WO2021042323A1 - Method for extracting heavy oil genomic deoxyribonucleic acid, and kit and application thereof - Google Patents
Method for extracting heavy oil genomic deoxyribonucleic acid, and kit and application thereof Download PDFInfo
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- the invention belongs to the technical field of microbial geology, and relates to a method, kit and application for extracting heavy oil genome deoxyribonucleic acid (DNA).
- DNA heavy oil genome deoxyribonucleic acid
- °API ⁇ 32 °API is 20-30( Is 0.8654-0.9340), °API is 10-20( 0.9340-1) and °API ⁇ 10( ), respectively indicate light crude oil, medium crude oil, heavy crude oil and extra-heavy crude oil.
- crude oil with a viscosity> 50-10000 mPa ⁇ s and a relative density greater than 0.9200 g ⁇ cm -3 (20°C) is an ordinary heavy oil; viscosity> 10000-50000, the crude oil with relative density greater than 0.9500g ⁇ cm -3 (20°C) is extra-heavy oil; the crude oil with viscosity greater than 50000 and relative density greater than 0.9800g ⁇ cm -3 (20°C) is super-heavy oil.
- High viscosity and high density are the most important characteristics of heavy oil, as well as the main indicators that distinguish it from ordinary thin oil.
- the purpose of the present invention is to provide a kit for extracting heavy oil genome deoxyribonucleic acid and a method for extracting heavy oil genome deoxyribonucleic acid using the kit;
- the purpose of the present invention is also to provide the application of the kit in the extraction of heavy oil genome deoxyribonucleic acid.
- the present invention improves cell lysis and DNA extraction liquid components, increases the effectiveness of heavy oil DNA extraction; simplifies and shortens some extraction steps and time such as shaking and thermal reaction, and enhances DNA extraction efficiency; at the same time, it improves the environmental protection of the pretreatment process and uses green Reagents replace conventional organic reagents such as petroleum ether and isooctane.
- the present invention provides a method for extracting heavy oil genome deoxyribonucleic acid, which comprises the following steps:
- Step 1 Add snailase, prionase K, DNA extract containing Triton X-100 (Triton X-100), and decontamination solution to the heavy oil to lyse cells;
- Step 2 After standing still, centrifugation removes the sediment to obtain the upper layer liquid, and the prion precipitation liquid is added to the upper layer liquid to remove the organic macromolecular components, and the upper layer liquid is collected by centrifugation;
- Step 3 Transfer the upper layer collected by centrifugation to the adsorption column for adsorption, and then rinse with the rinsing solution and elution with the DNA elution solution to collect the heavy oil genome deoxyribonucleic acid.
- Triton X-100 is used, which can effectively dissolve cell membranes and improve the quality of DNA amplified by polymerase chain reaction after DNA extraction; because the heavy oil system is complex and the extraction is the total genome Therefore, the use of the snail enzyme of the present invention is more conducive to the breaking of fungal cells.
- the step 1 further includes a step of pre-treating the heavy oil.
- the pre-processing is to add a pretreatment reagent to the heavy oil for treatment to obtain the pre-treated heavy oil.
- ⁇ -valerolactone is used as a pretreatment reagent.
- ⁇ -valerolactone is a green and non-toxic chemical that can reduce oil viscosity and is easy to collect microorganisms.
- the method specifically includes the following steps:
- Step 1 Add 10-20 ⁇ L of snail enzyme to every 300-500mg of heavy oil, shake at 30-37°C, 90-120rpm for 20-30min, and then add 10-20 ⁇ L of prionase K and 1-2mL in sequence
- the DNA extract containing Triton X-100 is shaken at 30-37°C and 90-120 rpm for 20-30 minutes, and finally 100-200 ⁇ L of decontamination solution is added, and placed at 50-65°C for 30-60 minutes;
- Step 2 Centrifuge at room temperature and 8000rpm (7870.72 ⁇ g) for 2-3min to remove the precipitate to obtain the supernatant, transfer the supernatant to a new centrifuge tube, add the same volume of prion precipitation to the supernatant, and Centrifuge for 2-3min at 8000-10000rpm, transfer the upper layer to a new centrifuge tube, repeat the operation of adding the prion precipitation solution once, and collect the upper layer by centrifugation;
- Step 3 Transfer the upper layer collected by centrifugation to the adsorption column for adsorption, put the adsorption column into the collection tube, centrifuge at 10000-12000rpm (12298-17709.12 ⁇ g) for 1-2min to remove the waste liquid, and then transfer it to the adsorption column Add pre-cooled rinsing solution to rinse, centrifuge at 10000-12000 rpm for 1 min to remove waste liquid, repeat the rinsing step once; place the adsorption column at room temperature for 10-20 minutes to dry the residual rinsing in the adsorption membrane in the adsorption column Finally, drop the DNA eluate into the middle of the adsorption membrane in the adsorption column, let it stand at room temperature for 5-10 minutes, centrifuge at 10000-12000 rpm for 2-3 minutes, and collect the centrifugal supernatant to be thick oil Genomic DNA.
- the step one further includes the step of pretreating the heavy oil, the pretreatment is to add 150-250 ⁇ L of pretreatment reagent to every 300-500 mg of heavy oil, and vortex to mix. After homogenization, the lower layer liquid is removed to obtain the pretreated heavy oil.
- the mass volume concentration of the snail enzyme is 10-20 mg/mL (a snail enzyme aqueous solution).
- the pretreatment reagent is ⁇ -valerolactone.
- the mass volume concentration of prion K is 5-20 mg/mL (aqueous solution of prion K).
- each liter of DNA extraction solution containing Triton X-100 includes 50-200mmol of Trishydroxymethylaminomethane hydrochloride, 50-200mmol of Triton X-100, 50 -200mmol of Na 3 PO 4 and 0.5-2mol of NaCl.
- the decontamination solution is a sodium deoxycholate (SDC) solution with a mass volume concentration of 50-100 mg/mL (aqueous solution of sodium deoxycholate).
- SDC sodium deoxycholate
- a solution of sodium deoxycholate (SDC) is used as the decontamination solution.
- the sodium deoxycholate of the present invention does not have a polar head group, and its polar groups are distributed in various parts of the molecular chain.
- the sodium deoxycholate of the present invention has better solubility and is easier to prepare, and it can be used with other extraction reagents of the present invention to make the extraction effect of heavy oil total DNA better.
- the prion precipitation liquid is a mixed liquid of phenol, chloroform and isoamyl alcohol, and the mixing volume ratio of phenol, chloroform and isoamyl alcohol is (24-26):(23-25):( 0.5-1.5).
- the rinsing liquid is chromatographically pure ethanol, and the volume concentration of the ethanol is 70%.
- the DNA eluate is sterile ultrapure water.
- the adsorption membrane used in the adsorption column is a silica gel membrane.
- the present invention also provides a kit for extracting heavy oil genome deoxyribonucleic acid.
- the kit includes: snailase, prionase K, DNA extraction solution containing Triton X-100, decontamination solution, prion Precipitation liquid and adsorption column.
- the kit further includes a pretreatment reagent, and the pretreatment reagent is ⁇ -valerolactone.
- the kit further includes a rinse solution and a DNA elution solution.
- the kit further includes glass beads, and the glass beads are monodisperse glass beads with a particle size of 1.5-2.0 mm.
- the present invention also provides the application of the above kit in the extraction of heavy oil genome deoxyribonucleic acid.
- the method for extracting heavy oil genomic DNA has more advantages for the extraction of heavy oil.
- the present invention can directly extract heavy oil as it is, or select ⁇ -valerolactone as the pretreatment reagent according to the oil condition.
- the pretreatment reagent is a green reagent, which is more environmentally friendly than using isooctane, petroleum ether and other reagents for pretreatment.
- the present invention is specific to heavy oil samples.
- the combined application of snail enzyme, Triton X-100-containing extract and SDC solution has better cell lysis and decontamination of microorganisms in high-density and viscous oils. effect.
- the present invention simplifies the extraction steps, and also shortens the extraction time.
- the entire extraction process can be completed within one and a half hours at the fastest, and the extraction concentration is also high, the amount of dimer produced is minimal, and the subsequent qPCR detection, high Throughput sequencing and metagenomic analysis.
- the kit simplifies the operation method, and can be conveniently used for the extraction of heavy oil genomic DNA to achieve the purpose of efficiently extracting the total deoxyribonucleic acid in the heavy oil.
- the present invention has a shorter time (a savings of more than 100 minutes compared to the same period last year), a better effect, and is more environmentally friendly and economical.
- Figure 1 is an electrophoresis chart of PCR product amplification of genomic DNA extracted in Example 1 of the present invention (wherein: 1 to 4 are parallel samples of the same oil sample; M is a molecular weight marker Marker);
- Figure 2 is the electrophoresis pattern of PCR product amplification of genomic DNA extracted in Examples 2 and 3 of the present invention (wherein: 5 to 6 are parallel samples of the same oil sample in Example 2; 7-8 are the same oil sample in Example 3 Parallel samples; M is the molecular weight marker Marker).
- Fig. 3 is an electrophoresis pattern of PCR product amplification of genomic DNA extracted in Example 4 of the present invention (a, 9 to 10 in Fig. 3 are parallel samples of the same oil sample in Example 4) and the genome extracted in Comparative Example 2 of the present invention
- the electrophoresis patterns of DNA PCR product amplification (b, 11 to 12 in Fig. 3 are the parallel samples of the same oil sample in Comparative Example 2; M is the comparison chart of the molecular weight marker Marker).
- a nucleic acid prion detector was used to determine the concentration and purity of the DNA extract (A260/A280), and the concentration of the DNA extract was determined in combination with the amount of Qubit.
- This embodiment provides a kit for extracting heavy oil genome deoxyribonucleic acid.
- the kit includes: pretreatment reagent, glass beads, snail enzyme, prionase K, DNA extract containing Triton X-100, and decontamination
- pretreatment reagent glass beads
- snail enzyme prionase K
- DNA extract containing Triton X-100 DNA extract containing Triton X-100
- decontamination The components and materials of liquid, prion precipitation, rinse, DNA eluate, adsorption column, collection tube, centrifuge tube, etc.
- the content and material requirements of each component are as follows:
- Pretreatment reagent ⁇ -valerolactone
- Glass beads 20 monodisperse glass beads with a particle size of 1.5mm;
- Snail enzyme mass volume concentration 20mg/mL
- Prionase K mass volume concentration 20mg/mL
- Extraction solution (pH8.0): Each liter of extraction solution contains 100mmol of tris-hydroxymethylaminomethane hydrochloride (Tris-HCl), 100mmol of Triton X-100 (Triton-X), 100mmol of Na 3 PO 4 and 1.5 mol NaCl;
- Decontamination solution 100mg/mL SDC solution with mass volume concentration
- Prion precipitation solution a mixed solvent of phenol/chloroform/isoamyl alcohol with a volume ratio of 25:24:1;
- Rinsing solution chromatographically pure grade ethanol with a volume concentration of 70%
- DNA eluate sterile ultrapure water
- Adsorption column contains silica gel adsorption membrane
- This implementation also provides a method for extracting heavy oil genome deoxyribonucleic acid, which includes the following steps:
- Step 1 Take 500mg of heavy oil, add 200-300 ⁇ L of ⁇ -valerolactone, vortex and mix, remove the lower layer to obtain pretreated heavy oil;
- Step two take the pretreated heavy oil into a centrifuge tube, add 10-20 ⁇ L of snailase, shake at 37°C, 120rpm for 30min, and then add 10-20 ⁇ L of prion K and 1-2mL of snailase in turn Pass the DNA extraction solution of X-100, shake at 37°C and 120rpm for 30min, finally add 100-200 ⁇ L of decontamination solution, place it at 65°C for 1h, and centrifuge at room temperature and 6000-12000rpm for 3min to remove the precipitate to obtain the supernatant , Transfer the upper layer to a new centrifuge tube, add the same volume of prion precipitation to the upper layer, centrifuge at 6000-12000 rpm for 3 minutes, transfer the upper layer to a new centrifuge tube, repeat adding the prion precipitation solution Operate once and collect the supernatant by centrifugation;
- Step 3 Transfer 500-1000 ⁇ L of the upper layer liquid collected by centrifugation to the adsorption column for adsorption, put the adsorption column into the collection tube, centrifuge at 6000-12000 rpm for 1 min to remove the waste liquid, repeat this step until the upper layer has mostly passed Adsorption column filtration (note: the prion precipitation layer cannot be absorbed when sucking the upper layer liquid, so keep the upper layer liquid with a thickness of 3-5mm above the prion precipitation layer), and then add 500-1000 ⁇ L low-temperature pre-cooled rinsing solution to the adsorption column for rinsing.
- DNA heavy oil genome deoxyribonucleic acid
- the forward primer (Primer1) is 515F: 5'-GTGYCAGCMGCCGCGGTAA-3',
- the reverse primer (Primer2) is 806R: 5'-GGACTACVSGGGTATCTAAT-3'.
- Y, M, V, S are degenerate bases.
- Y represents that the base can be selected from C or T;
- M represents that the base can be selected from A or C
- V represents that the base can be selected from A, C or G;
- S represents that the base can be selected from C or G;
- the base sequence of the forward primer can be selected from one of the following sequences:
- the base sequence of the reverse primer can be selected from one of the following sequences:
- the amplified products were electrophoresed on a 1% agarose gel with a voltage of 100V for 45 minutes and photographed with an ultraviolet gel imaging system.
- L2YHC23-1 and L2YHC23-2 are a set of parallel samples, and L2YHC23p is the average value and standard deviation of the oil sample (Table 1).
- the DNA extracted in Example 1 is relatively pure, the ratio of A260/A280 is about 1.6, and the concentration is also relatively high (Table 1).
- No. 1 and No. 2 electrophoresis (Figure 1) showed that the DNA amplification product had a single and clear band. It can be seen that the DNA extracted by the present invention has a better effect.
- the pretreatment method is the same as in Example 1, add 200-300 ⁇ L of ⁇ -valerolactone, vortex and mix, remove the lower layer to obtain the pretreatment liquid, and the rest of the extraction steps follow the QIAGEN kit method get on.
- L2YHC23-3 and L2YHC23-4 are a set of parallel samples, and L2YHC23p is the average and standard deviation of the oil sample (Table 2).
- the purity and concentration of the DNA extracted by the QIAGEN kit method (Table 2) are lower than those of the method of the present invention (Example 1), and the difference seems to be small.
- subsequent sequencing shows that only the method of the present invention can be used for subsequent experiments.
- Example 1 The only difference between this example and Example 1 is the lack of step one, that is, no pretreatment reagent ( ⁇ -valerolactone) is used, and heavy oil is directly used for extraction, and the rest of the operations are completely the same.
- L2YHC23-5 and L2YHC23-6 are a set of parallel samples, and L2YHC23p is the average value and standard deviation of the oil sample (Table 3).
- the extraction results and verification results show that the concentration of DNA extracted by the present invention is relatively high (Table 3), and the electrophoresis bands No. 5 and No. 6 ( Figure 2) are single and clear, indicating that the heavy oil DNA extraction effect is better.
- Example 2 Compared with Example 1, this example omitted step one and directly used heavy oil for extraction.
- the specific process is as follows: take 500 mg of heavy oil in a centrifuge tube, add 10-20 ⁇ L of snail enzyme, and then add 10-20 ⁇ L of Prion K and 1-2 mL of DNA extract containing Triton X-100, finally add 100-200 ⁇ L of decontamination solution, place it at 65°C for 1 h, and centrifuge at room temperature and 8000 rpm for 3 min to remove the precipitate to obtain the upper layer.
- L2YHC23-7 and L2YHC23-8 are a set of parallel samples, and L2YHC23p is the average value and standard deviation of the oil sample (Table 4).
- the extraction results and verification results show that the concentration of DNA extracted by the present invention is higher (Table 4), and the electrophoresis bands No. 7 and No. 8 ( Figure 2) are the clearest and brightest, indicating that the heavy oil DNA extraction effect is better.
- Example 3 uses the same heavy oil (different storage conditions after collection), and the dosage is exactly the same as the experimental operation.
- L2YHC23-9 and L2YHC23-10 are a set of parallel samples, and L2YHC23p is the average value and standard deviation of the oil sample (Table 5).
- the extraction results and verification results show that the concentration and purity of the DNA extracted by the present invention are higher (Table 5), and the electrophoresis bands No. 9 and No. 10 (a in Fig. 3) are clearer and brighter, indicating that the extraction effect of heavy oil DNA is better.
- Table 5 The extraction results and verification results show that the concentration and purity of the DNA extracted by the present invention are higher (Table 5), and the electrophoresis bands No. 9 and No. 10 (a in Fig. 3) are clearer and brighter, indicating that the extraction effect of heavy oil DNA is better.
- this comparative example 2 uses the same heavy oil, and the extraction method refers to the method of invention patent ZL201710116846.5.
- L2YHC23-11 and L2YHC23-12 are a set of parallel samples.
- L2YHC23p is the average and standard deviation of the oil sample (Table 6). The extraction and verification results show that the concentration and purity of DNA extracted by this method are higher than those of the method of the present invention (implementation).
- Example 4) is low (Table 6), and the electrophoretic bands No. 11 and No. 12 (b in Fig. 3) are not as bright as the method of the invention (a in Fig. 3), indicating that the extraction effect of the invention is better.
- the application of the present invention takes less time than our previous invention to extract DNA, and can be completed within 90 minutes at the fastest, and can save at least 100 minutes compared with the previous invention.
- the present invention does not use isooctane and other organic reagents in the pretreatment process, which is better than the previous invention. More environmentally friendly.
- the genomic DNA extracted by the method of the present invention can meet the analysis requirements of subsequent qPCR detection, high-throughput sequencing and metagenomics.
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Abstract
Provided are a method for extracting heavy oil genomic deoxyribonucleic acid, and a kit and an application thereof. The kit comprises: a snail enzyme, a prion enzyme K, a DNA extraction solution containing Triton X-100, a decontamination solution, a prion precipitation solution and an adsorption column. The described method is mainly for high-density and high-viscosity oils, and combines the application of a snail enzyme, an extraction solution containing Triton X-100 and an SDC solution. The described kit can be applied to the extraction of heavy oil genomic DNA.
Description
本发明属于微生物地质学技术领域,涉及一种提取稠油基因组脱氧核糖核酸(DNA)的方法及试剂盒和应用。The invention belongs to the technical field of microbial geology, and relates to a method, kit and application for extracting heavy oil genome deoxyribonucleic acid (DNA).
国际上常用°API≥32
°API为20-30(
为0.8654-0.9340),°API为10-20(
为0.9340-1)及°API≤10(
),分别表示轻质原油,中质原油,重质原油及特重原油。参照中国石油天然气行业标准《油藏分类》(SY/T 6169-1995),粘度>50-10000mPa·s,相对密度大于0.9200g·cm
-3(20℃)的原油为普通稠油;粘度>10000-50000,相对密度大于0.9500g·cm
-3(20℃)的原油为特稠油;粘度>50000,相对密度大于0.9800g·cm
-3(20℃)的原油为超稠油。高粘度和高密度是稠油最主要的特征,也是区别与普通稀油的主要指标。由于稠油非烃、沥青质和其它组分含量高,影响预处理过程生物量的收集以及后续的DNA提取的干扰,进而增大DNA提取难度,所以选择更具针对性的预处理方式和细胞裂解方式十分重要。目前,已报道过关于油藏样品DNA的提取方法,但未见有对稠油的报道。
Commonly used internationally °API≥32 °API is 20-30( Is 0.8654-0.9340), °API is 10-20( 0.9340-1) and °API≤10( ), respectively indicate light crude oil, medium crude oil, heavy crude oil and extra-heavy crude oil. According to China’s oil and natural gas industry standard "Reservoir Classification" (SY/T 6169-1995), crude oil with a viscosity> 50-10000 mPa·s and a relative density greater than 0.9200 g·cm -3 (20°C) is an ordinary heavy oil; viscosity> 10000-50000, the crude oil with relative density greater than 0.9500g·cm -3 (20°C) is extra-heavy oil; the crude oil with viscosity greater than 50000 and relative density greater than 0.9800g·cm -3 (20°C) is super-heavy oil. High viscosity and high density are the most important characteristics of heavy oil, as well as the main indicators that distinguish it from ordinary thin oil. Due to the high content of non-hydrocarbons, asphaltenes and other components in heavy oil, which affects the collection of biomass during the pretreatment process and the interference of subsequent DNA extraction, which in turn increases the difficulty of DNA extraction, more targeted pretreatment methods and cells are selected. The method of cracking is very important. At present, there have been reports on methods for extracting DNA from reservoir samples, but no reports on heavy oil have been seen.
发明内容Summary of the invention
为了克服上述现有技术的不足,进一步增强稠油DNA提取效果,本发明的目的在于提供一种提取稠油基因组脱氧核糖核酸的试剂盒以及利用该试剂盒提取稠油基因组脱氧核糖核酸的方法;本发明的目的还在于提供该试剂盒在稠油基因组脱氧核糖核酸提取中的应用。本发明改善细胞裂解和DNA提取液成分,增加稠油DNA提取的有效性;简化和缩短振荡、热反应等部分提取步骤和时间,增强DNA提取效率;同时改善预处理过程的环保性,使用绿色试剂替代常规的石油醚、异辛烷等有机试剂。In order to overcome the above shortcomings of the prior art and further enhance the effect of heavy oil DNA extraction, the purpose of the present invention is to provide a kit for extracting heavy oil genome deoxyribonucleic acid and a method for extracting heavy oil genome deoxyribonucleic acid using the kit; The purpose of the present invention is also to provide the application of the kit in the extraction of heavy oil genome deoxyribonucleic acid. The present invention improves cell lysis and DNA extraction liquid components, increases the effectiveness of heavy oil DNA extraction; simplifies and shortens some extraction steps and time such as shaking and thermal reaction, and enhances DNA extraction efficiency; at the same time, it improves the environmental protection of the pretreatment process and uses green Reagents replace conventional organic reagents such as petroleum ether and isooctane.
本发明的目的通过以下技术方案得以实现:The purpose of the present invention is achieved through the following technical solutions:
一方面,本发明提供一种提取稠油基因组脱氧核糖核酸的方法,其包括以下步骤:In one aspect, the present invention provides a method for extracting heavy oil genome deoxyribonucleic acid, which comprises the following steps:
步骤一,向稠油中加入蜗牛酶、朊酶K、含有曲拉通X-100(Triton X-100)的DNA提取液、去污液进行裂解细胞;Step 1: Add snailase, prionase K, DNA extract containing Triton X-100 (Triton X-100), and decontamination solution to the heavy oil to lyse cells;
步骤二,静置后离心去除沉淀获得上层液,并向上层液中加入朊沉淀液去除有机大 分子组分,离心收集上层液;Step 2: After standing still, centrifugation removes the sediment to obtain the upper layer liquid, and the prion precipitation liquid is added to the upper layer liquid to remove the organic macromolecular components, and the upper layer liquid is collected by centrifugation;
步骤三,将离心收集的上层液转移至吸附柱中进行吸附,然后通过漂洗液漂洗和DNA洗脱液洗脱,收集得到稠油基因组脱氧核糖核酸。Step 3: Transfer the upper layer collected by centrifugation to the adsorption column for adsorption, and then rinse with the rinsing solution and elution with the DNA elution solution to collect the heavy oil genome deoxyribonucleic acid.
本发明的方法中,采用的是含有曲拉通X-100,其能够有效的溶解细胞膜,改进提取DNA后聚合酶链反应扩增DNA的质量;由于稠油体系复杂,并且提取为总的基因组,采用本发明的蜗牛酶更有利于真菌细胞的破碎。In the method of the present invention, Triton X-100 is used, which can effectively dissolve cell membranes and improve the quality of DNA amplified by polymerase chain reaction after DNA extraction; because the heavy oil system is complex and the extraction is the total genome Therefore, the use of the snail enzyme of the present invention is more conducive to the breaking of fungal cells.
上述的方法中,优选地,所述步骤一前还包括对稠油进行预处理的步骤,所述预处理是向稠油中加入预处理试剂进行处理,获得预处理后的稠油。In the above method, preferably, the step 1 further includes a step of pre-treating the heavy oil. The pre-processing is to add a pretreatment reagent to the heavy oil for treatment to obtain the pre-treated heavy oil.
本发明的方法中,采取γ-戊内酯作为预处理试剂,γ-戊内酯不同于异辛烷,是一种绿色、无毒的化学品,可以降低油品粘度,易于微生物的收集。In the method of the present invention, γ-valerolactone is used as a pretreatment reagent. Different from isooctane, γ-valerolactone is a green and non-toxic chemical that can reduce oil viscosity and is easy to collect microorganisms.
上述的方法中,优选地,该方法具体包括以下步骤:In the above method, preferably, the method specifically includes the following steps:
步骤一,向每300-500mg的稠油中加入10-20μL的蜗牛酶,于30-37℃、90-120rpm下振荡20-30min,然后再依次加入10-20μL的朊酶K和1-2mL含有曲拉通X-100的DNA提取液,于30-37℃、90-120rpm下振荡20-30min,最后加入100-200μL的去污液,50-65℃下放置30-60min;Step 1: Add 10-20μL of snail enzyme to every 300-500mg of heavy oil, shake at 30-37℃, 90-120rpm for 20-30min, and then add 10-20μL of prionase K and 1-2mL in sequence The DNA extract containing Triton X-100 is shaken at 30-37°C and 90-120 rpm for 20-30 minutes, and finally 100-200 μL of decontamination solution is added, and placed at 50-65°C for 30-60 minutes;
或者,直接向稠油中依次加入10-20μL的蜗牛酶、10-20μL的朊酶K、1-2mL含有曲拉通X-100、100-200μL去污液,50-65℃下放置30-60min;Or, directly add 10-20μL of snailase, 10-20μL of prionase K, 1-2mL containing Triton X-100, 100-200μL of decontamination solution to the heavy oil, and place it at 50-65℃ for 30- 60min;
步骤二,在室温、8000rpm(7870.72×g)条件下离心2-3min去除沉淀获得上层液,转移上层液于新的离心管中,向上层液中加入与上层液等体积的朊沉淀液,于8000-10000rpm条件下离心2-3min,转移上层液于新的离心管中,重复加入朊沉淀液操作一次,离心收集上层液;Step 2: Centrifuge at room temperature and 8000rpm (7870.72×g) for 2-3min to remove the precipitate to obtain the supernatant, transfer the supernatant to a new centrifuge tube, add the same volume of prion precipitation to the supernatant, and Centrifuge for 2-3min at 8000-10000rpm, transfer the upper layer to a new centrifuge tube, repeat the operation of adding the prion precipitation solution once, and collect the upper layer by centrifugation;
步骤三,将离心收集的上层液转移至吸附柱中进行吸附,吸附柱放入收集管中,于10000-12000rpm(12298-17709.12×g)条件下离心1-2min去除废液,接着向吸附柱中加入预冷的漂洗液进行漂洗,于10000-12000rpm条件下离心1min去除废液,重复漂洗步骤一次;将吸附柱于室温下放置10-20min,以晾干吸附柱中吸附膜中残余的漂洗液;最后向吸附柱中的吸附膜的中间部位悬空滴加DNA洗脱液,室温下静置5-10min,于10000-12000rpm条件下离心2-3min,收集离心后的上层液即为稠油基因组脱氧核糖核酸。Step 3: Transfer the upper layer collected by centrifugation to the adsorption column for adsorption, put the adsorption column into the collection tube, centrifuge at 10000-12000rpm (12298-17709.12×g) for 1-2min to remove the waste liquid, and then transfer it to the adsorption column Add pre-cooled rinsing solution to rinse, centrifuge at 10000-12000 rpm for 1 min to remove waste liquid, repeat the rinsing step once; place the adsorption column at room temperature for 10-20 minutes to dry the residual rinsing in the adsorption membrane in the adsorption column Finally, drop the DNA eluate into the middle of the adsorption membrane in the adsorption column, let it stand at room temperature for 5-10 minutes, centrifuge at 10000-12000 rpm for 2-3 minutes, and collect the centrifugal supernatant to be thick oil Genomic DNA.
上述的方法中,优选地,所述步骤一前还包括对稠油进行预处理的步骤,所述预处理是向每300-500mg的稠油中加入150-250μL的预处理试剂,涡旋混匀后去除下层液, 得到预处理后的稠油。In the above method, preferably, the step one further includes the step of pretreating the heavy oil, the pretreatment is to add 150-250 μL of pretreatment reagent to every 300-500 mg of heavy oil, and vortex to mix. After homogenization, the lower layer liquid is removed to obtain the pretreated heavy oil.
上述的方法中,优选地,所述蜗牛酶的质量体积浓度为10-20mg/mL(蜗牛酶水溶液)。In the above method, preferably, the mass volume concentration of the snail enzyme is 10-20 mg/mL (a snail enzyme aqueous solution).
上述的方法中,优选地,所述预处理的试剂为γ-戊内酯。In the above method, preferably, the pretreatment reagent is γ-valerolactone.
上述的方法中,优选地,所述朊酶K的质量体积浓度为5-20mg/mL(朊酶K的水溶液)。In the above method, preferably, the mass volume concentration of prion K is 5-20 mg/mL (aqueous solution of prion K).
上述的方法中,优选地,所述含有曲拉通X-100的每升DNA提取液包括50-200mmol的三羟甲基氨基甲烷盐酸盐、50-200mmol的曲拉通X-100、50-200mmol的Na
3PO
4和0.5-2mol的NaCl。
In the above method, preferably, each liter of DNA extraction solution containing Triton X-100 includes 50-200mmol of Trishydroxymethylaminomethane hydrochloride, 50-200mmol of Triton X-100, 50 -200mmol of Na 3 PO 4 and 0.5-2mol of NaCl.
上述的方法中,优选地,所述去污液为脱氧胆酸钠(SDC)溶液,其质量体积浓度为50-100mg/mL(脱氧胆酸钠的水溶液)。In the above method, preferably, the decontamination solution is a sodium deoxycholate (SDC) solution with a mass volume concentration of 50-100 mg/mL (aqueous solution of sodium deoxycholate).
本发明的方法中,采取脱氧胆酸钠(SDC)溶液作为去污液,本发明的脱氧胆酸钠没有一个极性头端基团,其极性基团分布于分子链的各个部分,相比常规的阴离子去污剂,本发明的脱氧胆酸钠溶解性更佳,配制更容易,搭配本发明其他提取试剂能够使得稠油总DNA提取效果更佳。In the method of the present invention, a solution of sodium deoxycholate (SDC) is used as the decontamination solution. The sodium deoxycholate of the present invention does not have a polar head group, and its polar groups are distributed in various parts of the molecular chain. Compared with conventional anionic detergents, the sodium deoxycholate of the present invention has better solubility and is easier to prepare, and it can be used with other extraction reagents of the present invention to make the extraction effect of heavy oil total DNA better.
上述的方法中,优选地,所述朊沉淀液为苯酚、氯仿和异戊醇的混合液,苯酚、氯仿和异戊醇的混合体积比为(24-26):(23-25):(0.5-1.5)。In the above method, preferably, the prion precipitation liquid is a mixed liquid of phenol, chloroform and isoamyl alcohol, and the mixing volume ratio of phenol, chloroform and isoamyl alcohol is (24-26):(23-25):( 0.5-1.5).
上述的方法中,优选地,所述漂洗液为色谱纯级的乙醇,所述乙醇的体积浓度为70%。In the above method, preferably, the rinsing liquid is chromatographically pure ethanol, and the volume concentration of the ethanol is 70%.
上述的方法中,优选地,所述DNA洗脱液为无菌超纯水。In the above method, preferably, the DNA eluate is sterile ultrapure water.
上述的方法中,优选地,所述吸附柱中采用的吸附膜为硅胶膜。In the above method, preferably, the adsorption membrane used in the adsorption column is a silica gel membrane.
另一方面,本发明还提供一种提取稠油基因组脱氧核糖核酸的试剂盒,该试剂盒包括:蜗牛酶、朊酶K、含有曲拉通X-100的DNA提取液、去污液、朊沉淀液和吸附柱。On the other hand, the present invention also provides a kit for extracting heavy oil genome deoxyribonucleic acid. The kit includes: snailase, prionase K, DNA extraction solution containing Triton X-100, decontamination solution, prion Precipitation liquid and adsorption column.
上述的试剂盒中,优选地,该试剂盒还包括预处理试剂,所述预处理试剂为γ-戊内酯。In the above kit, preferably, the kit further includes a pretreatment reagent, and the pretreatment reagent is γ-valerolactone.
上述的试剂盒中,优选地,该试剂盒还包括漂洗液和DNA洗脱液。In the above kit, preferably, the kit further includes a rinse solution and a DNA elution solution.
上述的试剂盒中,优选地,该试剂盒还包括玻璃珠,所述玻璃珠是粒径为1.5-2.0mm的单分散玻璃珠。In the above kit, preferably, the kit further includes glass beads, and the glass beads are monodisperse glass beads with a particle size of 1.5-2.0 mm.
再一方面,本发明还提供上述试剂盒在稠油基因组脱氧核糖核酸提取中的应用。In another aspect, the present invention also provides the application of the above kit in the extraction of heavy oil genome deoxyribonucleic acid.
本发明的有益效果:The beneficial effects of the present invention:
本发明提供的提取稠油基因组DNA方法对于稠油的提取更具优势,首先,本发明可以直接用稠油原样进行提取,也可以根据油品情况选择γ-戊内酯作为预处理试剂,该预处理试剂是一种绿色试剂,比采用异辛烷、石油醚等试剂进行预处理更为环保。其次,本发明对稠油样品具有针对性,联合应用蜗牛酶、含曲拉通X-100的提取液及SDC溶液,对高密度和粘度油品中微生物具有更好的细胞的裂解和去污效果。最后,本发明简化了提取步骤,同时也缩短了提取时间,最快可以在1个半小时内完成整个提取过程,并且提取浓度也较高,二聚体产生量极微,后续qPCR检测、高通量测序及宏基因组等分析。该试剂盒简化了操作方法,可方便的应用稠油基因组DNA的提取,以达到高效提取稠油中总脱氧核糖核酸的目的。本发明相对于申请人之前针对普通原油的基因组DNA提取方法(ZL 20170116846.5),其时间更短(同比节省100min以上),效果更好,更环保经济等。The method for extracting heavy oil genomic DNA provided by the present invention has more advantages for the extraction of heavy oil. First of all, the present invention can directly extract heavy oil as it is, or select γ-valerolactone as the pretreatment reagent according to the oil condition. The pretreatment reagent is a green reagent, which is more environmentally friendly than using isooctane, petroleum ether and other reagents for pretreatment. Secondly, the present invention is specific to heavy oil samples. The combined application of snail enzyme, Triton X-100-containing extract and SDC solution has better cell lysis and decontamination of microorganisms in high-density and viscous oils. effect. Finally, the present invention simplifies the extraction steps, and also shortens the extraction time. The entire extraction process can be completed within one and a half hours at the fastest, and the extraction concentration is also high, the amount of dimer produced is minimal, and the subsequent qPCR detection, high Throughput sequencing and metagenomic analysis. The kit simplifies the operation method, and can be conveniently used for the extraction of heavy oil genomic DNA to achieve the purpose of efficiently extracting the total deoxyribonucleic acid in the heavy oil. Compared with the applicant's previous genomic DNA extraction method for ordinary crude oil (ZL 20170116846.5), the present invention has a shorter time (a savings of more than 100 minutes compared to the same period last year), a better effect, and is more environmentally friendly and economical.
图1为本发明实施例1中提取基因组DNA PCR产物扩增的电泳图谱(其中:1至4分别为同一油样的平行样品;M为分子量标记物Marker);Figure 1 is an electrophoresis chart of PCR product amplification of genomic DNA extracted in Example 1 of the present invention (wherein: 1 to 4 are parallel samples of the same oil sample; M is a molecular weight marker Marker);
图2为本发明实施例2和3中提取基因组DNA PCR产物扩增的电泳图谱(其中:5至6分别为实施例2同一油样的平行样品;7-8为实施例3同一油样的平行样品;M为分子量标记物Marker)。Figure 2 is the electrophoresis pattern of PCR product amplification of genomic DNA extracted in Examples 2 and 3 of the present invention (wherein: 5 to 6 are parallel samples of the same oil sample in Example 2; 7-8 are the same oil sample in Example 3 Parallel samples; M is the molecular weight marker Marker).
图3为本发明实施例4中提取基因组DNA PCR产物扩增的电泳图谱(图3中的a,9至10分别为实施例4同一油样的平行样品)及本发明对比例2中提取基因组DNA PCR产物扩增的电泳图谱(图3中的b,11至12分别为对比例2同一油样的平行样品;M为分子量标记物Marker)的对比图。Fig. 3 is an electrophoresis pattern of PCR product amplification of genomic DNA extracted in Example 4 of the present invention (a, 9 to 10 in Fig. 3 are parallel samples of the same oil sample in Example 4) and the genome extracted in Comparative Example 2 of the present invention The electrophoresis patterns of DNA PCR product amplification (b, 11 to 12 in Fig. 3 are the parallel samples of the same oil sample in Comparative Example 2; M is the comparison chart of the molecular weight marker Marker).
为了对本发明的技术特征、目的和有益效果有更加清楚的理解,现对本发明的技术方案进行以下详细说明,但不能理解为对本发明的可实施范围的限定。In order to have a clearer understanding of the technical features, objectives, and beneficial effects of the present invention, the technical solutions of the present invention are now described in detail below, but they should not be understood as limiting the scope of implementation of the present invention.
利用核酸朊检测仪测定DNA提取液浓度和纯度(A260/A280),结合口比特(Qubit)量检测其浓度。A nucleic acid prion detector was used to determine the concentration and purity of the DNA extract (A260/A280), and the concentration of the DNA extract was determined in combination with the amount of Qubit.
实施例中所有涉及到的稠油样品采自辽河油田,L2YHC23,密度为0.994g/cm
3,粘度为5860mPa·s,胶质+沥青质含量为46.8%,根据中国标准SY/T 6169-1995属于普通 稠油,根据国际常用°API归类方式属于重质原油。
All the heavy oil samples involved in the examples are collected from Liaohe Oilfield, L2YHC23, density is 0.994g/cm 3 , viscosity is 5860mPa·s, content of gum + asphaltene is 46.8%, according to Chinese standard SY/T 6169-1995 It belongs to ordinary heavy oil and belongs to heavy crude oil according to the international common °API classification method.
实施例中的所采用的原料、试剂若无特殊说明,均为市售获得。Unless otherwise specified, the raw materials and reagents used in the examples are all commercially available.
实施例1Example 1
本实施例提供一种提取稠油基因组脱氧核糖核酸的试剂盒,该试剂盒包括:预处理试剂、玻璃珠、蜗牛酶、朊酶K、含有曲拉通X-100的DNA提取液、去污液、朊沉淀液、漂洗液、DNA洗脱液、吸附柱、收集管和离心管等组分和材质,各组分的内容和材质要求如下:This embodiment provides a kit for extracting heavy oil genome deoxyribonucleic acid. The kit includes: pretreatment reagent, glass beads, snail enzyme, prionase K, DNA extract containing Triton X-100, and decontamination The components and materials of liquid, prion precipitation, rinse, DNA eluate, adsorption column, collection tube, centrifuge tube, etc. The content and material requirements of each component are as follows:
预处理试剂:γ-戊内酯;Pretreatment reagent: γ-valerolactone;
玻璃珠:粒径为1.5mm的单分散玻璃珠20颗;Glass beads: 20 monodisperse glass beads with a particle size of 1.5mm;
蜗牛酶:质量体积浓度20mg/mL;Snail enzyme: mass volume concentration 20mg/mL;
朊酶K:质量体积浓度20mg/mL;Prionase K: mass volume concentration 20mg/mL;
提取液(pH8.0):每升提取液含有100mmol的三羟甲基氨基甲烷盐酸盐(Tris-HCl)、100mmol曲拉通X-100(Triton-X),100mmol Na
3PO
4及1.5mol NaCl;
Extraction solution (pH8.0): Each liter of extraction solution contains 100mmol of tris-hydroxymethylaminomethane hydrochloride (Tris-HCl), 100mmol of Triton X-100 (Triton-X), 100mmol of Na 3 PO 4 and 1.5 mol NaCl;
去污液:质量体积浓度100mg/mL SDC溶液;Decontamination solution: 100mg/mL SDC solution with mass volume concentration;
朊沉淀液:体积比为25:24:1的苯酚/氯仿/异戊醇的混合溶剂;Prion precipitation solution: a mixed solvent of phenol/chloroform/isoamyl alcohol with a volume ratio of 25:24:1;
漂洗液:色谱纯级的体积浓度70%乙醇;Rinsing solution: chromatographically pure grade ethanol with a volume concentration of 70%;
DNA洗脱液:无菌超纯水;DNA eluate: sterile ultrapure water;
吸附柱:含有硅胶吸附膜;Adsorption column: contains silica gel adsorption membrane;
收集管和离心管:EP管。Collection tube and centrifuge tube: EP tube.
采用以上试剂盒可方便的应用本实施例下述的提取方法,以达到高效提取稠油中总脱氧核糖核酸的目的。Using the above kit can conveniently apply the following extraction method in this embodiment to achieve the purpose of efficiently extracting total deoxyribonucleic acid in heavy oil.
本实施还提供一种提取稠油基因组脱氧核糖核酸的方法,其包括以下步骤:This implementation also provides a method for extracting heavy oil genome deoxyribonucleic acid, which includes the following steps:
步骤一,取稠油500mg,加入200-300μL的γ-戊内酯,涡旋混匀,去除下层液后获得预处理的稠油;Step 1: Take 500mg of heavy oil, add 200-300μL of γ-valerolactone, vortex and mix, remove the lower layer to obtain pretreated heavy oil;
步骤二,取预处理后的稠油于离心管中,加入10-20μL的蜗牛酶,于37℃、120rpm下振荡30min,然后再依次加入10-20μL的朊酶K和1-2mL含曲拉通X-100的DNA提取液,于37℃、120rpm下振荡30min,最后加入100-200μL的去污液,65℃下放置1h,并于室温、6000-12000rpm条件下离心3min去除沉淀获得上层液,转移上层液于新的离心管中,向上层液中加入与上层液等体积的朊沉淀液,于6000-12000rpm条件下离心3min,转移上层液于新的离心管中,重复加入朊沉淀液操作一次,离心收集上层液;Step two, take the pretreated heavy oil into a centrifuge tube, add 10-20μL of snailase, shake at 37℃, 120rpm for 30min, and then add 10-20μL of prion K and 1-2mL of snailase in turn Pass the DNA extraction solution of X-100, shake at 37°C and 120rpm for 30min, finally add 100-200μL of decontamination solution, place it at 65°C for 1h, and centrifuge at room temperature and 6000-12000rpm for 3min to remove the precipitate to obtain the supernatant , Transfer the upper layer to a new centrifuge tube, add the same volume of prion precipitation to the upper layer, centrifuge at 6000-12000 rpm for 3 minutes, transfer the upper layer to a new centrifuge tube, repeat adding the prion precipitation solution Operate once and collect the supernatant by centrifugation;
步骤三,将离心收集的上层液取500-1000μL转移至吸附柱中进行吸附,吸附柱放入收集管中,于6000-12000rpm条件下离心1min去除废液,重复此步骤至上层液大部分经吸附柱过滤(注意:吸取上层液时不能吸到朊沉淀层,故保留朊沉淀层上方3-5mm厚度的上层液),接着向吸附柱中加入500-1000μL低温预冷的漂洗液进行漂洗,于6000-12000rpm条件下离心1min去除废液,重复漂洗步骤;将吸附柱于室温下放置10min,以晾干吸附柱中吸附膜中残余的漂洗液;最后向吸附柱中的吸附膜的中间部位悬空滴加110μL的DNA洗脱液,室温下静置8min,于10000-12000rpm条件下离心2min,收集离心后的上层液即为稠油基因组脱氧核糖核酸(DNA)。Step 3: Transfer 500-1000μL of the upper layer liquid collected by centrifugation to the adsorption column for adsorption, put the adsorption column into the collection tube, centrifuge at 6000-12000 rpm for 1 min to remove the waste liquid, repeat this step until the upper layer has mostly passed Adsorption column filtration (note: the prion precipitation layer cannot be absorbed when sucking the upper layer liquid, so keep the upper layer liquid with a thickness of 3-5mm above the prion precipitation layer), and then add 500-1000μL low-temperature pre-cooled rinsing solution to the adsorption column for rinsing. Centrifuge at 6000-12000rpm for 1 min to remove the waste liquid, repeat the rinsing step; place the adsorption column at room temperature for 10 minutes to dry the residual rinsing liquid in the adsorption membrane in the adsorption column; and finally to the middle part of the adsorption membrane in the adsorption column Add 110 μL of DNA eluate dropwise in the air, let it stand for 8 min at room temperature, and centrifuge at 10000-12000 rpm for 2 min. The supernatant after centrifugation is collected, which is the heavy oil genome deoxyribonucleic acid (DNA).
对本实施例提取的稠油基因组DNA进行PCR扩增验证其纯度,具体步骤如下:Perform PCR amplification on the heavy oil genomic DNA extracted in this example to verify its purity, and the specific steps are as follows:
正向引物(Primer1)为515F:5′-GTGYCAGCMGCCGCGGTAA-3′,The forward primer (Primer1) is 515F: 5'-GTGYCAGCMGCCGCGGTAA-3',
反向引物(Primer2)为806R:5′-GGACTACVSGGGTATCTAAT-3′。The reverse primer (Primer2) is 806R: 5'-GGACTACVSGGGTATCTAAT-3'.
其中:Y、M、V、S为简并碱基。Among them: Y, M, V, S are degenerate bases.
Y表示碱基可选自C或T;Y represents that the base can be selected from C or T;
M表示碱基可选自A或C;M represents that the base can be selected from A or C;
V表示碱基可选自A、C或G;V represents that the base can be selected from A, C or G;
S表示碱基可选自C或G;S represents that the base can be selected from C or G;
因此,正向引物的碱基序列可以选自如下序列中的一种:Therefore, the base sequence of the forward primer can be selected from one of the following sequences:
5′-GTGCCAGCAGCCGCGGTAA-3′(如SEQ ID NO:1所示);5'-GTGCCAGCAGCCGCGGTAA-3' (as shown in SEQ ID NO:1);
5′-GTGCCAGCCGCCGCGGTAA-3′(如SEQ ID NO:2所示);5'-GTGCCAGCCGCCGCGGTAA-3' (as shown in SEQ ID NO: 2);
5′-GTGTCAGCAGCCGCGGTAA-3′(如SEQ ID NO:3所示);5'-GTGTCAGCAGCCGCGGTAA-3' (as shown in SEQ ID NO: 3);
5′-GTGTCAGCCGCCGCGGTAA-3′(如SEQ ID NO:4所示)。5'-GTGTCAGCCGCCGCGGTAA-3' (as shown in SEQ ID NO: 4).
反向引物的碱基序列可以选自如下序列中的一种:The base sequence of the reverse primer can be selected from one of the following sequences:
5′-GGACTACACGGGTATCTAAT-3′(如SEQ ID NO:5所示);5'-GGACTACACGGGTATCTAAT-3' (as shown in SEQ ID NO: 5);
5′-GGACTACCCGGGTATCTAAT-3′(如SEQ ID NO:6所示);5'-GGACTACCCGGGTATCTAAT-3' (as shown in SEQ ID NO: 6);
5′-GGACTACGCGGGTATCTAAT-3′(如SEQ ID NO:7所示);5'-GGACTACGCGGGTATCTAAT-3' (as shown in SEQ ID NO: 7);
5′-GGACTACAGGGGTATCTAAT-3′(如SEQ ID NO:8所示);5'-GGACTACAGGGGTATCTAAT-3' (as shown in SEQ ID NO: 8);
5′-GGACTACCGGGGTATCTAAT-3′(如SEQ ID NO:9所示);5'-GGACTACCGGGGTATCTAAT-3' (as shown in SEQ ID NO: 9);
5′-GGACTACGGGGGTATCTAAT-3′(如SEQ ID NO:10所示)。5'-GGACTACGGGGGTATCTAAT-3' (as shown in SEQ ID NO: 10).
将扩增产物于1%的琼脂糖凝胶上100V电压,电泳45min,用紫外凝胶成像系统进行拍摄。L2YHC23-1和L2YHC23-2为一组平行样品,L2YHC23p为该油样的平均值和 标准偏差(表1)。利用本实施例1提取的DNA较纯,A260/A280比值约为1.6,浓度也较高(表1)。1号和2号电泳(图1)显示DNA扩增产物条带单一、清晰,由此可知,应用本发明提取的DNA效果较好。The amplified products were electrophoresed on a 1% agarose gel with a voltage of 100V for 45 minutes and photographed with an ultraviolet gel imaging system. L2YHC23-1 and L2YHC23-2 are a set of parallel samples, and L2YHC23p is the average value and standard deviation of the oil sample (Table 1). The DNA extracted in Example 1 is relatively pure, the ratio of A260/A280 is about 1.6, and the concentration is also relatively high (Table 1). No. 1 and No. 2 electrophoresis (Figure 1) showed that the DNA amplification product had a single and clear band. It can be seen that the DNA extracted by the present invention has a better effect.
表1本实施1提取稠油基因组DNA的浓度和纯度Table 1 Concentration and purity of genomic DNA extracted from heavy oil in Example 1
对比例1Comparative example 1
取稠油500mg,预处理方式同实施例1,加入200-300μL的γ-戊内酯,涡旋混匀,去除下层液后获得预处理液,其余提取步骤按照凯杰(QIAGEN)试剂盒法进行。L2YHC23-3和L2YHC23-4为一组平行样品,L2YHC23p为该油样的平均值和标准偏差(表2)。凯杰试剂盒法(表2)提取稠油DNA的纯度和浓度均比本发明方法(实施例1)低,差异似乎较小,但后续测序表明,仅有本发明方法才可以进行后续实验。Take 500mg of heavy oil, the pretreatment method is the same as in Example 1, add 200-300μL of γ-valerolactone, vortex and mix, remove the lower layer to obtain the pretreatment liquid, and the rest of the extraction steps follow the QIAGEN kit method get on. L2YHC23-3 and L2YHC23-4 are a set of parallel samples, and L2YHC23p is the average and standard deviation of the oil sample (Table 2). The purity and concentration of the DNA extracted by the QIAGEN kit method (Table 2) are lower than those of the method of the present invention (Example 1), and the difference seems to be small. However, subsequent sequencing shows that only the method of the present invention can be used for subsequent experiments.
表2对比例1提取稠油基因组DNA的浓度和纯度Table 2 Concentration and purity of genomic DNA extracted from heavy oil in Comparative Example 1
实施例2Example 2
本实施例与实施例1中的惟一区别是缺少步骤一,即不使用预处理试剂(γ-戊内酯),直接使用稠油进行提取,其余操作完全一致。L2YHC23-5和L2YHC23-6为一组平行样品,L2YHC23p为该油样的平均值和标准偏差(表3)。提取结果和验证结果显示,应用本发明提取DNA浓度较高(表3),5号和6号电泳条带(图2)单一、清晰,表明稠油DNA提取效果较好。The only difference between this example and Example 1 is the lack of step one, that is, no pretreatment reagent (γ-valerolactone) is used, and heavy oil is directly used for extraction, and the rest of the operations are completely the same. L2YHC23-5 and L2YHC23-6 are a set of parallel samples, and L2YHC23p is the average value and standard deviation of the oil sample (Table 3). The extraction results and verification results show that the concentration of DNA extracted by the present invention is relatively high (Table 3), and the electrophoresis bands No. 5 and No. 6 (Figure 2) are single and clear, indicating that the heavy oil DNA extraction effect is better.
表3本实施2提取稠油基因组DNA的浓度和纯度Table 3 Concentration and purity of genomic DNA extracted from heavy oil in this implementation 2
实施例3Example 3
本实施例与实施例1相比,省略步骤一,直接使用稠油进行提取,具体过程如下:取稠油500mg于离心管中,加入10-20μL的蜗牛酶,然后再依次加入10-20μL的朊酶K和1-2mL含有曲拉通X-100的DNA提取液,最后加入100-200μL的去污液,65℃下放置1h,并于室温、8000rpm条件下离心3min去除沉淀获得上层液,转移上层液于新的离心管中,向上层液中加入与上层液等体积的朊沉淀液,于8000rpm条件下离心3min,转移上层液于新的离心管中,重复加入朊沉淀液操作一次,离心收集上层液;后续操作与实施例1完全一致。Compared with Example 1, this example omitted step one and directly used heavy oil for extraction. The specific process is as follows: take 500 mg of heavy oil in a centrifuge tube, add 10-20 μL of snail enzyme, and then add 10-20 μL of Prion K and 1-2 mL of DNA extract containing Triton X-100, finally add 100-200 μL of decontamination solution, place it at 65°C for 1 h, and centrifuge at room temperature and 8000 rpm for 3 min to remove the precipitate to obtain the upper layer. Transfer the upper layer to a new centrifuge tube, add the same volume of prion precipitation to the upper layer, centrifuge at 8000 rpm for 3 minutes, transfer the upper layer to a new centrifuge tube, and repeat the operation of adding prion precipitation once. The supernatant was collected by centrifugation.
L2YHC23-7和L2YHC23-8为一组平行样品,L2YHC23p为该油样的平均值和标准偏差(表4)。提取结果和验证结果显示,应用本发明提取的DNA浓度较高(表4),7号和8号电泳条带(图2)最清晰、明亮,表明稠油DNA提取效果较好。L2YHC23-7 and L2YHC23-8 are a set of parallel samples, and L2YHC23p is the average value and standard deviation of the oil sample (Table 4). The extraction results and verification results show that the concentration of DNA extracted by the present invention is higher (Table 4), and the electrophoresis bands No. 7 and No. 8 (Figure 2) are the clearest and brightest, indicating that the heavy oil DNA extraction effect is better.
表4本实施3提取稠油基因组DNA的浓度和纯度Table 4 Concentration and purity of genomic DNA extracted from heavy oil in Example 3
实施例4Example 4
本实施例与实施例3相比,使用相同稠油(采集后保存条件不同),且用量和实验操作完全一致。L2YHC23-9和L2YHC23-10为一组平行样品,L2YHC23p为该油样的平均值和标准偏差(表5)。提取结果和验证结果显示,应用本发明提取的DNA浓度和纯度较高(表5),9号和10号电泳条带(图3中的a)较清晰、明亮,表明稠油DNA提取效果较好。Compared with Example 3, this example uses the same heavy oil (different storage conditions after collection), and the dosage is exactly the same as the experimental operation. L2YHC23-9 and L2YHC23-10 are a set of parallel samples, and L2YHC23p is the average value and standard deviation of the oil sample (Table 5). The extraction results and verification results show that the concentration and purity of the DNA extracted by the present invention are higher (Table 5), and the electrophoresis bands No. 9 and No. 10 (a in Fig. 3) are clearer and brighter, indicating that the extraction effect of heavy oil DNA is better. Great.
表5本实施4提取稠油基因组DNA的浓度和纯度Table 5 Concentration and purity of genomic DNA extracted from heavy oil in Example 4
对比例2Comparative example 2
本对比例2与实施例4相比,使用相同稠油,提取方法参照发明专利ZL201710116846.5方法进行。L2YHC23-11和L2YHC23-12为一组平行样品,L2YHC23p为该油样的平均值和标准偏差(表6)提取结果和验证结果显示,应用该方法提取的DNA浓度和纯度比本发明方法(实施例4)低(表6),11号和12号电泳条带(图3中的b)也没本发明方法(图3中的a)亮,表明本发明提取效果较好。此外,应用本发明比我们前发明提取DNA所用时间短,最快可在90min内完成,比前发明至少可节省100min;同时本发明在前处理过程可不使用异辛烷等有机试剂,比前发明更具环保性。Compared with Example 4, this comparative example 2 uses the same heavy oil, and the extraction method refers to the method of invention patent ZL201710116846.5. L2YHC23-11 and L2YHC23-12 are a set of parallel samples. L2YHC23p is the average and standard deviation of the oil sample (Table 6). The extraction and verification results show that the concentration and purity of DNA extracted by this method are higher than those of the method of the present invention (implementation). Example 4) is low (Table 6), and the electrophoretic bands No. 11 and No. 12 (b in Fig. 3) are not as bright as the method of the invention (a in Fig. 3), indicating that the extraction effect of the invention is better. In addition, the application of the present invention takes less time than our previous invention to extract DNA, and can be completed within 90 minutes at the fastest, and can save at least 100 minutes compared with the previous invention. At the same time, the present invention does not use isooctane and other organic reagents in the pretreatment process, which is better than the previous invention. More environmentally friendly.
表6本对比例2提取稠油基因组DNA的浓度和纯度Table 6 Concentration and purity of genomic DNA extracted from heavy oil in this comparative example 2
应用本发明方法提取的基因组DNA可以满足后续qPCR检测、高通量测序及宏基因组等分析要求。The genomic DNA extracted by the method of the present invention can meet the analysis requirements of subsequent qPCR detection, high-throughput sequencing and metagenomics.
Claims (15)
- 一种提取稠油基因组脱氧核糖核酸的方法,其包括以下步骤:A method for extracting heavy oil genome deoxyribonucleic acid, which comprises the following steps:步骤一,向稠油中加入蜗牛酶、朊酶K、含有曲拉通X-100的DNA提取液、去污液进行裂解细胞;Step 1: Add snailase, prionase K, DNA extract containing Triton X-100, and decontamination solution to the heavy oil to lyse the cells;步骤二,静置后离心去除沉淀获得上层液,并向上层液中加入朊沉淀液去除有机大分子组分,离心收集上层液;Step 2: After standing still, the sediment is removed by centrifugation to obtain the upper liquid, and the prion sediment is added to the upper liquid to remove the organic macromolecular components, and the upper liquid is collected by centrifugation;步骤三,将离心收集的上层液转移至吸附柱中进行吸附,然后通过漂洗液漂洗和DNA洗脱液洗脱,收集得到稠油基因组脱氧核糖核酸。Step 3: Transfer the upper layer collected by centrifugation to the adsorption column for adsorption, and then rinse with the rinsing solution and elution with the DNA elution solution to collect the heavy oil genome deoxyribonucleic acid.
- 根据权利要求1所述的方法,其中,所述步骤一前还包括对稠油进行预处理的步骤,所述预处理是向稠油中加入预处理试剂进行处理,获得预处理后的稠油。The method according to claim 1, wherein, before the first step, it further comprises a step of pretreating the heavy oil, and the pretreatment is to add a pretreatment reagent to the heavy oil for treatment to obtain the pretreated heavy oil .
- 根据权利要求1所述的方法,其中,该方法具体包括以下步骤:The method according to claim 1, wherein the method specifically comprises the following steps:步骤一,向每300-500mg的稠油中加入10-20μL的蜗牛酶,于30-37℃、90-120rpm下振荡20-30min,然后再依次加入10-20μL的朊酶K和1-2mL含有曲拉通X-100的DNA提取液,于30-37℃、90-120rpm下振荡20-30min,最后加入100-200μL的去污液,50-65℃下放置30-60min;Step 1: Add 10-20μL of snail enzyme to every 300-500mg of heavy oil, shake at 30-37℃, 90-120rpm for 20-30min, and then add 10-20μL of prionase K and 1-2mL in sequence The DNA extract containing Triton X-100 is shaken at 30-37°C and 90-120 rpm for 20-30 minutes, and finally 100-200 μL of decontamination solution is added, and placed at 50-65°C for 30-60 minutes;或者,直接向每300-500mg的稠油中依次加入10-20μL的蜗牛酶、10-20μL的朊酶K、1-2mL含有曲拉通X-100的DNA提取液、100-200μL去污液,50-65℃下放置30-60min;Or, directly add 10-20μL of snailase, 10-20μL of prionase K, 1-2mL of DNA extract containing Triton X-100, and 100-200μL of decontamination solution to every 300-500mg of heavy oil. , Placed at 50-65℃ for 30-60min;步骤二,在室温、8000-10000rpm条件下离心2-3min去除沉淀获得上层液,转移上层液于新的离心管中,向上层液中加入与上层液等体积的朊沉淀液,于8000-10000rpm条件下离心2-3min,转移上层液于新的离心管中,重复加入朊沉淀液操作,离心收集上层液;Step 2: Centrifuge for 2-3min at room temperature and 8000-10000rpm to remove the precipitate to obtain the supernatant. Transfer the supernatant to a new centrifuge tube. Add the same volume of prion precipitation to the supernatant at 8000-10000rpm. Centrifuge for 2-3min under conditions, transfer the upper layer to a new centrifuge tube, repeat the operation of adding prion precipitation solution, and collect the upper layer by centrifugation;步骤三,将离心收集的上层液转移至吸附柱中进行吸附,吸附柱放入收集管中,于10000-12000rpm条件下离心1-2min去除废液,接着向吸附柱中加入预冷的漂洗液进行漂洗,于10000-12000rpm条件下离心1-2min去除废液,重复漂洗步骤;将吸附柱于室温下放置10-20min,以晾干吸附柱中吸附膜中残余的漂洗液;最后向吸附柱中的吸附膜的中间部位悬空滴加的DNA洗脱液,室温下静置5-10min,于10000-12000rpm条件下离心2-3min,收集离心后的上层液即为稠油基因组脱氧核糖核酸。Step 3: Transfer the upper layer liquid collected by centrifugation to the adsorption column for adsorption, put the adsorption column into the collection tube, centrifuge at 10000-12000rpm for 1-2min to remove the waste liquid, and then add the pre-cooled rinsing solution to the adsorption column Carry out rinsing, centrifuge at 10000-12000rpm for 1-2min to remove the waste liquid, repeat the rinsing step; place the adsorption column at room temperature for 10-20min to dry the residual rinsing liquid in the adsorption membrane in the adsorption column; finally transfer to the adsorption column The DNA eluate suspended in the middle part of the adsorption membrane in the medium, left standing at room temperature for 5-10min, centrifuged at 10000-12000rpm for 2-3min, and the supernatant collected after centrifugation is the heavy oil genome deoxyribonucleic acid.
- 根据权利要求3所述的方法,其中,所述步骤一前还包括对稠油进行预处理的步骤,所述预处理是向每300-500mg的稠油中加入150-250μL的预处理试剂,涡旋混匀后去除下层液,得到预处理后的稠油。The method according to claim 3, wherein, before the step one, it further comprises a step of pretreating the heavy oil, and the pretreatment is to add 150-250 μL of pretreatment reagent to every 300-500 mg of heavy oil, After vortexing and mixing, the lower layer liquid is removed to obtain the pretreated heavy oil.
- 根据权利要求1-4任一项所述的方法,其中,所述蜗牛酶的质量体积浓度为10-20mg/mL。The method according to any one of claims 1 to 4, wherein the mass volume concentration of the snail enzyme is 10-20 mg/mL.
- 根据权利要求2或4所述的方法,其中,所述预处理的试剂为γ-戊内酯。The method according to claim 2 or 4, wherein the pretreatment reagent is γ-valerolactone.
- 根据权利要求1-4任一项所述的方法,其中,所述朊酶K的质量体积浓度为5-20mg/mL。The method according to any one of claims 1 to 4, wherein the mass volume concentration of prion K is 5-20 mg/mL.
- 根据权利要求1-4任一项所述的方法,其中,所述含有曲拉通X-100的每升DNA提取液包括50-200mmol的三羟甲基氨基甲烷盐酸盐、50-200mmol的曲拉通X-100、50-200mmol的Na 3PO 4和0.5-2mol的NaCl。 The method according to any one of claims 1 to 4, wherein each liter of DNA extraction solution containing Triton X-100 comprises 50-200mmol of tris hydrochloride, 50-200mmol of Triton X-100, 50-200 mmol of Na 3 PO 4 and 0.5-2 mol of NaCl.
- 根据权利要求1-4任一项所述的方法,其中,所述去污液为脱氧胆酸钠溶液,其质量体积浓度为50-100mg/mL。The method according to any one of claims 1 to 4, wherein the decontamination liquid is a sodium deoxycholate solution with a mass volume concentration of 50-100 mg/mL.
- 根据权利要求1-4任一项所述的方法,其中,所述朊沉淀液为苯酚、氯仿和异戊醇的混合液,苯酚、氯仿和异戊醇的混合体积比为(24-26):(23-25):(0.5-1.5)。The method according to any one of claims 1 to 4, wherein the prion precipitation liquid is a mixed liquid of phenol, chloroform and isoamyl alcohol, and the mixing volume ratio of phenol, chloroform and isoamyl alcohol is (24-26) : (23-25): (0.5-1.5).
- 根据权利要求1-4任一项所述的方法,其中,所述漂洗液为色谱纯级的乙醇,所述乙醇的体积浓度为70%;The method according to any one of claims 1 to 4, wherein the rinsing liquid is chromatographically pure ethanol, and the volume concentration of the ethanol is 70%;优选地,所述DNA洗脱液为无菌超纯水;Preferably, the DNA eluate is sterile ultrapure water;优选地,所述吸附柱中采用的吸附膜为硅胶膜。Preferably, the adsorption membrane used in the adsorption column is a silica gel membrane.
- 一种提取稠油基因组脱氧核糖核酸的试剂盒,其中,该试剂盒包括:蜗牛酶、朊酶K、含有曲拉通X-100的DNA提取液、去污液、朊沉淀液和吸附柱。A kit for extracting heavy oil genome deoxyribonucleic acid, wherein the kit includes: snailase, prionase K, DNA extraction solution containing Triton X-100, decontamination solution, prion precipitation solution and adsorption column.
- 根据权利要求12所述的试剂盒,其中,该试剂盒还包括预处理试剂,所述预处理试剂为γ-戊内酯;The kit according to claim 12, wherein the kit further comprises a pretreatment reagent, and the pretreatment reagent is γ-valerolactone;优选地,该试剂盒还包括漂洗液和DNA洗脱液。Preferably, the kit further includes a rinse solution and a DNA elution solution.
- 根据权利要求12所述的试剂盒,其中,该试剂盒还包括玻璃珠,所述玻璃珠是粒径为1.5-2.0mm的单分散玻璃珠。The kit according to claim 12, wherein the kit further comprises glass beads, and the glass beads are monodisperse glass beads with a particle size of 1.5-2.0 mm.
- 权利要求12-14任一项所述试剂盒在稠油基因组脱氧核糖核酸提取中的应用。The use of the kit according to any one of claims 12-14 in the extraction of heavy oil genome deoxyribonucleic acid.
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Cited By (1)
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CN115386574A (en) * | 2022-09-02 | 2022-11-25 | 苏州英泽生物医药科技有限公司 | Nucleic acid extraction method without using chloroform |
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