Specification
DESCRIPTION SOLUTION FOR EXTRACTION OF RNA
TECHNICAL FIELD
[0001]
The present invention relates to a solution for extracting substantially pure RNA from a biological sample. BACKGROUND ART
[0002]
Genetic information written in DNA is transcribed into RNA in various combinations, to produce complicated phenotypes of organisms. Contribution of RNA to phenotypes of organisms is known to be dependent on the types and expression levels of the RNA, and extraction of highly pure RNA from various biological materials is important for performing gene expression analysis. For achievement of this object, many methods for extraction of RNA have been developed so far. Examples of methods for isolation of RNA frequently employed include phenol extraction, precipitation from chaotropic salt solutions and adsorption to silica membranes.
[0003]
Patent Document 1 discloses a solution for RNA extraction comprising 2 to 5 M guanidine and 40 to 60% phenol. RNA extraction had required not less than 2 days of operation using an ultracentrifuge before, but use of this solution enabled efficient extraction of RNA in 3 hours.. This method is called the single-step method.
[0004]
By improvement of the method described in the above Patent Document 1, Patent Document 2 discloses an extraction solution for simultaneous extraction and separation of RNA, DN A and proteins from a sample comprising of these components. More specifically, the literature describes extraction and separation of RNA into an aqueous layer by using a 30 to 50% phenol solution containing 0.5 to 2 M guanidine.
[0005]
Although the solutions described in Patent Documents 1 and 2 have different compositions, RNA can be extracted by similar operations using the solutions. That is, each solution is used for homogenization of a biological tissue, and a hydrophobic organic solvent such as chloroform is used upon centrifugation of the homogenate to achieve layer separation. Thereafter, the aqueous layer in the uppermost part comprising RNA is recovered. RNA is then precipitated with alcohol and washed in order to extract RNA.
[0006]
However, RNA isolated using the solutions and the methods described in Patent Document 1 and 2 still shows contamination with (residual) genomic DNA in an amount which can be detected by the reverse transcription-polymerase chain reaction assay (RT-PCR), leading to problems such as loss of quantitativeness of RNA in cases of RT-PCR (Patent Document 3, e.g., paragraph 0005). Therefore, RNA isolated by these methods needs to be further purified for removal of DNA as a contaminant. [0007]
A commonly used method for removal of DNA contained as an impurity in an extracted RNA sample is treatment of the RNA sample with deoxyribonuclease (DNase). However, in cases where treatment with DNase is carried out in a liquid layer, it is necessary to perform phenol/chloroform extraction and denaturation of proteins again for removal of DNase after the treatment. Further, in cases where the extraction is performed using a combination of silica membrane columns, the operation of washing the columns needs to be carried out repeatedly. Although contamination with DNA is reduced by this treatment with DNase, such additional labor is required and loss of RNA occurs, resulting in a decreased amount of extracted RNA, which is problematic.
[0008]
As a method for avoiding contamination of an RNA sample with DNA without performing DNase treatment, Patent Document 3 reports a method using an RNA extraction reagent at a pH of less than 4. However, it is well known that nucleic acid is depurinated and degraded under acidic conditions, and it is therefore difficult to isolate substantially intact RNA. Further, since the solution equilibrium of DNA into the aqueous/organic layer under acidic conditions is biased toward distribution into the organic layer, the effect of suppressing contamination of the aqueous phase with genomic DNA can be expected to some extent by using a reagent for extraction of RNA at a pH of less than 4, but complete suppression of contamination with small DNA fragments having small numbers of bases is impossible.
PRIOR ART DOCUMENTS [Patent Documents]
[0009]
Patent Document 1: US 4843155 B Patent Document 2: JP 5-344886 A
Patent Document 3: Japanese Translated PCT Patent Application Laid-open No. 2007-532140
SUMMARY OF THE INVENTION PROBLEMS TO BE SOLVED BY THE INVENTION
[0010]
As described above, substantially pure RNA free from contamination with
DNA cannot be extracted with conventional solutions for extraction of RNA from biological samples even in cases where quantitativeness is required, which has been problematic. Therefore, for removal of DNA as a contaminant, an additional step such as DNase treatment has been necessary. The present invention aims to solve these problems and provides a solution for extracting substantially pure RNA from a biological sample.
MEANS FOR SOLVING THE PROBLEMS
[0011]
The present inventors studied compositions of conventional solutions for RNA extraction and discovered that the phenol concentration has an especially strong relationship with the effect of prevention of contamination with DNA, thereby completing the present invention. [0012]
That is, the present invention provides the following: [ 1 ] A solution for extracting RNA from a biological sample containing RNA and at least DNA, the solution comprising:
(a)phenol in an amount of more than 50% by volume based on the total amount of the solution;
(b)a polyol in an amount of 3 to 10% by volume based on the total amount of the solution;
(c)a guanidinium salt at a concentration of 0.5 to 2.0 M based on the total amount of the solution;
(d)a thiocyanate at a concentration of 0.1 to 0.5 M based on the total amount of the solution; and
(e)a buffer for maintaining the pH of the solution at 4 to 6.
[2]The solution according to [1], wherein the phenol concentration is 55 to 65% by volume based on the total amount of the solution.
[3The solution according to [1] or [2], further comprising an organic solvent for separating an aqueous layer.
[4]The solution according to any one of [1] to [3], wherein the biological sample is a culture liquid of cultured cells.
[5]The solution according to any one of [1] to [3], wherein the biological
sample is a body fluid component of an organism.
[6]The solution according to any one of [1] to [3], wherein the biological
sample is a blood component of an organism
[0013]
[7]A method for extracting RNA from a biological sample containing RNA and
at least DNA, the method comprising the steps of:
homogenizing the biological sample together with a solution comprising:
(a)phenol in an amount of more than 50% by volume based on the total amount of the solution;
(b)a polyol in an amount of 3 to 10% by volume based on the total amount of the solution;
(c)a guanidinium salt at a concentration of 0.5 to 2.0 M based on the total amount of the solution;
(d)a thiocyanate at a concentration of 0.1 to 0.5 M based on the total amount of the solution; and
(e)a buffer for maintaining the pH of the solution at 4 to 6; mixing the obtained homogenate with an organic solvent for separation of an aqueous layer; centrifuging the obtained mixture; and recovering an RNA-containing aqueous layer produced by the centrifugation. [0014]
[8]A method for extracting RNA from a biological sample containing RNA and at least DNA, the method comprising the steps of:
homogenizing the biological sample together with a solution comprising:
(a)phenol in an amount of more than 50% by volume based on the total amount of the solution;
(b)a polyol in an amount of 3 to 10% by volume based on the total amount of the solution;
(c)a guanidinium salt at a concentration of 0.5 to 2.0 M based on the total amount of the solution;
(d)a thiocyanate at a concentration of 0.1 to 0.5 M based on the total amount of the solution;
(e)a buffer for maintaining the pH of the solution at 4 to 6; and
(f)an organic solvent for separation of an aqueous layer; centrifuging the obtained homogenate; and recovering an RNA-containing aqueous layer produced by the centrifugation.
[0015]
[9]The method according to claim 7 or 8, wherein the phenol concentration is 55 to 65% by volume based on the total amount of the solution of (a) to (e). EFFECT OF THE INVENTION
[0016]
By using the solution of the present invention, substantially pure RNA free from contamination with DNA can be simply extracted from a biological sample. Further, by the present invention, RNA can be obtained without an additional treatment such as DNase treatment which may cause recovery loss, which RNA has purity that allows use of the RNA as it is even in uses wherein quantitativeness is required. In particular, an RNA of interest can be extracted with high purity even from, among biological samples, body fluids such as blood containing very large amounts of RNase and other contaminants. BRIEF DESCRIPTION OF THE DRAWINGS
[0017]
Fig. 1 shows electropherograms of nucleic acid extracted from serum in Example 1 using a solution of the present invention.
Fig. 2 shows electropherograms of nucleic acid extracted from serum in Comparative Example 1 using a solution described in Patent Document 2.
Fig. 3 shows an electropherogram of nucleic acid extracted from serum in Comparative Example 2 using a solution described in Patent Document 1.
Fig. 4 shows electropherograms of nucleic acid extracted from serum in Examples 2 to 5 using solutions of the present invention.
Fig. 5 shows electropherograms of nucleic acid extracted from serum in Examples 6 to 12 using solutions of the present invention.
Fig. 6 shows electropherograms of nucleic acid extracted from serum in Example 13 and Comparative Example 3 using a solution of the present invention and a solution described in Patent Document 3.
Fig. 7 shows electropherograms of nucleic acid extracted from cultured cells in Example 14 using a solution of the present invention.
Fig. 8 shows electropherograms of nucleic acid extracted from serum in Examples 15 and 16 using solutions of the present invention.
Fig. 9 shows electropherograms of nucleic acid extracted from serum in Comparative Example 4 using a solution described in Patent Document 3.
Fig. 10 shows electropherograms of nucleic acid extracted from serum in Examples 17 and 18 using solutions of the present invention.
BEST MODE FOR CARRYING OUT THE INVENTION
[0018]
The present invention is a solution for extracting RNA from a biological sample, which solution comprises as its components the following (a) to (e):
(a) phenol in an amount of more than 50% by volume based on the total amount of the solution;
i (b) a polyol in an amount of 3 to 10% by volume (not less than 3% by volume and not more than 10% by volume) based on the total amount of the solution;
(c) a guanidinium salt at a concentration of 0.5 to 2.0 M (not less than 0.5 M and not more than 2.0 M) based on the total amount of the solution;
(d) a thiocyanate at a concentration of 0.1 to 0.5 M (not less than 0.1 M and not more than 0.5 M) based on the total amount of the solution; and
(e) a buffer for maintaining the pH of the solution at 4 to 6.
[0019]
The biological sample used in the present invention comprises RNA and at least DNA. Further, by using the solution of the present invention, substantially
pure RNA can be extracted from the biological sample. The term "substantially pure RNA" herein means RNA from which DNA contained in the original biological sample has been separated and which is substantially free from contamination with the DNA. Whether or not RNA is substantially pure can be judged by seeing whether or not DNA is detected by electrophoresis. For example, since "Agilent
RNA 6000 pico kit" manufactured by Agilent Technologies Inc. (model number, 5067-1513) can be used for detection of nucleic acid in an amount of 50 pg/uLto 5000 pg/uL (recommendation), the kit can be used for evaluation of the presence/absence of DNA contamination. More specifically, the extracted nucleic acid may be treated with RNase and subjected to electrophoresis using "Agilent RNA 6000 pico kit". In cases where no peak was detected, it can be said that DNA contamination was sufficiently suppressed and substantially pure RNA could be obtained. Further, by analyzing the amount of DNA contamination by quantitative
PCR, the purity of RNA can be evaluated. For example, in cases where a real-time PCR apparatus and "SYBR Green" (fluorescent dye) are used, double-stranded DNA in an amount of 60 pg can be detected, so that the evaluation can be carried out using these. More specifically, extracted nucleic acid is added to a PCR reaction solution containing primers, DNA polymerase and "SYBR Green" to perform PCR amplification, and the result is compared with a preliminarily prepared calibration curve. By this, the amount of DNA contamination can be quantitatively analyzed.
[0020]
In the present invention, the total amount of a solution means the total volume comprising all of the above-described (a) to (e). For example, "phenol in an amount of more than 50% by volume based on the total amount of the solution" means that more than 500 mL of phenol is contained in 1 L of the solution after mixing of all components. Further, for example, "a guanidinium salt at a concentration of 0.5 to 2.0 M based on the total amount of the solution" means that the final concentration in the solution is not less than 0.5 M and not more than 2.0 M, that is, the guanidinium salt is contained in an amount of not less than 0.5 mol and not more than 2 mol in 1 L of the solution after mixing of all components.
[0021]
The solution of the present invention comprises (a) phenol in an amount of more than 50% by volume based on the total amount of the solution. It was found that employing a phenol concentration of more than 50% by volume, which is different from the concentration employed in conventional techniques, produces the effect of reducing contamination of the aqueous layer, into which RNA is extracted, with DNA as an impurity. For example, the solution of the present invention comprises phenol in an amount of not less than 51% by volume, not less than 52% by volume, not less than 53% by volume, not less than 54% by volume or not less than 55% by volume. The solution of the present invention comprises phenol in an
amount of preferably not less than 53% by volume, more preferably not less than 55% by volume. Further, the concentration of phenol is preferably not more than 75% by volume in view of preparing the solution of the present invention in the state where other components of the solution of the present invention, (b) polyalcohol, (c) 0.5 to 2.0 M guanidinium salt and (d) 0.1 to 0.5 M thiocyanate are uniformly mixed at the respective predetermined concentrations. Further, the concentration of phenol is more preferably not more than 65% by volume in view of reducing the influence of oxidation of phenol. The range of the phenol concentration is preferably one determined by an arbitrary combination of these upper limits and lower limits, and is more preferably not less than 52% by volume and not more than 65% by volume, not less than 53% by volume and not more than 65% by volume, especially preferably not less than 55% by volume and not more than 65% by volume.
[0022]
The solution of the present invention comprises (b) a polyol in an amount of 3 to 10% by volume based on the total amount of the solution. The polyol in the present invention may be an aliphatic alcohol having a plurality of hydroxyl groups, which allows mixing of the (a) phenol component and the aqueous solutions of (c) and (d) in the solution of the present invention, to keep the solution of the present invention uniform. As the polyol, a C2-C6 aliphatic alcohol having 2 to 4 hydroxyl groups is preferred. Examples of the polyol include glycerol, ethylene glycol, propylene glycol and erythritol, and the polyol is more preferably glycerol. The polyol may be used in an amount of 3 to 10% by volume based on the total amount of the solution of the present invention in order to maintain the solution of the present invention as a uniform solution and to prevent excessive distribution of the phenol component into the aqueous layer.
[0023]
The solution of the present invention comprises (c) a guanidinium salt at a concentration of 0.5 to 2.0 M based on the total amount of the solution. Specific preferred examples of the guanidinium salt include guanidinium thiocyanate and guanidinium hydrochloride. Guanidinium salts have an effect to protect RNA from degradation and to keep phenol in the solution state in an aqueous solution
[0024]
The solution of the present invention comprises (d) a thiocyanate at a concentration of 0.1 to 0.5 M based on the total amount of the solution. As the thiocyanate, an inorganic salt of thiocyanic acid may be preferably used, and ammonium thiocyanate and sodium thiocyanate may be more preferably used. Further, the thiocyanate may be a mixture of a plurality of different inorganic salts of thiocyanic acid, and, for example, a mixture of ammonium thiocyanate and sodium thiocyanate may be preferably used. Thiocyanate is considered to enhance RNA extraction from a biological sample. In cases where the solution of the present invention comprises guanidinium thiocyanate, the concentration of guanidinium thiocyanate is included in the concentration of the above-described guanidinium salt, and not included in the concentration of thiocyanate.
[0025]
The solution of the present invention comprises (e) a buffer for maintaining the pH of the solution at 4 to 6. As the buffer, organic salts and inorganic salts which are conventionally used for maintaining the pH within a desired range and show buffering capacity may be used. Specific examples of the buffer include organic salts and inorganic salts, such as phosphate, acetate, citrate, phthalate, tartrate and lactate, of sodium, potassium, lithium and ammonium. Among the combinations of these, sodium acetate and sodium citrate are more preferably used. Further, a plurality of these organic salts and/or inorganic salts may be used in combination. The concentration of the buffer is not restricted as long as it is sufficient for maintaining the pH within the desired range of 4 to 6, and the concentration is preferably 0.02 to 0.2 M based on the total amount of the solution of the present invention. In order to adjust the pH of the solution of the present invention, an appropriate aqueous acid or alkaline solution such as a hydrochloric acid or sodium hydroxide solution may be added as appropriate in addition to the buffer.
[0026]
The solution of the present invention may contain a surfactant(s) such as polyoxyethylene sorbitan, sodium dodecyl sulfate and/or sarcosine for supporting purification of the RNA of interest by denaturing proteins in the biological sample. Further, the solution of the present invention may contain an antioxidant(s) such as hindered amine phenol and/or quinoline for prevention of oxidation of phenol.
[0027]
In cases where the biological sample is in the liquid state when the RNA of interest is to be extracted, the solution of the present invention may be used in an amount of not less than 1 volume, preferably not less than 3 volumes of the sample.
[0028]
An example of the procedure for extraction of the RNA of interest using the solution of the present invention is shown below. First, the biological sample is homogenized in the solution of the present invention to form a homogenate. The method of homogenization is not restricted, and examples of the method include stirring by vortexing or the like, crushing with an injection needle or the like, and use of a conventional homogenizer. Subsequently, an organic solvent is added to the homogenate for separation of the aqueous layer, and the resulting mixture is subjected to centrifugation. The organic solvent to be added in this step is preferably used in an amount of about 2% by volume to about 40% by volume based on the homogenate. The centrifugation may be carried out usually at 6,000*G to 20,000>
(1)Preparation of Solution for RNA Extraction
The respective components of the solution were mixed such that their final concentrations were as described below, to prepare a solution for RNA extraction.
■ 58 vol% Phenol
■ 5 vol% Glycerol
• 0.8 M Guanidinium thiocyanate (mixed as an aqueous solution)
■ 0.4 M Ammonium thiocyanate (mixed as an aqueous solution)
• 0.1 M Sodium acetate buffer (mixed as an aqueous solution), adjusted to
pH5.
[0041]
(2)RNA Extraction from Biological Sample
As a biological sample containing RNA as well as DNA and proteins, serum was used for RNA extraction. By mixing 900 uL of the solution prepared in the above (1) and 3 00 uL of serum by vortexing, the sample was homogenized. To the resulting homogenate, 60 uL of p-bromoanisole was added, and the resulting mixture was mixed, followed by centrifuging the mixture at room temperature at 12,000>
(1) Preparation of Solution for RNA Extraction
The solution described in Patent Document 2 was prepared with the same composition as in Example 1 except that the phenol concentration was 50% by volume in terms of the final concentration of the solution.
[0047]
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (3b) Purification and Concentration of RNA from Aqueous Layer - With RNase Treatment -
The operation was carried out in the same manner as in Example 1. (3c) Purification and Concentration of RNA from Aqueous Layer - With DNase Treatment -
The operation was carried out in the same manner as in (3 b) in Example 1 except that the aqueous layer containing RNA was treated with DNase instead of the RNase in (3b), to obtain a purified and concentrated sample. Other conditions were the same as in Example 1.
[0048]
(4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The results are shown in Fig. 2.
In the sample wherein enzyme treatment was not carried out, two strong peaks (corresponding to numbers of bases of about 200 and about 500) and one weak peak (corresponding to the same number of bases as in Example 1) were detected (lane 1). In the sample treated with RNase, the peaks of 200 bases and 500 bases hardly changed, and it was therefore found that the two peaks were not due to RNA (lane 2). On the other hand, the single weak peak has disappeared, and this peak was therefore confirmed to be due to RNA as in the case of Example 1. In the DNase-treated sample, the two strong peaks have disappeared, and very short fragments due to degradation were detected (lane 3). Therefore, these two strong peaks were found to be due to contamination with DNA fragments .
[0049]
Thus, when the solution containing 50% by volume of phenol was used, contamination with DNA was observed, and pure RNA could not be extracted.
The above results are summarized in Table 3.
[0050]
(1) Preparation of Solution for RNA Extraction
The same solution as the extraction solution described in Patent Document 1 I was prepared except that the phenol concentration was 60% by volume. That is, the solution contained 60% by volume of phenol, 2M guanidinium thiocyanate, 0.1 M sodium acetate and 0.2% by volume of 2-mercaptoethanol in terms of the final concentrations, and the pH of the solution was 4.
[0051]
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3 a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. [0052] (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in Fig. 3.
Three peaks similar to those in Comparative Example 1 were observed. Therefore, contamination with DNA fragments could be confirmed.
The above result is summarized in Table 3.
[0053]
(1) Preparation of Solution for RNA Extraction
A solution was prepared such that the composition of the solution is the same as in Example 1 except that the phenol concentration was 55% by volume in terms of the final concentration.
(2) RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (3b) Purification and Concentration of RNA from Aqueous Layer - With RNase Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The results are shown in Fig. 4. [0054]
The same peak as in Example 1 was detected (lane 1), and it could be confirmed that only RNA was extracted with high purity. Since the peak in the RNase-treated sample (lane 5; RNase (+)) was as weak as that in BLANK, it could be confirmed that the extracted nucleic acid contained only RNA.
The above results are summarized in Table 1.
[0055]
(1) Preparation of Solution for RNA Extraction A solution was prepared such that the composition of the solution is the same as in Example 1 except that the phenol concentration was 65% by volume in terms of the final concentration.
(2) RNA Extraction from Biological Sample
[ The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. )
(4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 2 in Fig. 4.
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity,
I The above result is summarized in Table 1.
[0056]
(1)Preparation of Solution for RNA Extraction
A solution was prepared such that the composition of the solution is the I same as in Example 1 except that the phenol concentration was 53% by volume in terms of the final concentration.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3a) Purification and Concentration of RNA from Aqueous Layer- Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1.
I
(4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 3 in Fig. 4.
The same peak as in Example 1 was detected, and it could be confirmed that I only RNA was extracted with high purity.
The above result is summarized in Table 1.
[0057]
(1)Preparation of Solution for RNA Extraction
)The solution having the same composition as in Example 1 was prepared.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample, except that 240 pL of chloroform was added instead of 60 JJ.L of p-bromoanisole to the homogenate. i (3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The i result is shown in lane 4 in Fig. 4.
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity.
The above result is summarized in Table 1.
[0058]
(1) Preparation of Solution for RNA Extraction
The solution having the same composition as in Example 1 was prepared.
(2) RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample, except that 100 uL of 4-bromoveratrole was added instead of 60 uL of p-bromoanisole to the homogenate.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 1 in Fig. 5.
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity.
The above result is summarized in Table 1.
[0059]
(1)Preparation of Solution for RNA Extraction
The solution having the same composition as in Example 1 was prepared.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample, except that 100 uL of 6-bromo-l,4-benzodioxane was added instead of 60 uL of p-bromoanisole to the homogenate. (3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 2 in Fig. 5.
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity.
The above result is summarized in Table 1.
[0060]
(1)Preparation of Solution for RNA Extraction
The solution having the same composition as in Example 1 was prepared.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using ) serum as the biological sample, except that 100 uL of l-bromo-4-trifluoromethoxybenzene was added instead of 60 pL of p-bromoanisole to the homogenate.
(3 a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme
Treatment -
I The operation was carried out in the same manner as in Example 1.
(4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 3 in Fig. 5.
The same peak as in Example 1 was detected, and it could be confirmed that | only RNA was extracted with high purity.
The above result is summarized in Table 1.
[0061]
(1)Preparation of Solution for RNA Extraction
The solution having the same composition as in Example 1 was prepared.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using
"""^ "" ■■!■■■ ■ II. - _ ,.._ M„i
serum as the biological sample, except that 100 μ L of l-bromo-2,4-dimethoxybenzene was added instead of 60 uL of p-bromoanisole to the homogenate.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme
Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 4 in Fig. 5.
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity.
The above result is summarized in Table 1.
[0062]
(1) Preparation of Solution for RNA Extraction The solution having the same composition as in Example 1 was prepared.
(2) RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample, except that 100 uL of 4-fluoroanisole was added instead of 60 uL of p-bromoanisole to the homogenate.
(3 a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 5 in Fig. 5.
The same peak as in Example 1 was detected, and it could be confirmed that
j
inly RNA was extracted with high purity.
The above result is summarized in Table 2. ;
0063]
'Example 11> '1) Preparation of Solution for RNA Extraction
The solution having the same composition as in Example 1 was prepared. 2) RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample, except that 100 \xL of 4-bromotoluene was added nstead of 60 uL of p-bromoanisole to the homogenate.
3a) Purification and Concentration of RNA from Aqueous Layer - "Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. 4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The esult is shown in lane 6 in Fig. 5.
The same peak as in Example 1 was detected, and it could be confirmed that mly RNA was extracted with high purity.
The above result is summarized in Table 2.
0064]
^Example 12>
1) Preparation of Solution for RNA Extraction
The solution having the same composition as in Example 1 was prepared.
2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using ;erum as the biological sample, except that 100 uL of ethyl 4-bromobutyrate was idded instead of 60 uL of p-bromoanisole to the homogenate.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 7 in Fig. 5.
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity.
The above result is summarized in Table 2.
[0065]
(1)Preparation of Solution for RNA Extraction
A solution was prepared by adding hydrochloric acid to the solution prepared in Example 1 such that the pH of the solution was adjusted to 4.2.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 1 in Fig. 6.
The same peak as in Example 1 was detected also in the case where the pH of the solution was 4.2, and it could be confirmed that only RNA was extracted with high purity.
The above result is summarized in Table 2.
[0066]
(1)Preparation of Solution for RNA Extraction
A solution was prepared by adding hydrochloric acid to the solution prepared in Comparative Example 1 such that the pH of the solution was adjusted to 3.6.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3 a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The result is shown in lane 2 in Fig. 6. The same three peaks as in Comparative Example 1 were observed. By this, it could be confirmed that, in cases where the solution containing 50% by volume of phenol is used, contamination with DNA fragments occurs also at a pH of 3.6.
The above result is summarized in Table 3.
[0067]
(1)Preparation of Solution for RNA Extraction
The solution having the same composition as in Example 1 was prepared.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 except that cultured cells (HEK293 cells) suspended in 300 nL of PBS were used as the biological sample, instead of 300 μ L of serum.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1 except that 1.25 volumes, instead of 1.5 volumes, of ethanol was added to the aqueous layer. (3b) Purification and Concentration of RNA from Aqueous Layer - With RNase Treatment -
The operation was carried out in the same manner as in Example 1 except that 1.25 volumes, instead of 1.5 volumes, of ethanol was added to the aqueous layer. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1 except that "Agilent RNA 6000 nano kit" (model number, 5067-1511) (manufactured by Agilent Technologies Inc.) was used as the kit, instead of "Agilent RNA 6000 pico kit". The results are shown in Fig. 7.
[0068]
It could be confirmed that, in the sample without enzyme treatment in (3a), 18S and 28S ribosome RNAs were extracted almost without degradation (RIN value: 2.3) (lane 1). The amount of nucleic acid calculated in this case was 79 ng/uL. In the result obtained with the RNase-treated sample in (3 b), the same peak as in Example 1 was not detected at all (lane 2). The amount of nucleic acid calculated in this case was 4 ng/uL. The noise produced in the detection system when no sample was subjected to electrophoresis was investigated (lane 3) and, as a result, the amount of nucleic acid in this case was 2 ng/ μ L. Thus, the amount of nucleic acid in lane 2 was considered to be due to the noise. Based on these results, the extracted nucleic acid was confirmed to be entirely RNA.
The above results are summarized in Table 2.
[0069]
(1) Preparation of Solution for RNA Extraction
The respective components of the solution were mixed such that their final concentrations were as described below, to prepare a solution for RNA extraction. That is, 60 uL of additional p-bromoanisole was added to 900 uL of the solution having the same composition as in Example 1, to prepare the solution.
■ 58 vol% Phenol
■ 5 vol% Glycerol
• 0.8 M Guanidinium thiocyanate (mixed as an aqueous solution)
■ 0.4 M Ammonium thiocyanate (mixed as an aqueous solution)
■ 0.1 M Sodium acetate buffer (mixed as an aqueous solution), adjusted to pH5.
■ 6.6 vol% p-Bromoanisole based on the total amount (100%) of the above
components
[0070]
(2)RNA Extraction from Biological Sample
By mixing 900 uL of the solution prepared in the above (1) and 300 uL of serum by vortexing, the sample was homogenized. The resulting homogenate was centrifuged at room temperature at 12,000XG for 10 minutes. By this, an aqueous layer containing RNA, and an organic layer and an intermediate layer containing DNA and proteins were formed. From these, 350 uL of the aqueous layer was separated into another tube.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (3b) Purification and Concentration of RNA from Aqueous Layer - With RNase Treatment -
The operation was carried out in the same manner as in Example 1.
[ i
(4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The results are shown in lanes 1, 3 and 5 in Fig. 8.
[0071]
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity (lane 1). Since the peak in the RNase-treated sample (lane 3; RNase (+)) was as weak as that in BLANK (lane 5), it could be confirmed that the extracted nucleic acid contained only RNA.
The above results are summarized in Table 2.
[0072]
(1)Preparation of Solution for RNA Extraction
The respective components of the solution were mixed such that their final concentrations were as described below, to prepare a solution for RNA extraction. That is, 90 uL of additional chloroform was added to 900 uL of the solution having the same composition as in Example 1, to prepare the solution.
• 58 vol% Phenol
■ 5 vol% Glycerol
■ 0.8 M Guanidinium thiocyanate (mixed as an aqueous solution)
■ 0.4 M Ammonium thiocyanate (mixed as an aqueous solution)
• 0.1 M Sodium acetate buffer (mixed as an aqueous solution), adjusted to
pH5.
• 10 vol% chloroform based on the total amount (100%) of the above components
(2) RNA Extraction from Biological Sample
By mixing 900 uL of the solution prepared in the above (1) and 300 uL of serum by vortexing, the sample was homogenized. The resulting homogenate was
1
centrifuged at room temperature at 12,000XG for 10 minutes. By this, an aqueous layer containing RNA, and an organic layer and an intermediate layer containing DNA and proteins were formed. From these, 350 uL of the aqueous layer was separated into another tube.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (3 b) Purification and Concentration of RNA from Aqueous Layer - With RNase Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The results are shown in lanes 2,4 and 5 in Fig. 8.
[0073]
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity (lane 2). Since the peak in the RNase-treated sample (lane 4; RNase (+)) was as weak as that in BLANK (lane 5), it could be confirmed that the extracted nucleic acid contained only RNA.
The above results are summarized in Table 2.
[0074]
(1)Preparation of Solution for RNA Extraction
The solution having the same composition as in Comparative Example 3 was prepared except that the phenol concentration was 55% by volume.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (3b) Purification and Concentration of RNA from Aqueous Layer - With RNase Treatment —
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The results are shown in Fig. 9.
[0075]
In the sample without enzyme treatment in (3a), a rather broader peak compared to the peak in Example 1 was detected (lane 1), and the RNase-treated sample in (3b) also showed a peak (lane 2). Since the peak obtained with the RNase-treated sample (RNase(+)) was also broader than the peak in BLANK (lane 2), contamination with nucleic acid other than RNA (DNA) could be confirmed.
The above results are summarized in Table 3.
[0076]
(1)Preparation of Solution for RNA Extraction
The solution having the same composition as in Example 1 in terms of the final concentrations was prepared, except that the pH of was adjusted to 4.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3 a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1.
(3b) Purification and Concentration of RNA from Aqueous Layer - With RNase Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The results are shown in Fig. 10 (lanes 1, 2 and 5).
[0077]
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity (lane 1). Since the peak in the RNase-treated sample (lane 2; RNase (+)) was as weak as that in BLANK (lane 5), it could be confirmed that the extracted nucleic acid contained only RNA.
The above results are summarized in Table 2.
[0078]
(1)Preparation of Solution for RNA Extraction
The solution having the same composition as in Example 1 in terms of the final concentrations was prepared, except that the pH was adjusted to 6.
(2)RNA Extraction from Biological Sample
The operation was carried out in the same manner as in Example 1 using serum as the biological sample.
(3 a) Purification and Concentration of RNA from Aqueous Layer - Without Enzyme Treatment -
The operation was carried out in the same manner as in Example 1. (3b) Purification and Concentration of RNA from Aqueous Layer - With RNase Treatment -
The operation was carried out in the same manner as in Example 1. (4) Evaluation of Purity by Electrophoresis
The operation was carried out in the same manner as in Example 1. The results are shown in Fig. 10 (lanes 3,4 and 5).
[0079]
The same peak as in Example 1 was detected, and it could be confirmed that only RNA was extracted with high purity (lane 3). Since the peak in the RNase-treated sample (lane 4; RNase (+)) was as weak as that in BLANK (lane 5), it could be confirmed that the extracted nucleic acid contained only RNA.
The above results are summarized in Table 2.
CLAIMS
1.A solution for extracting RNA from a biological sample containing RNA and at
least DNA, said solution comprising:
(a)phenol in an amount of more than 50% by volume based on the total amount of said solution;
(b)a polyol in an amount of 3 to 10% by volume based on the total amount of said solution;
(c)a guanidinium salt at a concentration of 0.5 to 2.0 M based on the total amount of said solution;
(d)a thiocyanate at a concentration of 0.1 to 0.5 M based on the total amount of said solution; and
(e)a buffer for maintaining the pH of said solution at 4 to 6.
2.The solution according to claim 1, wherein the phenol concentration is 55 to 65% by volume based on the total amount of said solution.
3.The solution according to claim 1 or 2, further comprising an organic solvent for separating an aqueous layer.
4.The solution according to any one of claims 1 to 3, wherein said biological sample is a culture liquid of cultured cells.
5.The solution according to any one of claims 1 to 3, wherein said biological sample is a body fluid component of an organism.
6.The solution according to any one of claims 1 to 3, wherein said biological sample is a blood component of an organism.
7.A method for extracting RNA from a biological sample containing RNA and at least DNA, said method comprising the steps of:
homogenizing said biological sample together with a solution comprising:
(a)phenol in an amount of more than 50% by volume based on the total amount of said solution;
(b)a polyol in an amount of 3 to 10% by volume based on the total amount of said solution;
(c)a guanidinium salt at a concentration of 0.5 to 2.0 M based on the total amount of said solution;
(d)a thiocyanate at a concentration of 0.1 to 0.5 M based on the total amount of said solution; and
(e)a buffer for maintaining the pH of said solution at 4 to 6;
mixing the obtained homogenate with an organic solvent for separation of an aqueous layer;
centrifuging the obtained mixture; and recovering an RNA-containing aqueous layer produced by the centrifugation.
8.A method for extracting RNA from a biological sample containing RNA and at
least DNA, said method comprising the steps of:
homogenizing said biological sample together with a solution comprising:
(a)phenol in an amount of more than 50% by volume based on the total amount of said solution;
(b)a polyol in an amount of 3 to 10% by volume based on the total amount of said solution;
(c)a guanidinium salt at a concentration of 0.5 to 2.0 M based on the total amount of said solution;
(d)a thiocyanate at a concentration of 0.1 to 0.5 M based on the total amount of said solution;
(e)a buffer for maintaining the pH of said solution at 4 to 6; and
(f)an organic solvent for separation of an aqueous layer;
centrifuging the obtained homogenate; and
recovering an RNA-containing aqueous layer produced by the centrifugation.
9.The method according to claim 7 or 8, wherein the phenol concentration is 55
to 65% by volume based on the total amount of said solution of (a) to (e).