EP0403503A1 - Nucleic acid isolation - Google Patents
Nucleic acid isolationInfo
- Publication number
- EP0403503A1 EP0403503A1 EP89902588A EP89902588A EP0403503A1 EP 0403503 A1 EP0403503 A1 EP 0403503A1 EP 89902588 A EP89902588 A EP 89902588A EP 89902588 A EP89902588 A EP 89902588A EP 0403503 A1 EP0403503 A1 EP 0403503A1
- Authority
- EP
- European Patent Office
- Prior art keywords
- biological sample
- protein
- salt
- dna
- precipitate
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Withdrawn
Links
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
Definitions
- the present invention relates to a method for isolating, i.e., separating, nucleic acids from a biological composition. More particularly, this invention relates to the separation of protein from a biological sample containing nucleic acids using salt. The protein is removed prior to the isolation of the nucleic acids.
- RNA from cellular debris is an important and routine procedure in the area of biotechnology. Thus, numerous researchers have attempted to simplify this isolation procedure. If the nucleic acids are purified from complex mixtures of molecules such as cell lysates, generally a proteolytic enzyme such as pronase, proteinase K, chymotrypsin, trypsin, subtilisin, . carboxypeptidase and the like or an ionic detergent such as sodium dodecyl sulfate (SDS) , sarkosyl and the like is used to dissociate or denature most of the protein which is present.
- the proteolytic enzymes used are generally selected to be active against a broad spectrum of proteins in order to effectively degrade as much as possible.
- the protein must be separated or removed from the cell lysate prior to the isolation of the nucleic acids otherwise the protein copurifies along with the nucleic acids. In addition, the protein may interfere with restriction enzymes and with the separation. A poor spectrophotometer reading may also be obtained.
- the dissociation of protein from the nucleic acid as well as the subsequent removal of protein is an important step in the isolation of nucleic acids. After degrading the protein, the nucleic acid is typically extracted using an organic solvent.
- the most common technique used to remove the inactivated or digested protein from a biological composition containing nucleic acids is to use a combination of phenol and chloroform. It is generally believed that two different organic solvents are more efficient than one.
- the nucleic acid solution is extracted once with phenol, once with a 1:1 mixture of phenol and chloroform, and once with chloroform.
- a final extraction with chloroform or similar compound removes any lingering traces of phenol from the nucleic acid preparation. This phenol/chloroform extraction procedure is described in Molecular Cloning by
- Ether is used to remove any residual traces of phenol or chloroform from the DNA solution.
- Ether of course, is highly volatile and extremely flammable and should be worked with and stored in an explosion- proof chemical hood.
- the aqueous layer containing the nucleic acids in solution is transferred to another tube and the nucleic acids are isolated by precipitating the nucleic acids with about 2 volumes of absolute ethanol. This procedure results in about a 67% ethanol final solution. The precipitated nucleic acids are then recovered by centrifuging or filtering.
- Phenol may be absorbed through the skin in sufficient amounts to result in death due to its effects upon the central nervous system as well as damage to the kidneys, liver, pancreas, spleen and lungs.
- Chronic exposure to low concentrations of phenol vapor may result in digestive disturbances, nervous disorders and dermatitis.
- Chronic poisoning may be terminal where there has been extensive damage to the kidney or liver. Dermatitis resulting from contact with phenol or phenol-containing products is fairly common in industry.
- Chloroform is a suspected carcinogen and has the ability to cause neoplastic growths. Exposure to chloroform vapors can result in conjunctivitis and dilation of the pupils. Prolonged inhalation will cause paralysis accompanied by cardiac respiratory failure and finally death. Exposure to chloroform may also cause profound toxemia and damage to the liver, heart and kidneys.
- Gautreau, C. et al "Comparison of Two Methods of High-Molecular-Weight DNA Isolation from Human Leucocytes," Analytical Biochemistry. Vol. 134, pp. 320-324 (1983) describes two methods of DNA extraction using phenol and chloroform for deproteinization after protein digestion with proteinase K and sodium dodecyl sulfate.
- One method involves removal of phenol by extensive dialysis with 0.01 M sodium tetraborate and 0.01 M EDTA at pH 9.1.
- Cell lysis and digestion with SDS and protease K are carried out on the filter.
- the solution is allowed to flow through the filter by gravity.
- the DNA is then removed from the filters by treatment with DNase and 0.5 ml water.
- the DNA can also be removed from the filter by irradiation with 1000-1500 rad gamma rays followed by an aqueous wash.
- Smith, K.C. et al described the use of ammonium sulfate fractionation to separate amino-acid specific RNA. They begin with transfer RNA extracted from guinea pig liver using a phenol procedure to eliminate protein.
- Three methods of processing the supernatant fluid that have been used are: 1) addition of 2 to 2.5 volumes of ethanol to the supernatant to precipitate the nucleic acids and recovery of the precipitated nucleic acids by centrifugation; 2) removal of the NaCl and residual SDS by dialysis against a buffer; and 3) extraction of the supernatant fluid using phenol and/or chloroform to remove residual protein and SDS prior to ethanol preciptation or dialysis.
- the prior art has long sought a more efficient, simple and less tedious method to remove protein from a biological sample prior to isolation or separation of nucleic acids.
- the time involved in the phenol-chloroform separation procedure, the expense related to waste disposal and the precautions required in handling these two chemicals does not make this procedure well-suited for large-scale mass extraction or for small laboratory use.
- An object of the present invention is to develop a fast and efficient method for isolating nucleic acids from a biological sample such as a cell digest or cell lysate.
- a further object of the present invention is to provide a method for isolating nucleic acids which does not require the use of hazardous chemicals and maintains a high level of occupational safety for the technician.
- An additional object of the present invention is to provide a method for precipitating protein present in a biological sample which uses economical and convenient materials.
- a method for isolating nucleic acids from a biological sample which involves dissociating protein present in a biological sample containing nucleic acids; adding a sufficient amount of organic or inorganic salt to precipitate the protein; mixing the biological sample containing the salt for a time sufficient to achieve a satisfactory dispersion of salt through the biological sample to obtain a protein precipitate; separating the precipitated protein from the biological sample; and finally separating the nucleic acid remaining in the biological sample.
- a biological sample for the purpose of the present invention is defined as any sample or composition which contains nucleic acids.
- samples may include a cell lysate, a cell digest, a sample containing cell leucocytes, a tissue sample, a urine sample, a blood stain or the like.
- Suitable samples may be obtained from the spleen, kidney, heart, muscle, spermatozoa, intestine, skin, blood and the like from a variety of living creatures whose cells contain nucleic acids including mammalian organisms such as humans.
- Suitable samples may also include microorganisms such as bacterial cells. Those skilled in the art would recognize suitable biological samples from which nucleic acids such as DNA and RNA may be extracted.
- nucleic acid isolations are preferably used when describing the present invention since numerous techniques in the area of biotechnology require the isolation of nucleic acids. Typical uses include restriction enzyme digestion, ligation, cloning and the like. The type of sample used for such nucleic, acid isolations may vary.
- the proteins including nucleoproteins present in the biological sample are dissociated.
- denaturing is used to describe this step.
- Such techniques are well-known in the art.
- the use of proteinase K and SDS is preferred as noted in Molecular Cloning, supra.
- the product obtained is oftentimes referred to as a cell digest.
- Any type of salt may be used in the practice of the present invention. Obviously, the salt must be selected so as not to interfere with the compounds used in any of the other steps during the isolation of the nucleic acids. Suitable salts include all organic salts and all inorganic salts. A representative listing of salts may be obtained by reference to any standard chemistry text. One such text is Lance's Handbook of Chemistry, thirteenth edition, editor John A. Dean, 1985, which is incorporated herein by reference in its entirety.
- a salt in its simplest terms can be thought of as an association between a cation and an anion.
- Suggested anions in the practice of the present invention include but are not limited to chloride, bromide, fluoride, iodide, borate, hypobromite, hypochlorite, nitrate, nitrite, hyponitrite, sulfate, disulfate, sulfite, sulfonate, phosphate, diphosphate, phosphite, phosphonate, diphosphonate, perchlorate, perchlorite, oxalate, alonate, succinate, lactate, carbonate, acetate, benzoate, citrate, tosylate, permanganate, manganate, propanolate, propanoate, ethandioate, butanoate, propoxide, chromate, dichromate, selenate, orthosilicate, metasilicate, pertechnetate, technet
- Suggested cations include but are not limited to sodium, potassium, calcium, magnesium, ethylamine, diethylamine, triethylamine, benzylamine, di ethylaniline, N-methylmorpholine, amyloride. ammonium, lithium, berylium, cesium, zinc, chromium, copper, aluminum, barium, strontium, iron, tin, nickel, barium, silver, platinum, palladium, titanium and the like.
- the preferred salt depends on a variety of factors, for instance, if ethanol is used in the final extraction, the salt should preferably be soluble in ethanol so that the residual salt does not precipitate out along with the nucleic acids in the final isolation.
- Sulfate salts are typically not soluble in ethanol. It would also be advantageous for the salt to be neutral so as not to significantly change the pH or denature the DNA. Further, if SDS is used to digest the protein, it would be preferable if the cation of the salt did not react with anionic SDS which may be present in the nucleic acid digest since it may result in the formation of a sludge which could float on top of the aqueous layer. Under certain conditions and in certain concentrations, heavy metal salts may damage nucleic acids by causing cleavage of phosphodiester bonds. Thus, care must be taken when selecting a heavy metal salt so as not to damage the DNA. and RNA present in the biological sample.
- any inorganic or organic salt is suitable to precipitate the protein in the biological sample of the present invention.
- Preferred inorganic salts include sodium chloride, potassium chloride, magnesium chloride and calcium chloride. Sodium chloride is more preferred.
- organic salts ammonium acetate, sodium acetate, potassium acetate and sodium benzoate are preferred. Ammonium acetate is the most preferred salt among both the inorganic and organic salts. -li ⁇ lt is believed that the salt dehydrates and thus precipitates cellular proteins which may be present in the biological sample.
- the salt have a high solubility in water to allow enough salt molecules to tie up water molecules so that the protein readily dehydrates and precipitates.
- the amount of salt necessary in the practice of the present invention is an amount sufficient to precipitate protein contained in the biological sample.
- a wide variety of types of biological samples are suitable in the practice of the present invention. And depending on the origin of the sample varying amounts of protein and nucleic acid may be present. Further, some of the biological samples may require a substantial amount of clean-up prior to isolation of the nucleic acids.
- the amount of salt may range from about 0.01 weight % to about 500 weight % based on the total weight of the biological sample. Preferably, the range is from about 0.1 weight % to about 50 weight %.
- the salt is preferably added in the form of a saturated solution, however, the salt may be added in solid form or as a dilute solution.
- a saturated solution is about a 35% (w/v) solution.
- the biological sample must be mixed in order to obtain a desirable dispersion of salt throughout the biological sample. In most cases, shaking the biological sample containing the salt for approximately fifteen seconds is sufficient.
- the time for mixing can range anywhere from approximately three seconds to approximately twenty minutes. The precise mixing time is not critical but rather the biological sample containing salt must be mixed for a sufficient time to achieve a satisfactory dispersion of salt throughout 5 the biological sample and thereby obtain a protein precipitate.
- the precipitated protein may be separated from the biological sample and the nucleic acid-rich supernatant recovered by any 0 technique known in the art.
- One such technique is centrifuging the biological sample and the protein precipitate. A single 15 minute spin is generally sufficient and the nucleic acid-rich supernatant may then be readily separated from the precipitated 5 protein.
- the biological sample containing the precipitated protein may simply be filtered to obtain the nucleic acid-rich liquid.
- the nucleic acids in the nucleic acid-rich supernatant may then be separated from the biological
- General methods for precipitating nucleic acid include the use of alcohols, for example, ethanol, isopropanol and the like, or alternatively, polymin-P, streptomycin sulfate, a metal such as copper and the
- the most widely used method for concentrating nucleic acids is precipitation with ethanol.
- the ethanol is preferably at ambient temperature, however,
- a wide range of temperatures is suitable in the practice of the present invention.
- the temperature must be sufficient to allow the precipitation of nucleic acid.
- any other substances also present in the sample not precipitate out along with the nucleic acid.
- the precipitate in this widely used method is recovered by centrifugation and redissolved in an appropriate buffer at the desired concentration. This technique is rapid and quantitative even with nanogram amounts of nucleic acid. If the concentration of monovalent cations present in the nucleic acid sample is too high it can be diluted with TE (pH 8.0). If the concentration of salts is too low, an appropriate salt solution may be added. Suggested salt solutions include sodium acetate, sodium chloride and ammonium acetate.
- RNA requires a slightly higher concentration of ethanol to be precipitated from solution than does DNA. RNA generally requires about 2.5 volumes of ethanol resulting in 71% ethanol final concentration. However, obviously a variety of techniques are known in the art to obtain DNA and/or RNA. A detailed description of methods for the concentration or precipitation of nucleic acids is set forth in Maniatis et al, supra. The entire reference by Maniatis et al is incorporated herein by reference in its entirety. The isolated DNA and/or RNA can then be used in any standard molecular biological application, including restriction enzyme digestion, ligation and cloning. Additionally, samples can be further processed using DNase and organic extraction to yield RNA suitable for northern blot analysis.
- EXAMPLE 1 SODIUM CHLORIDE A tube of anticoagulated blood was centrifuged for approximately 20 minutes at 2000 RPM to separate the cells from the plasma. The white cell (leucocyte) buffy coat was transferred to a 15 ml polypropylene tube. Approximately 9 ml of red cell lysis buffer (0.144 M NH 4 C1, 0.001 M NaHC0 3 ) was added to the polypropylene tube to hemolyze red blood cells. The polypropylene tube was inverted several times and maintained at room temperature for approximately 20 minutes. The tube was spun for 15 minutes at 2000 RPM to separate out the white blood cells. The supernatant was discarded. A white cell pellet remained.
- nuclei lysis buffer (10 mM Tris-HCl, 400 mM NaCl and 2 mM Na 2 EDTA, pH 8.2) was added to resuspend the white cell pellet.
- DNA quantity/residual protein quantitation was then diluted 1 to 100 in deionized water and quantitated at 260/280 nm (DNA quantity/residual protein quantitation) on a spectrophotometer. Five separate runs were conducted using NaCl and the following 260/280 values were obtained: 1.8, 1.77, 1.9, 1.76 and 1.78. A value of 1.5 or greater is considered desirable.
- Example 2 POTASSIUM CHLORIDE Example 2 was conducted in a similar manner as Example 1 except that approximately 1.0 ml of a saturated solution of KC1 was added to the cell digest. Fluffy, white strands of DNA were obtained.
- Example 3 was conducted in a similar manner as Example 1 except that approximately 1.0 ml of a saturated solution of MgCl 2 was added to the cell digest. Fluffy, white strands of DNA were obtained.
- EXAMPLE 4 SODIUM ACETATE Example 4 was conducted in a similar manner as Example 1 except that approximately 1.0 ml of a saturated solution of sodium acetate was added to the cell digest. Six separate runs were conducted using sodium acetate and the following 260/280 values were obtained: 1.76, 1.83, 1.8, 1.82, 1.84 and 1.9.
- Example 5 was conducted in a similar manner as Example 1 except that approximately 1.0 ml of a saturated solution of ammonium acetate was added to the cell ⁇ digest.
- the white blood cell sample provided the following 260/280 values: 1.87, 1.84, 1.86, 1.87,
- Example 6 AMMONIUM ACETATE Example 6 was conducted in a similar manner as Example 5 using ammonium acetate, however, the biological sample for Example 6 was derived from tissue. A 260/280 value of 1.77 was obtained.
- Example 7 was conducted in a similar manner as Example 1 except that DNA was extracted from anticoagulated blood from five separate individuals. After extraction the samples were quantitated and five ug of each sample was restricted with 8 U/ug of Apa I. DNA was incubated according to manufacturer specifications (New England Biolabs, Inc.). DNA was electrophoresed in agarose gels, stained with ethidium bromide to check for completeness of restriction and Southern blotted. Membranes were hybridized with human DNA probes specific for detecting Apa I restriction fragment length polymorphisms.
- Example 8 was conducted in the same manner as Example 7 except that extracted DNA samples were restricted separately with 6 U/ug of Tag I and 9 U/ug of Msp I. Observed bands after hybridization and non- isotopic detection demonstrated complete restriction.
- Example 9 RFLP STUDY USING DNA SAMPLE Example 9 was conducted in the same manner as Example 7 except that extracted DNA samples were restricted with 10 U/ug of Rsa I. Observed bands after hybridization and non-isotopic detection demonstrated complete restriction.
Abstract
Un procédé permet d'isoler des acides nucléiques à partir d'un échantillon biologique en dissociant la protéine présente dans ledit échantillon, en ajoutant une quantité suffisante d'un sel inorganique ou organique afin de précipiter la protéine, en mélangeant l'échantillon biologique renfermant le sel pendant une durée suffisante pour obtenir une dispersion satisfaisante du sel à travers ledit échantillon biologique en vue d'obtenir un précipitat de protéine, en séparant la protéine précipitée de l'échantillon biologique, et en séparant l'acide nucléique subsistant dans ce dernier. Le sel est de préférence un acétate d'ammonium et on utilise de préférence de l'éthanol à température ambiante pour précipiter et receuillir l'acide nucléique.A method makes it possible to isolate nucleic acids from a biological sample by dissociating the protein present in said sample, by adding a sufficient quantity of an inorganic or organic salt in order to precipitate the protein, by mixing the biological sample containing the salt for a sufficient time to obtain a satisfactory dispersion of the salt through said biological sample in order to obtain a protein precipitate, by separating the precipitated protein from the biological sample, and by separating the nucleic acid remaining in the latter . The salt is preferably an ammonium acetate and ethanol is preferably used at room temperature to precipitate and collect the nucleic acid.
Description
Claims
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US15402488A | 1988-02-09 | 1988-02-09 | |
US154024 | 1988-02-09 |
Publications (2)
Publication Number | Publication Date |
---|---|
EP0403503A1 true EP0403503A1 (en) | 1990-12-27 |
EP0403503A4 EP0403503A4 (en) | 1992-06-24 |
Family
ID=22549702
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
EP19890902588 Withdrawn EP0403503A4 (en) | 1988-02-09 | 1989-02-09 | Nucleic acid isolation |
Country Status (3)
Country | Link |
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EP (1) | EP0403503A4 (en) |
JP (1) | JPH03503481A (en) |
WO (1) | WO1989007603A1 (en) |
Families Citing this family (10)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
AU2907995A (en) * | 1994-06-23 | 1996-01-19 | Dade International Inc. | Method for the rapid isolation of nucleic acid |
US5538870A (en) * | 1994-09-21 | 1996-07-23 | Boehringer Mannheim Corporation | Method for preparing nucleic acids for analysis and kits useful therefor |
US5817798A (en) * | 1997-09-17 | 1998-10-06 | Abbott Laboratories | Rapid RNA isolation procedure in the presence of a transition metal ion |
DE19903507A1 (en) * | 1999-01-29 | 2000-08-10 | Roche Diagnostics Gmbh | Process for the preparation of endotoxin-free or endotoxin-depleted nucleic acids and their use |
ES2328446T5 (en) | 2000-02-04 | 2014-02-27 | Children's Hospital Research Foundation | Use of lysosomal acid lipase to treat atherosclerosis and associated diseases |
JP2003528701A (en) * | 2000-04-03 | 2003-09-30 | バテル メモリアル インスティチュート | Dispensing device and liquid compound |
WO2002012559A1 (en) * | 2000-08-02 | 2002-02-14 | Oriental Yeast Co., Ltd. | Kits for extracting nucleic acid and method of extracting nucleic acid by using the kits |
JP2005501810A (en) | 2001-03-22 | 2005-01-20 | バテル メモリアル インスティチュート | Liquid form for electrohydrodynamic spraying containing polymer and suspended particles |
AU2002255555B2 (en) * | 2002-02-15 | 2006-07-27 | Qiagen North American Holdings, Inc. | Method to isolate DNA |
JP2006238822A (en) * | 2005-03-04 | 2006-09-14 | Fuji Photo Film Co Ltd | Method for separating and purifying nucleic acid |
Family Cites Families (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US4427580A (en) * | 1982-09-01 | 1984-01-24 | Cornell Research Foundation, Inc. | Method for separation and recovery of proteins and nucleic acids from nucleoproteins using water destructuring salts |
-
1989
- 1989-02-09 WO PCT/US1989/000463 patent/WO1989007603A1/en not_active Application Discontinuation
- 1989-02-09 JP JP50240489A patent/JPH03503481A/en active Pending
- 1989-02-09 EP EP19890902588 patent/EP0403503A4/en not_active Withdrawn
Non-Patent Citations (2)
Title |
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No further relevant documents have been disclosed. * |
See also references of WO8907603A1 * |
Also Published As
Publication number | Publication date |
---|---|
EP0403503A4 (en) | 1992-06-24 |
JPH03503481A (en) | 1991-08-08 |
WO1989007603A1 (en) | 1989-08-24 |
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