The present invention relates to a method for the isolation and purification of nucleic acids by elution of the nucleic acids from nucleic acid-containing samples, and biological materials. Furthermore, the present invention relates to a kit for carrying out the method of the present invention.
An efficient method for the isolation and purification of nucleic acids, already known in the prior art, is based on the adsorption of nucleic acids on glass or silica particles in the presence of chaotropic salts, and the subsequent recovery of the adsorbed nucleic acids (Vogelstein, B. and Gillespie, D. (1979); “Preparative and analytical purification of DNA from agarose”, Proc. Natl. Acad. Sci. USA 76: 615-619). According to this method, DNA is isolated and purified on agarose using high concentrations of chaotropic salts, such as sodium iodide, sodium perchlorate or guanidinium thiocyanate. The RNA or DNA may also be isolated or purified from various mixtures (Boom, R. (1990); “Rapid and simple method for purification of nucleic acids”, J. Clin. Microbiol. 28: 495-503).
After purification, nucleic acids are often used in polymerase chain reaction (PCR). The PCR amplifies polynucleic acids in a sequence-specific manner and is therefore widely used in genetic diagnosis or DNA diagnosis. The use of PCR technology in clinical routine methods entails several problems. It is known that inhibitory substances that have not been removed from the purified nucleic acid preparation may inhibit the PCR. Such inhibitory substances are, e.g., hemoglobin and surfactants, which were used in the nucleic acid extraction process. Against this background it is apparent that the methods for the extraction and purification of nucleic acids are extremely important and relevant (Oshima et al., JJCL A, 22(2) 145-150 (1997)).
Methods for the extraction and purification of nucleic acids are frequently automated. The prior art already knows automated nucleic acid extraction methods, as described, e.g., in JP-A-107854/1999 and in JP-A-266864/1999. In most methods for the isolation and purification of nucleic acids, a solution containing a high concentration of salts and a high concentration of alcohol, and in which the nucleic acids are present, is brought into contact with an adsorption surface. Here, the adsorption surface may be a column. Subsequently the nucleic acids are adsorbed on this surface and later eluted using solutions containing less concentrated salt solutions.
The problem with most methods for the isolation and purification of nucleic acids consists in that the yield of nucleic acids is comparatively small. A further problem is that, according to the IATA (International Air Transportation Association) Regulations, ethanol-containing solutions are classified as dangerous materials (HAZMAT; hazardous materials). According to the IATA Regulations, all products, materials and goods are categorized in nine main classes. Where goods are classified as dangerous, additional fees and taxes become due for air transport. It was therefore the object of the present invention to replace as far as possible ethanol (or isopropanol) in the method for the purification and extraction of nucleic acids to facilitate the isolation and purification of nucleic acids, to provide an ethanol-free method, and to facilitate the transport of air cargo.
The prior art discloses substitutes for alcohol in methods for the purification of nucleic acids, which, however, solve the above discussed problems only in part (US 2004/0167324). The majority of the substances described therein either fall under the HAZMAT IATA Regulations or have an acrid smell so that they may only be used in a fume hood.
To better solve the above mentioned problems there was a need for further alcohol substitutes in methods for the isolation and purification of nucleic acids.
The present invention relates to a method for the extraction of nucleic acids from a solution, comprising the steps of:
In the binding process of the nucleic acid preparation, the person skilled in the art can also successfully replace ethanol by mixtures of the mentioned binding mediators. Since ethanol-containing solutions of up to 24% (vol/vol) are not classified as HAZMAT, it is also possible to use mixtures of the binding mediators with ethanol.
If not otherwise stated, the concentrations mentioned in the invention are volume percentages (percent by volume, % by volume, % (v/v)). Concentrations in weight percent are represented by percent by weight (% by weight, % (w/v)).
Preferably, the binding mediators are present in the following concentrations:
Most of the binding mediators of the present invention are classified by IATA as not dangerous. In addition, good yields have been achieved with the binding mediators of the invention (see Example 9).
The nucleic acid-containing solution can be obtained by lysis from a biological sample material containing nucleic aid. This sample material may be, e.g., blood, tissue, smear preparations, bacteria, cell suspensions, urine and adherent cells. The nucleic acid-containing material may be human, animal or plant material.
The nucleic acid-containing solution may be obtained from a biochemical nucleic acid modification reaction or from polymerase chain reactions.
For example, the nucleic acid can be genomic DNA, total DNA, or short double-stranded DNA fragments.
In a preferred embodiment, the nucleic acid is genomic DNA.
In another preferred embodiment, the nucleic acid is total RNA.
In a further preferred embodiment, the nucleic acids are short double-stranded DNA fragments.
In a preferred embodiment, the nucleic acid-containing solution has been obtained by lysis from a nucleic acid-containing material.
In another preferred embodiment, the nucleic-acid containing solution has been obtained from a biochemical nucleic acid modification reaction.
Chaotropic conditions are achieved by adding chaotropic substances. Chaotropic substances are chemical substances which disrupt ordered hydrogen bonding in aqueous solutions. They thus reduce the hydrophobic effect and have a denaturing effect on proteins, since the driving force behind protein folding is the clustering of hydrophobic amino acids in water. Examples of chaotropic substances are barium salts, guanidinium hydrochloride, thiocyanates, such as guanidinium thiocyanate, perchlorates, or even sodium chloride. Depending on their solubility product, chaotropic salts may be used in concentration ranges between 1 M and 8 M.
High-salt conditions means highly concentrated salt solutions, wherein the salt concentration in the solution is at least 1 M, and preferably 1-4 M.
However, it is also possible to take alternative measures to reach chaotropic or high-salt conditions achieving the same effect, i.e. the binding of the nucleic acids to be purified to the surface.
The surface on which the nucleic acids are adsorbed is based on materials selected from the following group: silica materials, carboxylated surfaces, zeolites and titanium dioxide.
According to the present invention, the method of the invention is preferably characterized in that chaotropic conditions are achieved by the addition of chaotropic salts, such as potassium iodide, guanidinium hydrochloride, guanidinium thiocyanate or sodium chloride, to the nucleic-acid containing solution.
Preferably, surfactants are added to the nucleic acid-containing solution. These surfactants are preferably used in concentration ranges from 0.1% by volume to 10% by volume. In addition, agents preventing foam formation (antifoams) may be added, preferably in a range from 0.01 to 1% by weight.
Wash buffers and elution buffers that can be employed in the methods of the invention are known to the skilled person.
Wash buffers contain organic solvents, such as alcohol. Wash buffers remove the other components from the nucleic acid-containing solutions (other than the nucleic acids).
Elution buffers are usually buffered low-salt solutions with a neutral to slightly alkaline pH value (e.g., buffer TE of the company QIAGEN GmbH, Hilden). The skilled person sometimes also uses distilled water.
The present invention relates to a reagent kit for the extraction of nucleic acids from a solution, comprising
In addition to the mentioned binding mediators, a kit of the company QIAGEN for the purification of nucleic acids from biochemical nucleic acid modification reactions would, for example, further contain the following components:
In addition to the just mentioned binding mediators, a kit of the company QIAGEN for the purification of nucleic acids from biological sample materials would comprise, e.g., the following components:
Corresponding lysis buffers are known to the skilled person. They usually contain detergents, chelators for divalent cations, pH buffer substances and chaotropic salts.
In a preferred embodiment, the reagent kit according to the present invention for the extraction of nucleic acids may comprise wash buffers and elution buffers, as described in WO 99/22021, EP 1 121 460 and U.S. Pat. No. 7,074,916. The wash buffers and elution buffers described therein are part of the present disclosure.
In a preferred embodiment, the reagent kit according to the present invention for the extraction of nucleic acids may comprise as eluant, e.g., “buffer TE” or even distilled water.
In a preferred embodiment, the reagent kit according to the present invention for the extraction of nucleic acids from a solution contains a chaotropic salt in a buffer solution. The kit thus contains, for example, a chaotropic buffer, a lysis buffer and a binding mediator.
Preferably, the chaotropic salt is selected from the group comprising sodium iodide, guanidinium hydrochloride, guanidinium thiocyanate; sodium perchlorate and sodium chloride.
The present invention further relates to the use of the reagent kits according to the present invention for the purification of nucleic acids from biological materials, such as blood, tissue, smear preparations, bacteria, cells suspensions and adherent cells.
The present invention also relates to the use of reagent kits according to the present invention for the purification of nucleic acids from biochemical reactions, PCR reactions and in vitro nucleic acid modification reactions.
Unless otherwise stated, the products, buffers and protocols (process instructions) described in the present application are published documents and commercially available products of the company QIAGEN GmbH, Hilden, Germany.
Upper table: normalized results determined by means of β-actin qPCR; lower table: agarose gel with the individual samples
1A: 13.5% poly(2-ethyl-2-oxazoline)
1B: 22.5% poly(2-ethyl-2-oxazoline); 24% ethanol
Upper table: normalized results determined by means of β-actin qPCR; lower table: agarose gel with the individual samples
A: 99.0% diethylene glycol monoethyl ether
B: 74.3% diethylene glycol monoethyl ether; 24% ethanol
C, 61.9% diethylene glycol monoethyl ether; 24% ethanol
D: 80.0% diethylene glycol monoethyl ether; 16% ethanol
Table: normalized results determined by means of β-actin qPCR
A: 99.0% diethylene glycol monoethyl ether acetate
B: 74.3% diethylene glycol monoethyl ether acetate; 24% ethanol
C, 61.9% diethylene glycol monoethyl ether acetate; 24% ethanol
D: 80.0% diethylene glycol monoethyl ether acetate; 16% ethanol
Upper table: normalized results determined by means of β-actin qPCR; lower table: agarose gel with the individual samples
A: 12% poly(4-ammonium-styrene sulfonic acid) solution
B: 10% poly(4-ammonium-styrene sulfonic acid) solution
C: 12% poly(4-ammonium-styrene sulfonic acid) solution
D: 10% poly(4-ammonium-styrene sulfonic acid) solution
Upper table: normalized results determined by means of β-actin qPCR; lower table: agarose gel with the individual samples
1A: 13.5% poly(2-ethyl-2-oxazoline)
1B: 22.5% poly(2-ethyl-2-oxazoline); 24% ethanol
Upper table: normalized results determined by means of β-actin qPCR; lower table: agarose gel with the individual samples
A: 99.0% diethylene glycol monoethyl ether
B: 74.3% diethylene glycol monoethyl ether; 24% ethanol
C, 61.9% diethylene glycol monoethyl ether; 24% ethanol
D: 80.0% diethylene glycol monoethyl ether; 16% ethanol
Upper table: normalized results obtained by means of β-actin qPCR; lower table: agarose gel with the individual samples
A: 99.0% diethylene glycol monoethyl ether acetate
B: 74.3% diethylene glycol monoethyl ether acetate; 24% ethanol
C: 61.9% diethylene glycol monoethyl ether acetate; 24% ethanol
D: 80.0% diethylene glycol monoethyl ether acetate; 16% ethanol
Upper table: normalized results obtained by means of β-actin qPCR; lower table: agarose gel with the individual samples
A: 12% poly(4-ammonium-styrene sulfonic acid) solution
B: 8% poly(4-ammonium-styrene sulfonic acid) solution
C: 12% poly(4-ammonium-styrene sulfonic acid) solution
D: 8% poly(4-ammonium-styrene sulfonic acid) solution
Upper table: normalized results obtained by means of mouse GAPDH qPCR; lower table: agarose gel
1A: 13.5% poly(2-ethyl-2-oxazoline)
1B: 22.5% poly(2-ethyl-2-oxazoline); 24% ethanol
2B: 73.5% TetraGlyme; 24% ethanol
Upper table: normalized results obtained by means of mouse GAPDH qPCR; lower table: agarose gel
A: 99.0% diethylene glycol monoethyl ether acetate
B: 74.3% diethylene glycol monoethyl ether acetate; 24% ethanol
C, 61.9% diethylene glycol monoethyl ether acetate; 24% ethanol
D: 80.0% diethylene glycol monoethyl etheracetat; 16% ethanol
Upper table: normalized yields obtained by means of mouse GAPDH qPCR; lower table: agarose gel
A: 99.0% diethylene glycol monoethyl ether
B: 74.3% diethylene glycol monoethyl ether; 24% ethanol
C, 61.9% diethylene glycol monoethyl ether; 24% ethanol
D: 80.0% diethylene glycol monoethyl ether; 16% ethanol
Table: normalized results obtained by means of mouse GAPDH qPCR
Table: normalized results obtained by means of mouse GAPDH qPCR
A: 99.0% diethylene glycol monoethyl ether acetate
B: 74.3% diethylene glycol monoethyl ether acetate; 24% ethanol
C, 61.9% diethylene glycol monoethyl ether acetate; 24% ethanol
D: 80.0% diethylene glycol monoethyl ether acetate; 16% ethanol
Upper table: normalized results obtained by means of mouse GAPDH qPCR; lower table: agarose gel
A: 99.0% diethylene glycol monoethyl ether
B: 74.3% diethylene glycol monoethyl ether; 24% ethanol
C, 61.9% diethylene glycol monoethyl ether; 24% ethanol
D: 80.0% diethylene glycol monoethyl ether acetate; 16% ethanol
Table: normalized results obtained by means of lamin RT-qPCR; the cells used were “293” and MCF7
Upper table: normalized results obtained by means of mouse GAPDH qPCR; lower table: agarose gel
Binding additive 01=12% poly(4-ammonium-styrene sulfonic acid) solution (failed in PCR)
Binding additive 02=98% TetraGlyme
Binding additive 03=73.5% TetraGlyme; 24% ethanol
Binding additive 04=99% diethylene glycol monoethyl ether acetate
Binding additive 05=80% diethylene glycol monoethyl ether acetate; 16% ethanol
RNeasy® inhibits small RNAs (5,8 S; tRNA; miRNA; . . . ) during purification. The exclusion size is about 150 base quantities. In this experiment it is demonstrated that the size inhibition of the test chemicals is comparable to the reference values of ethanol.
Binding additive 1=98% TetraGlyme;
Binding additive 2=80% diethylene glycol monoethyl ether acetate; 16% ethanol
Buffer ML in position 1
Upper left table: normalized results obtained by means of β-actin qPCR; right table: “Delta-Delta-CT” analysis of different sample starting amounts. In the calculation process, the measured Delta-CT is compared with the theoretical Delta-CT whereby the numerical value of the PCR inhibition degree is disclosed; lower table: agarose gel
Upper table: cartridge alignment of the EZ1® DNA Blood 200 μl reagent cartridge; middle table: normalized results obtained by means of MapK2 RT qPCR; lower table: agarose gel
1: EGDME (ethylene glycol dimethyl ether); 2: DX (1,4-dioxane); 3: AC (acetone); 4: THF (tetrahydrofuran); 5: EL (ethyl lactate); 6: DIGLYME (diethylene glycol dimethyl ether); 7: reference—MagAttract® Blood Protocol
1: EGDME (ethylene glycol dimethyl ether); 2: DX (1,4-dioxane); 3: AC (acetone); 4: THF (tetrahydrofuran); 5: EL (ethyl lactate); 6: DIGLYME (diethylene glycol dimethyl ether); 7: reference—MagAttract® Blood Protocol
The reagents and buffers listed in Table 1 as well as the protocols described therein are publications and commercially available products of the company QIAGEN GmbH, Hilden.
BioSprint® 96 with Protocol File: “BS96_DNA_Blut—200”
Replacement buffers
Replacement buffers
Blood and buffers
Method: Preparation of Genomic DNA from 100 μl Blood Using QIAamp® Spin Columns:
The results of the comparison are shown in
In the given system, the organic solvents used in US 2004/167324 A1 failed as additives of DNA on silica membranes. On the agarose gel very low yields can be observed, while the UV OD measurements indicate an overquantitation.
Method: Preparation of Genomic DNA from 100 μl Blood Using Magnetic Silica Particles:
As shown by the agarose gel in
Number | Date | Country | Kind |
---|---|---|---|
08163623.5 | Sep 2008 | EP | regional |
Filing Document | Filing Date | Country | Kind | 371c Date |
---|---|---|---|---|
PCT/EP09/61360 | 9/2/2009 | WO | 00 | 3/29/2011 |