml. Alkaline lysis solution II Alkaline lysis solution III Antibiotic for plasmid selection Ethanol Isopropanol Phenol:chloroform (1:1, v/v) STE TE (pH 8.0) containing 20 µg/ml RNase A Media Rich medium METHOD 1. Inoculate 10 ml of rich medium (LB, YT, or Terrific Broth) containing the appropriate antibiotic with a single colony of transformed bacteria. Incubate the culture overnight at 37°C with vigorous shaking. 2. Transfer the culture into a 15-ml tube and recover the bacteria by centrifugation at 2000g (4000 rpm in a Sorvall SS-34 rotor) for 10 minutes at 4°C. 3. Remove the medium by gentle aspiration, leaving the bacterial pellet as dry as possible. 4. Resuspend the bacterial pellet in 200 µl of ice-cold Alkaline lysis solution I by vigorous vortexing, and transfer the suspension to a microfuge tube. 5. Add 400 µl of freshly prepared Alkaline lysis solution II to each bacterial sus