Kit for simultaneously extracting and purifying DNA and RNA of complex plant and extraction method
Technical Field
The invention belongs to the field of molecular biology, and particularly relates to a kit for simultaneously extracting and purifying DNA and RNA of a complex plant and an extraction method.
Background
Extraction of DNA and RNA is one of the fundamental contents of plant molecular biology experiments. High quality DNA samples are the basis for molecular biological studies such as restriction, PCR amplification, molecular hybridization, genetic polymorphism analysis, genomics, etc. The high quality RNA sample is a necessary precondition for gene cloning, expression level detection and functional analysis (the development of tests such as RT-PCR, northern, real-time PCR and cDNA library construction must obtain high-purity and complete RNA).
The higher plants such as Malus, pyrus, longan and Citrus have complex intracellular and extracellular components, and are rich in polysaccharides and phenols. Wherein, phenolic substances are easily oxidized into quinone substances during the homogenization operation, so that irreversible combination with DNA and RNA can occur, and the separation and purification of nucleic acid are affected. Many physicochemical properties of polysaccharides are similar to those of RNA, and are easily co-precipitated with RNA in the extraction process, so that the polysaccharide is difficult to separate, and the purity of an RNA sample is affected. The above characteristics of higher plant cells make the extraction of DNA and RNA difficult for other biological materials, thus making the research of molecular biology thereof difficult.
The conventional extraction methods of plant DNA and RNA are numerous, such as CTAB method, SDS method, guanidine salt method, phenol method, etc. The core of the methods is that on the basis of lysing plant cells, organic solvents are used for extraction for many times, proteins and the like are precipitated in the organic reagents, and nucleic acid is kept in a water phase, so that the purpose of separating nucleic acid is achieved, and therefore whether the interference of polysaccharide and phenolic compounds can be effectively removed is a key to the success or failure of extracting high-quality DNA and RNA. Although the existing commercial nucleic acid extraction kit has remarkable extraction effect, the raw materials are high in price and limited in extractable plant types, and the simultaneous extraction of DNA and RNA cannot be realized, and two sets of extraction kits of DNA and RNA are required to be used respectively, so that waste of test materials and reagents is caused. In addition, the traditional extraction method is complicated in operation, long in extraction time, can not ensure the extraction quality of DNA and RNA, and also adopts toxic irritants such as phenol, chloroform and the like, thereby having hidden danger to the operation safety of operators and being not beneficial to protecting the personal safety of the operators.
Therefore, developing a product which can be widely applicable and low in cost and can simultaneously extract and purify complex plant DNA and RNA has great significance in the fields of nucleic acid molecule detection and analysis.
Disclosure of Invention
The present invention aims to solve at least one of the technical problems in the prior art described above. Therefore, the product and the method for simultaneously extracting and purifying the DNA and the RNA of the complex plant are provided, the product can efficiently and rapidly extract the DNA and the RNA of the plant at the same time, and can independently obtain pure DNA or RNA according to the situation, and the product has high extraction rate, short time consumption and extremely high application value.
In a first aspect of the present invention, there is provided a plant nucleic acid extraction kit comprising: at least one of lysate, neutralization solution, deproteinized solution and rinse solution.
Wherein, the components of the lysate include: tris-HCl, EDTA-2Na, naCl, sodium dodecyl sulfate, polyvinylpyrrolidone K40, beta-mercaptoethanol;
the components of the neutralization solution comprise: sodium acetate, guanidine hydrochloride;
the deproteinized liquid comprises the following components: guanidine hydrochloride, tris-HCl and absolute ethyl alcohol;
the rinse liquid comprises the following components: tris-HCl, naCl, absolute ethanol.
In some embodiments of the invention, the plant nucleic acid extraction kit comprises: at least two of lysate, neutralization solution, deproteinized solution and rinsing solution.
In some embodiments of the invention, the plant nucleic acid extraction kit comprises: at least three of lysate, neutralization solution, deproteinized solution and rinsing solution.
In some embodiments of the invention, the plant nucleic acid extraction kit comprises: a combination of lysate, neutralization solution, deproteinized solution, and rinse solution.
According to a first aspect of the invention, in some embodiments of the invention, the composition of the lysate comprises, in 100 ml_: tris-HCl with a final concentration of 180-220 mM, EDTA-2Na with a final concentration of 90-110 mM, naCl with a final concentration of 550-650 mM, sodium dodecyl sulfate with a final concentration of 1.8-2.2 g, polyvinylpyrrolidone K40 with a final concentration of 2.5-3.5 g and beta-mercaptoethanol with a final concentration of 1.8-2.2 mL.
In some embodiments of the invention, the composition of the lysate, on a 100mL basis, comprises: tris-HCl with a final concentration of 200mM, EDTA-2Na with a final concentration of 100mM, naCl with a final concentration of 600mM, and 2g sodium dodecyl sulfate, 3g polyvinylpyrrolidone K40,2mL beta-mercaptoethanol.
According to a first aspect of the invention, in some embodiments of the invention, the components of the neutralization solution comprise, in 100 mL: sodium acetate with a final concentration of 750-850 mM and guanidine hydrochloride with a final concentration of 4.5-5.5M.
In some embodiments of the invention, the components of the neutralization solution include, in 100 mL: sodium acetate at a final concentration of 800mM and guanidine hydrochloride at a final concentration of 5M.
According to a first aspect of the invention, in some embodiments of the invention, the deproteinized fluid comprises, in 100 ml_: guanidine hydrochloride with the final concentration of 4.5-5.5M, 38-42 mM Tris-HCl and 38-42% absolute ethanol by weight percent.
In some embodiments of the invention, the deproteinized fluid comprises, in 100 ml_: guanidine hydrochloride at a final concentration of 5M, 40mM Tris-HCl,40% absolute ethanol by mass.
According to a first aspect of the invention, in some embodiments of the invention, the rinse solution comprises, in 100 mL: tris-HCl with a final concentration of 2.8-3.2 mM, naCl with a final concentration of 12-18 mM and absolute ethanol with a total mass percentage of 78-82%.
In some embodiments of the invention, the rinse solution comprises, in 100 ml_: tris-HCl with a final concentration of 3mM, 15mM NaCl, absolute ethanol with a total mass percentage of 80%.
According to a first aspect of the present invention, in some embodiments of the present invention, the plant nucleic acid extraction kit comprises at least one of DNase, RNase, and an adsorption column with a silica gel membrane.
In some embodiments of the invention, the plant nucleic acid extraction kit comprises at least two of DNase, RNase, and an adsorption column with a silica gel membrane.
In some embodiments of the invention, the plant nucleic acid extraction kit comprises a combination of DNase, RNase, and an adsorption column with a silica gel membrane.
In some embodiments of the invention, the DNase is selected from DNase I on-column digestion reagents; the adsorption column with the silica gel membrane comprises an RNA purification column and a DNA purification column. In the embodiment of the invention, the adsorption column with the silica gel membrane is a 6-layer RNA purification column.
In some embodiments of the invention, the plant nucleic acid comprises one of plant DNA, plant RNA, or a combination thereof.
In the invention, the extraction and purification mode of the plant nucleic acid extraction kit belongs to column purification by using a silica gel membrane, and can be suitable for extracting DNA and total RNA of various plants, but is not suitable for extracting small RNA (such as siRNA or miRNA extraction).
In a second aspect of the present invention, there is provided a method for extracting a plant nucleic acid, comprising the steps of:
Adding the lysate of the first aspect of the invention into the extracted sample for cracking, then adding the neutralizing solution of the first aspect of the invention, centrifuging to obtain a supernatant, adding an alcohol solvent, and then separating and purifying by using an adsorption column with silica gel films.
In some embodiments of the invention, the alcohol solvent comprises methanol, ethanol. The ratio of the alcohol solvent to the supernatant volume after centrifugation is 0.9-1.1:1.
In some embodiments of the invention, the content ratio of plant material to lysate is 0.1-0.2 g: 500-700 mu L.
In some embodiments of the invention, the plant material to neutralization solution ratio is from 0.1 to 0.2g: 500. Mu.L.
According to a second aspect of the present invention, in some embodiments of the present invention, the separation and purification step of the adsorption column comprises:
After adding the alcohol solvent, transferring the mixture into an adsorption column, centrifuging the mixture, and removing waste liquid; adding deproteinized liquid according to the first aspect of the present invention, centrifuging, and removing waste liquid; adding the rinsing liquid described in the first aspect of the invention, centrifuging, and removing waste liquid; eluting to obtain purified plant nucleic acid.
In some embodiments of the invention, the content ratio of plant material to deproteinized liquid is from 0.1 to 0.2g:600 mul.
In some embodiments of the invention, the content ratio of plant material to rinse liquid is from 0.1 to 0.2g:600 mul.
In some embodiments of the present invention, the extraction method specifically comprises:
(1) Taking plant material, pre-cooling with liquid nitrogen, and grinding to powder. Adding the lysate, and shaking vigorously. And (5) standing at room temperature.
(2) Adding the neutralization solution, centrifuging, and adding the absolute ethyl alcohol with the same volume.
(3) Transferring into adsorption column, centrifuging, and discarding the waste liquid.
(4) Adding the deproteinized solution, centrifuging, and discarding the waste liquid.
(5) Adding the above rinsing liquid, centrifuging, and discarding the waste liquid.
And adding preheated RNase-free water into the central position of a silica gel membrane of the adsorption column for eluting, and centrifuging to obtain a high-concentration plant DNA and total RNA mixture.
The traditional extraction method of the DNA and the total RNA of the plant containing the polysaccharide polyphenol has the defects of complicated steps, multiple repeated operations, long operation time and easiness in causing the degradation of the DNA and the total RNA. According to the method, the DNA and the total RNA are purified by adopting a silica gel membrane adsorption column, and alcohol-soluble impurities such as protein and the like are removed by utilizing deproteinizing liquid and rinsing liquid, so that the DNA and the total RNA with high purity and high concentration can be obtained rapidly according to test requirements, and the DNA and the total RNA can be extracted respectively.
In some embodiments of the invention, the plant nucleic acid comprises one of plant DNA, plant RNA, or a combination thereof.
In some embodiments of the present invention, if DNA purity is to be obtained separately, based on the above method, 2 μl of RNase free DNase (2 μl of RNase per 50 μl of eluate) is added when one eluate is obtained, and then the plant DNA purity is obtained after incubation and re-elution.
In some embodiments of the invention, if RNA purity is to be obtained separately, 50. Mu.L of DNase I working solution (i.e., DNase I digestion reagent on column) is added to the adsorption column prior to adding the rinse solution based on the method described above, and allowed to stand at room temperature for 15 minutes. 600. Mu.L of the deproteinized solution was again added to the column, and the mixture was centrifuged at 12000g for 1min, whereby the waste liquid was discarded. The subsequent steps are the same as the above method.
In a third aspect, the invention provides the use of a plant nucleic acid extraction kit according to the first aspect of the invention in the preparation of a plant nucleic acid extraction product.
According to a third aspect of the present invention, in some embodiments of the present invention, the plant nucleic acid extraction product further comprises at least one of DNase, RNase, and an adsorption column with a silica gel membrane.
In some embodiments of the invention, the plant nucleic acid extraction kit comprises at least two of DNase, RNase, and an adsorption column with a silica gel membrane.
In some embodiments of the invention, the plant nucleic acid extraction kit comprises a combination of DNase, RNase, and an adsorption column with a silica gel membrane.
In some embodiments of the invention, the DNase is selected from DNase I on-column digestion reagents; the adsorption column with the silica gel membrane comprises an RNA purification column and a DNA purification column. In the embodiment of the invention, the adsorption column with the silica gel membrane is a 6-layer RNA purification column.
The beneficial effects of the invention are as follows:
1. The invention provides a kit capable of simultaneously extracting DNA and total RNA of complex plants, which can efficiently and rapidly extract the DNA and the total RNA of the complex plants, can realize single extraction and purification of the DNA and the total RNA according to actual requirements, and has high extraction rate, high extraction speed and low use cost.
2. The invention provides a method for simultaneously extracting DNA and total RNA of complex plants based on the kit, which not only can extract the DNA and RNA of complex plants such as apples, but also can extract the DNA and total RNA of plants in common modes of arabidopsis and tobacco.
3. The extraction method does not use toxic reagents such as phenol, chloroform and the like, is environment-friendly and provides guarantee for the safety of operators.
Drawings
FIG. 1 is an agarose gel electrophoresis of DNA and total RNA from different organs of apple, arabidopsis and tobacco leaves extracted by the kit in the example.
FIG. 2 shows the comparison of the reverse transcription success rate of 6 apple leaf samples extracted by CTAB method with the kit in the example, and using Actin as reference gene.
Detailed Description
In order to make the objects, technical solutions and technical effects of the present invention more clear, the present invention will be described in further detail with reference to the following specific embodiments. It should be understood that the detailed description is presented herein for purposes of illustration only and is not intended to limit the invention.
The experimental materials and reagents used, unless otherwise specified, are those conventionally available commercially.
Product for simultaneously extracting and purifying DNA and RNA of complex plant
In the embodiments of the present invention, the inventors provide a product that can simultaneously extract and purify complex plant DNA and RNA. The product comprises the following components: lysate, neutralization solution, deproteinized solution, and rinsing solution.
Wherein, the total 100mL of the lysate is calculated according to the final concentration, and the components comprise: 200mM Tris-HCl (pH 8.0), 100mM EDTA-2Na (pH 8.0), 600mM NaCl, and 2g/100mL Sodium Dodecyl Sulfate (SDS), 3g/100mL polyvinylpyrrolidone K40 (PVP-40), 2mL/100mL β -mercaptoethanol (pH 8.0).
The total 100mL of the neutralization solution comprises the following components in terms of final concentration: 800mM sodium acetate and 5M guanidine hydrochloride.
The deproteinized solution is 100mL in total, and comprises the following components in terms of final concentration: 5M guanidine hydrochloride, 40mM Tris-HCl (pH 7.0), 40% absolute ethanol (w/w).
The total 100mL of the rinse solution comprises the following components in terms of final concentration: 3mM Tris-HCl (pH 8.0), 15mM NaCl,80% absolute ethanol (w/w).
The product also requires the use of DNase I on-column digestion reagents (available from Edley), RNase (available from TaKaRa) and RNA purification columns (optionally, edley 6-layer RNA purification columns).
The extraction and purification mode of the product belongs to column purification by using a silica gel membrane, and can be suitable for extracting DNA and total RNA of various plants, but is not suitable for extracting small RNA (such as siRNA or miRNA and the like).
Mode of use of the product in the above embodiment
Taking about 0.1-0.2 g of plant material, pre-cooling with liquid nitrogen, and fully grinding into powder. The powder was added to a 2mL centrifuge tube containing no DNase and RNase, 500-700. Mu.L of the above lysate was added, and shaking vigorously was performed for about 1min. Standing at room temperature for 10min to completely defoaming and cracking.
To the lysate was added 500. Mu.L of the above-mentioned neutralization solution, and the mixture was stirred upside down and centrifuged at 14000g for 10min. The supernatant was transferred to a new centrifuge tube without DNase and RNase, and centrifuged again at 14000g for 10min. Transferring the supernatant to a new centrifuge tube without DNase and RNase, slowly adding absolute ethyl alcohol with the same volume as the supernatant, and gently mixing.
Transferring the mixed solution into a DNA/RNA adsorption column (the adsorption column and a collection tube are soaked in 1%diethyl pyrocarbonate (DEPC) solution overnight and dried for use), centrifuging for 1min at 12000g, and discarding the waste liquid. The adding amount of the solution is smaller than the bearing capacity of the adsorption column, and if the volume of the solution exceeds the bearing capacity of the adsorption column, the solution needs to be transferred in multiple times. In this example, the maximum capacity of the column was 700. Mu.L.
600. Mu.L of the deproteinized solution was added to the column, and the mixture was centrifuged at 12000g for 30s, whereby the waste liquid was discarded.
600. Mu.L of the above-mentioned rinse solution was added to the column, and the mixture was centrifuged at 12000g for 30s, whereby the waste liquid was discarded. Repeated 2 times.
The adsorption column was placed back into the collection tube and centrifuged for 2min at 13000g to remove the rinse liquid sufficiently to avoid ethanol residue leading to inhibition of downstream reactions.
Taking out the adsorption column, putting the adsorption column into a new 1.5mL centrifuge tube without DNase and RNase, adding 30-50 mu L of RNase-free water (the RNase-free water is preheated at 70 ℃ to improve the RNA elution amount) at the center of a silica gel membrane of the adsorption column, standing for 2min at room temperature, and centrifuging for 2min with 13000g to obtain a primary eluent.
Repeatedly eluting the primary eluent with RNase-free water to obtain the high-concentration plant DNA and total RNA mixture.
Wherein, if necessary, the DNA pure product is obtained from the single DNA by the following method:
Based on the method, adding 2 mu L of RNase without DNase (2 mu L of RNase is added to each 50 mu L of eluent) into the primary eluent, incubating for 30min at 37 ℃, and repeatedly eluting with RNase-free water to obtain the high-concentration plant DNA pure product.
Wherein, if necessary, the total RNA pure product is further obtained from the single product, the method is as follows:
Based on the above method, 50. Mu.L of DNase I working solution (i.e., DNase I on-column digestion reagent) was added to the adsorption column and allowed to stand at room temperature for 15min before adding the rinse solution. 600. Mu.L of the deproteinized solution was again added to the column, and the mixture was centrifuged at 12000g for 1min, whereby the waste liquid was discarded. The subsequent steps are the same as the above method.
Note that: the working solution is directly dripped on the central position of the silica gel film of the adsorption column, and is not dripped on an O-shaped ring or a column wall of the adsorption column, so that the purity is not reduced.
After discarding the waste liquid, the rinse solution is continuously added into the adsorption column according to the method to continue the subsequent operation. The final product is the high-concentration plant total RNA pure product.
Practical application Effect of the products in the above embodiment
In order to fully explain the effectiveness of the above products, the inventors used the root, stem, leaf, pulp, seed of apple (Malus domestica), leaf of Arabidopsis thaliana (Arabidopsis thaliana) and leaf of tobacco (Nicotiana tabacum) as samples, respectively, and used the above products for DNA and total RNA extraction.
The specific method comprises the following steps:
Fresh apple root, stem, leaf, pulp and seed are respectively taken, 0.2g of arabidopsis leaf and tobacco leaf are respectively put into liquid nitrogen for quick freezing, fully ground into powder and respectively put into different 2mL centrifuge tubes.
700 Mu L of the lysate is added into a centrifuge tube, vortex oscillation is carried out, the lysate is fully and uniformly mixed, and the mixture is kept stand for 10min at room temperature.
500. Mu.L of the above-mentioned neutralization solution was added, and the mixture was stirred upside down and centrifuged at 14000g for 10min. All supernatants were transferred as much as possible to new 2mL centrifuge tubes and the centrifugation was repeated once at 14000 g.
Taking supernatant, slowly adding absolute ethanol with the same volume as the supernatant, gently mixing, transferring into a silica gel adsorption column (Aidelai 6-layer RNA purification column), centrifuging for 1min at 12000g, and discarding the waste liquid.
To the column, 500. Mu.L of the deproteinized solution was added, and the mixture was centrifuged at 12000g for 30s, whereby the waste liquid was discarded.
600. Mu.L of the above-mentioned rinse solution was added to the column, and the mixture was centrifuged at 12000g for 30s, whereby the waste liquid was discarded. Again 13000g of the tube was centrifuged for 2min.
Taking out the adsorption column, putting the adsorption column into a new 1.5mL centrifuge tube, suspending and dripping 30 mu L of RNase-free water preheated at 70 ℃ into the middle part of a silica gel film of the adsorption column, standing for 2min at room temperature, and centrifuging for 2min with 13000g to obtain a primary eluent.
And (3) suspending and dripping the primary eluent obtained at the bottom of the centrifuge tube in the middle of the silica gel membrane of the adsorption column, and centrifuging 13000g for 2min to obtain purified DNA and total RNA extracts.
Three groups of samples were repeated.
The purified DNA and total RNA extracts were identified using agarose gel electrophoresis.
As shown in FIG. 1, the product can be used for accurately extracting DNA and total RNA of each plant sample, the extraction effect is stable, and the brightness of partial strips is different due to different loading amounts and is only used for displaying the integrity of the extracted DNA and RNA. Therefore, the product provided in the embodiment can simultaneously and rapidly extract DNA and total RNA in different tissues of complex plants and common mode plants, selectively retain DNA or total RNA according to test requirements, is convenient and rapid, is economical and convenient, and has important application value for basic test requirements of plant molecular biology.
The effect of the product in the above examples was compared with that of the conventional extraction method
To fully illustrate the advantages of the products in the above examples over prior art extraction techniques, the inventors compared using the CTAB method (RNA or DNA extraction) and TRIZOL method (RNA extraction) as controls, which are conventional in the art.
Specific extraction methods of the CTAB method and the TRIZOL method are carried out by referring to a conventional test manual in the field, and an extracted sample is selected as apple leaves with equal quality. Each of the 3 groups was repeated.
The results are shown in tables 1 to 2 and FIG. 2.
Table 1 basic characteristic comparison of different methods
Extraction method |
CTAB method |
TRIZOL process |
Product in examples |
Extraction type |
RNA/DNA extraction |
RNA extraction |
DNA/RNA extraction |
Extraction time |
4h |
2h |
40min |
Cost of single sample (Yuan) |
2 |
3 |
1.2 |
Extraction range |
All plant samples |
Simple plant sample |
All plant samples |
TABLE 2 comparison of the extraction effects of the different methods
As can be seen from a combination of tables 1 to 2 and fig. 2, the products of the above examples have significant advantages in terms of extraction time, extraction cost and applicability over conventional nucleic acid extraction methods in the art. In addition, compared with the CTAB method (but note that the CTAB method is not used for simultaneously extracting the total RNA and the DNA) which can also extract the total RNA and the DNA, the extraction rate and the extraction purity of the product in the embodiment are obviously higher than those of the CTAB method, and the highest extraction amount can be 2.6 times of that of the CTAB method, so that the method has obvious technical advantages.
The above examples are preferred embodiments of the present invention, but the embodiments of the present invention are not limited to the above examples, and any other changes, modifications, substitutions, combinations, and simplifications that do not depart from the spirit and principle of the present invention should be made in the equivalent manner, and the embodiments are included in the protection scope of the present invention.