METHOD AND KIT FOR RAPIDLY DETECTING VIRAL GENOME SIZE
20240401155 ยท 2024-12-05
Assignee
Inventors
Cpc classification
C12Q2527/125
CHEMISTRY; METALLURGY
C12N15/1003
CHEMISTRY; METALLURGY
C12Q2527/125
CHEMISTRY; METALLURGY
G01N2333/015
PHYSICS
C12Q1/6806
CHEMISTRY; METALLURGY
International classification
Abstract
A method for rapidly detecting viral genome size based on an agarose gel electrophoresis technology belongs to the technical field of virus detection. The kit for detecting the genome size includes a lysis buffer and a sample loading buffer solution, and includes the following raw material components: 5% lauryl sodium sulfate, 0.5 M sodium chloride, 50 mM ethylenediamine tetraacetic acid and 6 DNA gel sample loading buffer dye. By adopting the detection method, a plurality of tedious steps of the existing method are omitted, a clearer gel imaging result can be obtained, the detection time is greatly shortened, and the method is particularly suitable for rapidly detecting virus genome size of parvoviridae family. The method has important application value, and is more in line with the needs of virus detection and quality control research work in the field of gene therapy drug development.
Claims
1. A method for rapidly detecting viral genome size, comprising: changing genomic single-stranded DNA of a virus into more stable double-stranded DNA, and then performing detection by agarose gel electrophoresis, wherein the virus is selected from viruses of Parvoviridae family.
2. The method according to claim 1, wherein the method comprises: adding a lysis buffer or a diluent thereof into a virus sample, subjecting virus capsid in the sample to lysis under suitable conditions, and then performing electrophoresis analysis using agarose gel; the lysis buffer, with water as a solvent, is selected from any one of the following types: (1) a detergent; (2) a detergent and NaCl; and (3) a detergent, NaCl and a chelating agent; and after the lysis buffer is added, a final concentration of the detergent in a system is 0%-0.1%, a final concentration of the NaCl in the system is 0 M-0.2 M, and a final concentration of the chelating agent in the system is 0 mM-6 mM.
3. The method according to claim 2, wherein the detergent is selected from mild detergents.
4. The method according to claim 2, wherein the chelating agent is ethylenediamine tetraacetic acid (EDTA).
5. The method according to claim 3, wherein a final concentration of the SDS in the system is 0.03%-0.1%.
6. The method according to claim 2, wherein the final concentration of the NaCl in the system is 0.02 M-0.08 M.
7. The method according to claim 2, wherein a final concentration of the EDTA in the system is 3 mM-6 mM.
8. The method according to claim 1, wherein the lysis buffer comprises 0.5% SDS, 0.5 M NaCl and 50 mM EDTA.
9. The method according to claim 1, wherein the suitable conditions comprise cooling on ice or at room temperature after heating treatment at 70 C.-100 C.
10. The method according to claim 9, wherein the suitable conditions comprise cooling at room temperature for 10 min-15 min after heating at 90 C.-100 C. for 10 min. 10 min-15 min.
11. A virus lysis buffer, wherein the virus lysis buffer, with water as a solvent, is selected from any one of the following types: (1) a 0.01%-1% detergent; (2) a 0.01%-1% detergent and 0.01 M-1 M NaCl; and (3) a 0.01%-1% detergent, 0.01 M-1 M NaCl and a 1.5 mM-100 mM chelating agent.
12. The virus lysis buffer according to claim 11, wherein the detergent is selected from mild detergents.
13. The virus lysis buffer according to claim 11, wherein the chelating agent is EDTA.
14. The virus lysis buffer according to claim 12, wherein a concentration of the SDS is 0.3%-1%.
15. The virus lysis buffer according to claim 11, wherein a concentration of the NaCl is 0.2 M-0.8 M.
16. The virus lysis buffer according to claim 11, wherein a concentration of the EDTA is 30 mM-60 mM.
17. The virus lysis buffer according to claim 11, wherein the lysis buffer comprises 0.5% SDS, 0.5 M NaCl and 50 mM EDTA.
18. A kit for detecting viral genome size, comprising the virus lysis buffer according to claim 11, wherein a virus is selected from viruses of Parvoviridae family.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DETAILED DESCRIPTION
[0049] The present disclosure is further described below in combination with accompanying drawings and specific examples, but the scope of the protection of the present disclosure is not limited to the following examples. It should also be understood that terms used in the examples of the present disclosure are intended to describe specific embodiments, rather than to limit the scope of the protection of the present disclosure. Without deviating from the spirit and scope of the concept of the present disclosure, all variations and advantages that can be thought of by persons skilled in the art are included in the present disclosure, and the scope of the protection of the present disclosure is defined by the attached claims and any equivalents thereof. In the specification and claims of the present disclosure, the singular forms a, one and the include plural forms, unless otherwise explicitly stated herein. Experimental methods without specific conditions specified in the following examples are general knowledge and common knowledge for persons skilled in the art, or are used in accordance with conditions suggested by manufacturers. Unless otherwise specified, all materials and reagents used in the examples are commercially available products.
[0050] In the present disclosure, a kit for rapidly detecting a genome of an adeno-associated virus includes: [0051] (1) a 6 DNA gel sample loading buffer dye (6 DNA gel loading purple dye, New England Biolabs, PN B7024); and [0052] (2) a lysis buffer, including components as shown in the following table.
TABLE-US-00001 Lysis buffer Component Lysis buffer 1 10X buffer 1 1% SDS Lysis buffer 2 10X buffer 2 0.5% SDS Lysis buffer 3 10X buffer 3 0.5% SDS, 0.1M NaCl Lysis buffer 4 10X buffer 4 0.5% SDS, 0.5M NaCl Lysis buffer 5 10X buffer 5 0.5% SDS, 0.25M NaCl Lysis buffer 6 10X buffer 6 0.5% SDS, 1M NaCl Lysis buffer 7 10X buffer 7 0.5% SDS, 2M NaCl Lysis buffer 8 10X buffer 8 0.5% SDS, 0.5M NaCl, 12 mM EDTA Lysis buffer 9 10X buffer 9 0.5% SDS, 0.5M NaCl, 25 mM EDTA Lysis buffer 10 10X buffer 10 0.5% SDS, 0.5M NaCl, 50 mM EDTA Lysis buffer 11 Tween20 50% Tween20 Lysis buffer 12 Triton-X 50% Triton-X Lysis buffer 13 Proteinase K 20 mg/ml Proteinase K Lysis buffer 14 10X buffer 3 0.1% SDS Lysis buffer 16 10X buffer 16 0.1% SDS, 0.5M NaCl, 1 mM EDTA Lysis buffer 17 10X buffer 17 1% SDS, 1M NaCl, 3 mM EDTA Lysis buffer 18 10X buffer 18 1% SDS, 2M NaCl, 5 mM EDTA
Example 1 Test of Virus Lysis Effects of Different Detergents
[0053] Step 1: Lysis buffers 1, 11, 12 and 13 were prepared.
[0054] Step 2: Samples were rewarmed at room temperature, and a metal bath was opened.
[0055] Step 3: 1% agarose gel was prepared.
[0056] (1) 0.25 g of agarose was accurately weighed and poured into a conical flask.
[0057] (2) About 25 ml of TAE was measured with a special measuring cylinder (to avoid excessive gel concentration caused by evaporation during heating), poured into the conical flask, and gently shaken for uniform mixing by a small force to prevent drug powder from attaching to a cup wall, which was not conducive to subsequent dissolution.
[0058] (3) A mixture obtained after uniform mixing was placed in a microwave oven, and heated for a certain period of time until liquid in the conical flask was boiled and a solution was clear and transparent (the solution was taken out and observed, and heating was continued when particles were observed), where the heating time was not too long so as to prevent the liquid from evaporating completely (a total of about 2 min).
[0059] (4) The solution was taken out and slightly cooled, and when the solution was cooled to a temperature acceptable to touch with hands, 1 l of a dye Gelred was added (when the dye was Goldenview, the addition amount was only 0.1 l, which might be judged based on experience to avoid a too yellow solution). Since the dye was attached to the head of a gun and was difficult to shoot out at a small addition amount, the dye was shoot out to a cup wall and then dissolved by shaking the conical flask.
[0060] (5) Then agarose gel was taken out and usually cooled for 30 min based on experience.
[0061] (6) When residual gel was difficult to clean during cleaning of the conical flask, a small amount of water was added, a mixture was heated slightly and directly poured into a waste liquid tank, and finally, the collected gel was wrapped with gloves and discarded or uniformly recycled.
[0062] Step 4: An adeno-associated virus to be detected was treated.
[0063] (1) The lysis buffers 1, 11, 12 and 13 were diluted to 2, respectively.
[0064] (2) Samples of an experimental group were prepared. 5 l of AAV2-GFP samples (210.sup.10/l) rewarmed at room temperature were mixed with 5 l of the 2 lysis buffers 1, 11, 12 and 13 or water, respectively.
[0065] (3) Samples of a negative control group were prepared. 5 l of AAV2 capsid (empty shell) samples rewarmed at room temperature were mixed with 5 l of the 2 lysis buffers 1, 11, 12 and 13 or water, respectively, and 5 l of AAV2 capsid samples and 5 l of the 2 lysis buffers 1, 11, 12 and 13 were used as a blank control group.
[0066] (4) The samples in steps (2) and (3) were treated in the metal bath at 95 C. for 10 min.
[0067] (5) Cooling was performed at room temperature for 10 min.
[0068] Step 5: Agarose gel electrophoresis was performed.
[0069] (1) 2 l of a 6DNA gel loading purple dye was added into the cooled samples.
[0070] (2) 3 l of a 5k Marker was added into a first pore channel.
[0071] (3) 8 l of the samples were sequentially added into pore channels.
[0072] (4) Electrophoresis was performed at 100 V and 200 mA for 50 min.
[0073] (5) Photographing was performed with a gel imager, where the genome size of AAV2-GFP was about 3.2 kb (
[0074] Agarose gel electrophoresis results of the samples treated with the lysis buffers 1, 11, 12 and 13 respectively are shown in
Example 2 Test of the Optimal Concentration of SDS
[0075] Lysis buffers 1, 2 and 14 were prepared, and experimental conditions and methods were used with reference to those in Example 1.
[0076] Agarose gel electrophoresis results of samples treated with the lysis buffers 1, 2 and 14 respectively are shown in
Example 3 Test of the Optimal Concentration of NaCl
[0077] Lysis buffers 2-7 were prepared, and experimental conditions and methods were used with reference to those in Example 1.
[0078] Agarose gel electrophoresis results of samples treated with the lysis buffers 2-7 respectively are shown in
Example 4 Test of Sample Cooling Conditions
[0079] Step 1: A lysis buffer 4 was prepared.
[0080] Step 2: Samples were rewarmed at room temperature, and a metal bath was opened.
[0081] Step 3: 1% agarose gel was prepared by the same method in Example 1.
[0082] Step 4: The samples to be detected were treated.
[0083] (1) The lysis buffer 4 was diluted to 2.
[0084] (2) A sample of an experimental group was prepared. 5 l of an AAV2-GFP sample (210.sup.10/l) rewarmed at room temperature was mixed with 5 l of the 2 lysis buffer 4.
[0085] (3) A sample of a negative control group was prepared. 5 l of an AAV2 capsid (empty shell) sample rewarmed at room temperature was mixed with 5 l of the 2 lysis buffer 4.
[0086] (4) The samples in steps (2) and (3) were treated in the metal bath at 95 C. for 10 min.
[0087] (5) The samples in step (4) were cooled on ice for 10 min, cooled at room temperature (25 C.) for 10 min, or cooled at 37 C. for 10 min, respectively.
[0088] Step 5: Agarose gel electrophoresis was performed.
[0089] (1) 2 l of a 6 DNA gel loading purple dye was added into the cooled samples.
[0090] (2) 3 l of a 5k Marker was added into a first pore channel.
[0091] (3) 8 l of the samples were sequentially added into pore channels.
[0092] (4) Electrophoresis was performed at a voltage of 100 V and a current of 200 mA for 50 min.
[0093] (5) Photographing was performed with a gel imager.
[0094] Agarose gel electrophoresis results of the samples treated with the lysis buffer 4 are shown in
Example 5 Test of Sample Lysis Conditions
[0095] Step 1: A lysis buffer 2 was prepared.
[0096] Step 2: Samples were rewarmed at room temperature, and a metal bath was opened.
[0097] Step 3: 1% agarose gel was prepared by the same method in Example 1.
[0098] Step 4: The samples to be detected were treated.
[0099] (1) The lysis buffer 2 was diluted to 2.
[0100] (2) A sample of an experimental group was prepared. 5 l of an AAV2-GFP sample (210.sup.10/l) rewarmed at room temperature was mixed with 5 l of the 2 lysis buffer 2 or water.
[0101] (3) A sample of a negative control group was prepared. 5 l of an AAV2 capsid (empty shell) sample rewarmed at room temperature was mixed with 5 l of the 2 lysis buffer 2 or water, and 5 l of an AAV capsid sample and 5 l of the 2 lysis buffer 2 were used as a blank control group.
[0102] (4) The samples in steps (2) and (3) were treated in the metal bath at 95 C. for 10 min or were not heated.
[0103] (5) Cooling was performed at room temperature (25 C.) for 10 min or was not performed.
[0104] Step 5: Agarose gel electrophoresis was performed.
[0105] (1) 2 l of a 6DNA gel loading purple dye was added into the cooled samples.
[0106] (2) 3 l of a 5k Marker was added into a first pore channel.
[0107] (3) 8 l of the samples were sequentially added into pore channels.
[0108] (4) Electrophoresis was performed at a voltage of 100 V and a current of 200 mA for 50 min.
[0109] (5) Photographing was performed with a gel imager.
[0110] Agarose gel electrophoresis results are shown in
Example 6 Test of the Optimal Concentration of EDTA
[0111] Lysis buffers 4, 8, 9 and 10 were prepared, and experimental conditions and methods were used with reference to those in Example 1.
[0112] Agarose gel electrophoresis results of samples treated with the lysis buffers 4, 8, 9 and 10 respectively are shown in
Example 7 Test of Lysis Buffers in Reasonable Concentration Ranges
[0113] Step 1: Lysis buffers 10, 15, 16 and 17 were prepared.
[0114] Step 2: Samples were rewarmed at room temperature, and a metal bath was opened.
[0115] Step 3: 1% agarose gel was prepared.
[0116] (1) 0.25 g of agarose was accurately weighed and poured into a conical flask.
[0117] (2) About 25 ml of TAE was measured with a special measuring cylinder (to avoid excessive gel concentration caused by evaporation during heating), poured into the conical flask, and gently shaken for uniform mixing by a small force to prevent drug powder from attaching to a cup wall, which was not conducive to subsequent dissolution.
[0118] (3) A mixture obtained after uniform mixing was placed in a microwave oven, and heated for a certain period of time until liquid in the conical flask was boiled and a solution was clear and transparent (the solution was taken out and observed, and heating was continued when particles were observed), where the heating time was not too long so as to prevent the liquid from evaporating completely (a total of about 2 min).
[0119] (4) The solution was taken out and slightly cooled, and when the solution was cooled to a temperature acceptable to touch with hands, 1 l of a dye Gelred was added (when the dye was Goldenview, the addition amount was only 0.1 l, which might be judged based on experience to avoid a too yellow solution). Since the dye was attached to the head of a gun and was difficult to shoot out at a small addition amount, the dye was shoot out to a cup wall and then dissolved by shaking the conical flask.
[0120] (5) Then agarose gel was taken out and usually cooled for 30 min based on experience.
[0121] (6) When residual gel was difficult to clean during cleaning of the conical flask, a small amount of water was added, a mixture was heated slightly and directly poured into a waste liquid tank, and finally, the collected gel was wrapped with gloves and discarded or uniformly recycled.
[0122] Step 4: An adeno-associated virus to be detected was treated.
[0123] (1) The lysis buffers 15, 16 and 17 were diluted to 2, respectively.
[0124] (2) Samples of an experimental group were prepared. 5 l of AAV2-GFP samples (210.sup.10/l) rewarmed at room temperature were mixed with 5 l of the 2 lysis buffers 15, 16 and 17, respectively.
[0125] (3) Samples of a negative control group were prepared. 5 l of AAV2 capsid (empty shell) samples rewarmed at room temperature were mixed with 5 l of the 2 lysis buffers 15, 16 and 17, respectively, and 5 l of AAV2 capsid samples and 5 l of the 2 lysis buffers 15, 16 and 17 were used as a blank control group.
[0126] (4) The samples in steps (2) and (3) were treated in the metal bath at 95 C. for 10 min.
[0127] (5) Cooling was performed at room temperature for 10 min.
[0128] Step 5: Agarose gel electrophoresis was performed.
[0129] (1) 2 l of a 6 DNA gel loading purple dye was added into the cooled samples.
[0130] (2) 3 l of a 5k Marker was added into a first pore channel.
[0131] (3) 8 l of the samples were sequentially added into pore channels.
[0132] (4) Electrophoresis was performed at 100 V and 200 mA for 50 min.
[0133] (5) Photographing was performed with a gel imager. Results are shown in
Example 8
[0134] Step 1: A lysis buffer 10 was prepared.
[0135] Step 2: Samples were rewarmed at room temperature, and a metal bath was opened.
[0136] Step 3: Operations were the same as those in Example 7.
[0137] Step 4: An adeno-associated virus to be detected was treated.
[0138] (1) The lysis buffer 10 was divided into two parts, where one part was not diluted (10), and the other part was diluted to 2.
[0139] (2) Samples of an experimental group were prepared. Sample in a pore channel 1:5 l of an AAV2-GFP sample (110.sup.11) rewarmed at room temperature was mixed with 5 l of the 2 lysis buffer 10. Sample in a pore channel 2:9 l of an AAV2-GFP sample (110.sup.11) rewarmed at room temperature was mixed with 1 l of the undiluted lysis buffer 10.
[0140] (3) Samples of a negative control group were prepared. 5 l of an AAV2 capsid (empty shell) sample rewarmed at room temperature was mixed with 5 l of the 2 lysis buffer 10 to serve as a negative control of the pore channel 1, and 9 l of an AAV2 capsid (empty shell) sample rewarmed at room temperature and 1 l of the undiluted lysis buffer 10 were mixed to serve as a negative control of the pore channel 2.
[0141] (4) The samples in steps (2) and (3) were treated in the metal bath at 95 C. for 10 min.
[0142] (5) Cooling was performed at room temperature for 10 min.
[0143] Step 5: Operations were the same as those in Example 7.
[0144] Results are shown in
[0145] All documents mentioned in the present disclosure are cited herein for reference in the present application. In addition, it should be understood that after reading the foregoing contents of the present disclosure, persons skilled in the art may make various changes or modifications to the present disclosure, and all the modifications of equivalent forms also fall within the scope defined by the claims of the present application.