KR20190065680A - DEVELOPMENT OF SINGLEPLEX REAL-TIME PCR KIT FOR RAPID DETECTION OF SALMONELLA TYPHIMURIUM USING ttr TARGET GENE - Google Patents

Abstract

The present invention relates to a primer set for detecting Salmonella typhimurium. Provided is a primer set for Salmonella typhimurium detection comprising a primer consisting of a nucleotide sequence of SEQ ID NO: 1 and a primer consisting of a nucleotide sequence of SEQ ID NO: 2.

Description

[0001] The present invention relates to a kit for detecting a Salmonella typhimurium infection, and a kit for detecting a Salmonella typhimurium infection.

The present invention relates to a primer set for the detection of Salmonella typhimurium real-time, and a real-time detection method and a detection kit for Salmonella typhimurium using the primer set.

Food poisoning refers to an infectious disease or toxic disease that is caused or caused by a microorganism or toxic substance harmful to human body due to food intake, and is accompanied by symptoms such as fever, nausea, vomiting, diarrhea and abdominal pain.

Food poisoning can be classified as microbiological food poisoning and chemical food poisoning. Microbiological food poisoning can be classified into bacterial food poisoning, viral food poisoning, and prototype food poisoning. Chemical poisoning can be classified as natural poisoning or chemical poisoning.

Representative pathogenic microbes which can cause food poisoning in food group is a S. typhimurium (Salmonella Typhimurium).

Salmonella spp . Is a very important cause of food poisoning. In the United States, more than 4 million people are reported to suffer from food poisoning by Salmonella spp . Each year, and it is recognized as an important cause of food poisoning in Korea and Japan. Salmonella spp. Is currently reported to be about 2,800 species. Although there are differences in the pathogenicity of Salmonella spp.

Salmonella has a wide variety of serotypes, but Salmonella typhimurium is known to be an important strain associated with food poisoning.

Molecular biological methods such as Polymerase Chain Reaction (PCR) have been used as a diagnostic method for quickly confirming the infection with Salmonella typhimurium and food contamination. However, existing real-time PCR detection kits have low activity, In some of the target genes, activity was not frequently observed despite the presence of the strain.

In addition, existing real-time polymerase chain reaction detection kits are not compatible with ABI 7500 and Bio-Rad CFX Connect, which are the most widely used real-time PCR devices.

As a result of intensive efforts to develop a PCR detection kit with improved sensitivity and accuracy, the present inventors have found that a target gene optimized for the detection of Salmonella typhimurium is identified and the primer sequence for the target gene is optimized to significantly improve the microorganism detection efficiency Respectively.

It is an object of the present invention to provide a kit for detecting Salmonella typhimurium with improved sensitivity and accuracy.

According to one aspect of the present invention, there is provided a primer set for detecting Salmonella Typhimurium binding to a ttr target gene.

In one embodiment, the primer set may include a primer consisting of the nucleotide sequence of SEQ ID NO: 1 and a primer consisting of the nucleotide sequence of SEQ ID NO: 2.

According to another aspect of the present invention, there is provided a method for detecting Salmonella typhimurium comprising the step of performing a polymerase chain reaction (PCR) using the primer set.

In one embodiment, the detection method is capable of detecting target DNA at a concentration of 0.0001 to 100 ng / μL.

According to another aspect of the present invention, there is provided a Salmonella typhimurium detection kit comprising the primer set and the PCR reaction mixture.

In one embodiment, the PCR reaction mixture may comprise reaction buffer, dNTP, and DNA polymerase.

Since the primer set of the present invention specifically binds to a specific target gene of Salmonella typhimurium, it can be usefully used in real-time PCR detection.

In particular, the primer set of the present invention is significantly superior in sensitivity and accuracy to the conventional detection kit.

It should be understood that the effects of the present invention are not limited to the effects described above, but include all effects that can be deduced from the description of the invention or the composition of the invention set forth in the claims.

Figure 1 shows the specificity of a primer set according to one embodiment of the present invention through crosscheck PCR verification.
2 is a graph illustrating the sensitivity of a primer set according to an embodiment of the present invention.
Figure 3 compares the activity of a primer set and a conventional primer set according to one embodiment of the present invention.
FIGS. 4 and 5 show positive control DNA sets and positive test results.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Hereinafter, the present invention will be described with reference to the accompanying drawings. The present invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein.

When an element is referred to as "comprising ", it means that it can include other elements, not excluding other elements unless specifically stated otherwise.

Unless otherwise defined, can be performed by molecular biology, microbiology, protein purification, protein engineering, and DNA sequencing and routine techniques commonly used in the art of recombinant DNA within the skill of those skilled in the art. These techniques are known to those skilled in the art and are described in many standardized textbooks and references.

Unless otherwise defined herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.

Various scientific dictionaries, including the terms contained herein, are well known and available in the art. Although any methods and materials similar or equivalent to those described herein are found to be used in the practice or testing of the present application, some methods and materials have been described. It is not intended that the invention be limited to the particular methodology, protocols, and reagents, as they may be used in various ways in accordance with the context in which those skilled in the art use them.

As used herein, the singular forms include plural objects unless the context clearly dictates otherwise. Also, unless otherwise indicated, nucleic acids are written from left to right, 5 'to 3', amino acid sequences from left to right, amino to carboxyl. Hereinafter, the present invention will be described in more detail.

According to one aspect of the present invention, there is provided a primer set for detecting Salmonella typhimurium which binds to the ttr gene.

The detection primer set specifically binds to the ttr gene of Salmonella typhimurium to effectively detect Salmonella typhimurium. The primer set includes a primer consisting of the nucleotide sequence of SEQ ID NO: 1 and a primer consisting of the nucleotide sequence of SEQ ID NO: 2 can do.

Salmonella Typhimurium is a typical pathogen causing food poisoning, and mainly shows symptoms of diarrhea and vomiting.

Since the primer set specifically binds to the ttr gene of Salmonella typhimurium, it can be usefully used for the early diagnosis of various diseases caused by Salmonella typhimurium and the possibility of disease development.

The primer may be a short nucleic acid sequence including a free 3 'hydroxyl group and form a base pair with a template of the complementary nucleic acid, and a strand copy of the nucleic acid template Can be used as a starting point.

The primer can initiate DNA synthesis in the presence of a reagent for polymerization and a different four nucleoside triphosphate at the appropriate buffer solution and temperature and hybridize with the nucleic acid present in the target microorganism to produce a specific gene of the target microorganism Can be used for amplification.

In consideration of the efficiency of amplification, the primer may preferably be a single-stranded or deoxyribonucleotide.

The primers may include naturally occurring dNMPs (i.e., dAMP, dGMP, dCMP and dTMP), modified nucleotides or non-natural nucleotides. In addition, the primers may also include ribonucleotides.

The primers include, but are not limited to, skeletal modified nucleotides such as peptide nucleic acid (PNA) (M. Egholm et al., Nature, 365: 566-568 (1993)), phosphorothioate DNA, phosphorodithioate DNA, DNA, amide-linked DNA, MMI-linked DNA, 2'-O-methyl RNA, alpha-DNA and methylphosphonate DNA, sugar modified nucleotides such as 2'-O-methyl RNA, 2'-fluoro 2'-O-alkyl DNA, 2'-O-allyl DNA, 2'-O-alkynyl DNA, hexose DNA, pyranosyl RNA and anhydrohexitol DNA, and a base Nucleotides with modifications such as C-5 substituted pyrimidines wherein the substituents are fluoro, bromo, chloro, iodo-, methyl-, ethyl-, vinyl-, formyl-, ethytyl-, propynyl 7-deazapurines having C-7 substituents (the substituents are fluoro, bromo, chloro, iodo, -, Methyl-, ethyl-, vinyl -, formyl-, alkynyl-, alkenyl-, thiazolyl-, imidazolyl-, pyridyl-), inosine and diaminopurine.

The hybridization means that two single-stranded nucleic acids form a duplex structure by pairing complementary base sequences.

The hybridization may occur in a perfect match between single stranded nucleic acid sequences or in the presence of some mismatching bases. The degree of complementarity required for the hybridization may vary depending on the hybridization reaction conditions, and can be controlled by temperature, in particular.

Generally, if the hybridization temperature is high, hybridization is likely to occur when the hybridization is complete, and hybridization may occur if the hybridization temperature is low, even if some mismatch exists.

The primer set can be hybridized to a characteristic gene of a target microorganism. When a desired microorganism exists in a sample, the base sequence of the characteristic gene is amplified by a polymerase chain reaction, so that the amplified product The presence or absence of the microorganism can be determined.

The PCR may be performed according to the general reaction conditions using a conventional PCR instrument known in the art, or may be carried out with some modifications.

According to another aspect of the present invention, there is provided a method for detecting Salmonella typhimurium comprising the step of performing a polymerase chain reaction (PCR) using the primer set.

The primer set can effectively detect a target microorganism through a polymerase chain reaction.

The above-mentioned " Polymerase Chain Reaction (PCR) " is a method of exponentially amplifying an initiating nucleic acid material by sequentially synthesizing nucleic acids using a polymerase, and is a method well known in the art. This is a concept that includes both qualitative PCR to check for the presence, quantitative PCR to measure the amount of specific nucleic acid, and real-time PCR, which enables real-time tracking and quantitative analysis. The polymerase chain reaction can be performed according to general PCR reaction conditions using a conventional PCR instrument known in the art, or can be carried out with some modifications.

The detection method may be performed by amplifying a specific DNA of each microorganism using the primer set and then confirming the amplification reaction of the specific DNA. Can be carried out by confirming whether or not it is consistent with the expected size of the DNA product through electrophoresis or the like.

The "amplification reaction" means a reaction for amplifying a nucleic acid molecule. A variety of amplification reactions have been extensively reported in the art and have been widely used in the art and include polymerase chain reaction (US Patent Nos. 4,683,195, 4,683,202 and 4,800,159), reverse transcription-polymerase chain reaction (Sambrook et al., Molecular Cloning. (LCR), Gap-LCR (WO 90/01069), the methods of Laplacet et al. (Spring Harbor Press, 2001), Miller, HI (WO 89/06700) and Davey, ), Repair chain reaction (EP 439,182), transcription-mediated amplification (TMA) (WO 88/10315), self sustained sequence replication (WO 90/06995) , Selective amplification of target polynucleotide sequences (U.S. Patent No. 6,410,276), consensus sequence primed polymerase chain reaction (CPPCR) (U.S. Patent No. 4,437,975), selective amplification of target polynucleotide sequences Arbitrary priming polymerase (US Patent 5,413,909 and 5,861, 245), nucleic acid sequence based amplification (NASBA) (U.S. Patent Nos. 5,130,238, 5,409,818, 5,554,517 No. 6,063,603), strand displacement amplification and loop mediated isothermal amplification. LAMP), but can be carried out through a real-time polymerase chain reaction.

The real-time polymerase chain reaction can quantitatively analyze more accurately the amount of the initial sample in which the exponential amplification occurs and the number of cycles at which the exponential increase of the fluorescent substance starts to be detected (cycle threshold) Can be analyzed.

The real-time polymerase chain reaction is an optical system module, such as a fluorescence photometer, which omits the step of measuring the intensity with an image analyzer by electrophoresis. The amplification degree of the amplification product is automated and quantified, Can be analyzed.

A sample of the template DNA used in the above detection method may be any substance, preferably food, feed, and sample, from which Salmonella typhimurium can be found, preferably from food.

The template DNA can be obtained through a DNA extraction method commonly used in the art and can be, for example, an alkaline extraction method, a hot water extraction method, a column extraction method and a phenol / chloroform extraction method, but is not limited thereto.

The detection method can detect a target DNA having a concentration of 0.0001 to 100 ng / μL.

The present inventors optimized the primer sequence for target gene detection, and the primer set is highly sensitive, so that it is possible to effectively amplify target DNA of a very low level, for example, 0.0001 ng / μL concentration.

According to another aspect of the present invention, there is provided a Salmonella typhimurium detection kit comprising the primer set and the PCR reaction mixture.

The PCR reaction mixture may include a reaction buffer, a dNTP, and a DNA polymerase, and may include all reagents available to a person skilled in the art for PCR reaction.

Hereinafter, embodiments of the present invention will be described in detail with reference to the accompanying drawings, but it should be apparent that the present invention is not limited by the following embodiments.

Examples: singleplex Real-time PCR

The real-time PCR was carried out in the same manner as in Example 1 except that 1 μl of template DNA (40 ng / μl), 2.65 μl of a primer (primer set of SEQ ID NO: 1 and SEQ ID NO: 2) and 2.65 μl of a probe set mixture were mixed with MG 2X qPCR MasterMix (TaqMan) Mu] l of distilled water and 6.35 [mu] l of distilled water.

The PCR reaction was performed by using a real-time gene amplification device (7500FAST, ABI, USA) at 50 ° C for 2 minutes to remove contamination of the PCR products. After pre-reading of the fluorescence value at 60 ° C for 1 minute, Amplification was performed.

The amplification reaction was pre-denaturation at 95 ° C for 10 minutes, followed by denaturation at 95 ° C for 15 seconds, annealing at 60 ° C for 1 minute, and extension for 40 cycles Respectively.

Genomic DNA extracted from Salmonella typhimurium was used as a template, and negative control was checked for cross contamination using distilled water.

Allelic discrimination plots and PCR amplification plots were verified using a software program (v. 2.0.6) of a real-time polymerase chain reaction (PCR) 7500.

Experimental Example 1: Evaluation of accuracy of primer

More efficient detection is possible by selecting a new target gene optimized for the strain. In the case of the existing Singleplex real-time PCR kit, the detection of other strains was frequently performed even though a specific strain was set as a target.

Through crosscheck PCR verification, it was confirmed whether there was activity against strains other than the target strain, and it was tested whether the above primers were specifically detected only in Salmonella typhimurium.

Referring to FIG. 1, the primers specifically detected strains in the left line, and no activity was observed on the other 15 strains except the target strains in the right line (-).

The results suggest that the primer set has an activity specific to Salmonella typhimurium.

Experimental Example 2: Evaluation of sensitivity of primer

Serial dilution experiments were conducted to evaluate the sensitivity of the primer set. Through serial dilution, the level at which template DNA was detected was assessed.

Referring to FIG. 2, the primer set detected a very low concentration of template DNA, and in particular, effectively detected a trace amount of DNA template (0.0001 ng / μL).

Experimental Example 3: Evaluation of primer activity

In the case of the conventional real-time PCR kit, the activity was low and real-time PCR was performed for a long time.

In order to evaluate the activity of the primer sets, the activities of the primer sets of other companies were compared and evaluated.

Referring to FIG. 3, since the primer set of the present invention is evaluated to have a much higher activity than the other primer sets, Salmonella typhimurium can be detected more rapidly and accurately.

Positive control DNA can also be used to set positive controls and conduct experiments accurately. Generally, DNA is purified to detect pathogen present in a food sample, and since the DNA may not be purified properly during the purification process, a positive control group can be set to ensure the accuracy of the experiment.

Referring to FIGS. 4 and 5, the primer set of the present invention exhibited high activity for the positive control, and excellent activity was confirmed especially in the real-time PCR equipment ABI 7500 and Bio-Rad CFX Connect.

It will be understood by those skilled in the art that the foregoing description of the present invention is for illustrative purposes only and that those of ordinary skill in the art can readily understand that various changes and modifications may be made without departing from the spirit or essential characteristics of the present invention. will be. It is therefore to be understood that the above-described embodiments are illustrative in all aspects and not restrictive. For example, each component described as a single entity may be distributed and implemented, and components described as being distributed may also be implemented in a combined form.

The scope of the present invention is defined by the appended claims, and all changes or modifications derived from the meaning and scope of the claims and their equivalents should be construed as being included within the scope of the present invention.

<110> Kyung Hee University <120> DEVELOPMENT OF SINGLEPLEX REAL-TIME PCR KIT FOR RAPID DETECTION          OF SALMONELLA TYPHIMURIUM USING TTR TARGET GENE <130> GKH17P-0109-KR <160> 2 <170> KoPatentin 3.0 <210> 1 <211> 23 <212> DNA <213> Artificial Sequence <220> <223> ttr <400> 1 ggatggctgg ctggctattc tcg 23 <210> 2 <211> 22 <212> DNA <213> Artificial Sequence <220> <223> ttr <400> 2 aacaggccat caattgcgcg tt 22

Claims (6)

A primer set for detection of Salmonella typhimurium that binds to the ttr gene. The method according to claim 1,
A primer set for detecting Salmonella typhimurium comprising a primer consisting of the nucleotide sequence of SEQ ID NO: 1 and a nucleotide sequence of SEQ ID NO: 2. A method for detecting Salmonella typhimurium comprising the steps of: performing a polymerase chain reaction (PCR) using the primer set of claim 1 or 2. The method of claim 3,
A method for detecting Salmonella typhimurium detecting target DNA at a concentration of 0.0001 to 100 ng / μL. A Salmonella typhimurium detection kit comprising the primer set of claim 1 or 2, and a PCR reaction mixture. 6. The method of claim 5,
Wherein the PCR reaction mixture comprises a reaction buffer, dNTP, and DNA polymerase.

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