Disclosure of Invention
It is an object of the present invention to provide a nucleic acid aptamer DT01 of diphtheria toxin with high specificity and high affinity; it is another object of the present invention to provide various applications of the aptamer DT01 in preparing a reagent for separating and enriching diphtheria toxin in a sample, preparing a reagent or kit for detecting diphtheria toxin, preparing a medicament for neutralizing or antagonizing diphtheria toxin, and the like.
The aim of the invention is realized by the following technical scheme: a diphtheria toxin aptamer DT01, the sequence of which is shown below:
5'-GTCGCATGGAAGGAGCGACGCCTTAGCCTCGCGTGTTCGCGTGCGGTGGAGCCGCGCAATCGGGACCGGCGGTCCAAGT-3'(SEQ ID NO:1)。
the nucleic acid aptamer DT01 of the diphtheria toxin is obtained by an in vitro SELEX screening technology based on the nucleic acid aptamer, wherein carboxyl magnetic beads are used as a solid phase medium, the diphtheria toxin is used as a target, and the nucleic acid aptamer which is specifically combined with the diphtheria toxin is obtained by screening a ssDNA library through the diphtheria toxin magnetic beads, and is named as the nucleic acid aptamer DT01.
The nucleic acid aptamer DT01 of diphtheria toxin can be subjected to chemical modification such as fluorescent group, amino group, biotin, digoxin or polyethylene glycol at the 5 'end or the 3' end.
The aptamer DT01 of the diphtheria toxin has the effect of antagonizing the toxicity of the diphtheria toxin and can be used as a potential neutralizing antagonist of the diphtheria toxin. The application of the aptamer DT01 of the diphtheria toxin in preparing medicaments for neutralizing or antagonizing the diphtheria toxin.
The application of the aptamer DT01 of the diphtheria toxin in preparing a reagent for separating and enriching diphtheria toxin in a sample.
The application of the nucleic acid aptamer DT01 of the diphtheria toxin in preparing diphtheria toxin detection reagents or kits.
The aptamer DT01 of the diphtheria toxin can also be applied to targeted treatment with the diphtheria toxin as an effector molecule.
Compared with the prior art, the invention has the advantages that:
1. the aptamer DT01 of the invention has no toxicity, small molecular weight, good permeability and easy synthesis and marking.
2. The synthesis cost of the aptamer DT01 is lower than that of antibody preparation, and the aptamer DT01 has short period and good reproducibility.
3. The aptamer DT01 of the invention can bind diphtheria toxin with high affinity and high specificity, has a dissociation constant of 23.7pM (95% IC:15.94-35.15 pM), and does not bind to other control proteins.
4. The aptamer DT01 of the invention has wide application prospect and important scientific and social value in the fields of diagnosis and treatment of diphtheria corynebacterium infection, diphtheria toxin mediated targeted treatment and the like, and particularly has the effect of antagonizing diphtheria toxin toxicity, and can be used as a potential neutralizing antagonist of diphtheria toxin.
Detailed Description
The present invention is described in detail below with reference to the drawings and examples of the specification:
a diphtheria toxin aptamer DT01, the sequence of which is as follows:
5'-GTCGCATGGAAGGAGCGACGCCTTAGCCTCGCGTGTTCGCGTGCGGTGGAGCCGCGCAATCGGGACCGGCGGTCCAAGT-3'(SEQ ID NO:1)。
the nucleic acid aptamer DT01 of diphtheria toxin is 100mM Na at 25 DEG C + ,1mM Mg 2+ The spatial structure is as follows:
the nucleic acid aptamer DT01 of the diphtheria toxin is subjected to chemical modification on the 5 'end or the 3' end of the nucleic acid aptamer DT01, including but not limited to fluorescent groups, amino groups, biotin, digoxin, polyethylene glycol and the like.
The nucleic acid aptamer DT01 of the diphtheria toxin is obtained by carrying out chemical modification on products obtained by carrying out truncated or prolonged or partial base substitution on the nucleic acid aptamer DT01, wherein the products comprise but are not limited to fluorophores, amino groups, biotin, digoxin, polyethylene glycol and the like.
The nucleic acid aptamer DT01 of the diphtheria toxin is obtained by an in vitro SELEX screening technology based on the nucleic acid aptamer, carboxyl magnetic beads are used as a solid phase medium, the diphtheria toxin is used as a target, and the nucleic acid aptamer specifically combined with the diphtheria toxin is obtained by screening a ssDNA library through the diphtheria toxin magnetic beads.
The screening method of the diphtheria toxin aptamer DT01 comprises the following steps:
(1) Preparation of screening library: a random ssDNA library shown in the following sequence was prepared:
5’-GTCGCATGGAAGGAGCGACGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGGGACCGGCGGTCCAAGT-3’;
(2) Coupling diphtheria toxin with carboxyl magnetic beads to prepare diphtheria toxin magnetic beads;
(3) Subjecting the ssDNA library to a heat activation treatment;
(4) Incubating the ssDNA library obtained in the step (3) with the diphtheria toxin magnetic beads obtained in the step (2);
(5) Magnetically separating the diphtheria toxin magnetic beads after the step (4), and washing off unbound, weakly bound and nonspecifically bound ssDNA on the surfaces of the diphtheria toxin magnetic beads; heating diphtheria toxin magnetic beads, and collecting ssDNA specifically bound with the diphtheria toxin magnetic beads, namely ssDNA enrichment library;
(6) And (3) PCR amplification: performing PCR amplification on the ssDNA enrichment library obtained in the step (5), wherein the primers used for the PCR amplification are as follows:
primer DTup:5'-FAM-GTCGCATGGAAGGAGCGACG-3'
Primer DTdown:5'-Biotin-ACTTGGACCGCCGGTCCCG-3';
(7) Purification of PCR products: purifying the PCR product by using a small fragment DNA purification kit; incubating the purified dsDNA with streptavidin magnetic beads, washing the streptavidin magnetic beads combined with the dsDNA, melting the dsDNA, separating by using a magnetic frame, and collecting the supernatant; the supernatant is subjected to ethanol precipitation to obtain a secondary ssDNA library for the next round of screening;
(8) And (3) circularly screening: taking the FAM-labeled secondary ssDNA library obtained in the step (7) as a secondary library for the next round of screening, and repeating the screening processes of the steps (3) to (7).
Embodiment one: screening of aptamer DT01
The screening method of the diphtheria toxin aptamer DT01 comprises the following steps:
(1) Preparation of screening library: designing a ssDNA random library, wherein the sequence of the ssDNA random library is as follows: 5'-GTCGCATGGAAGGAGCGACGNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNCGGGACCGGCGGTCCAAGT-3' comprising a fixed sequence region at both ends (20 nucleotides at the 5 'end and 19 nucleotides at the 3' end) and a random sequence region in the middle (40 random sequence nucleotides) and was assigned to the engineering company, inc.
(2) Diphtheria toxin is coupled with carboxyl magnetic beads: the diphtheria toxin is derived from a corynebacterium diphtheriae NCTC10648 strain with purity of >98%, and is purchased from the company The Native Antigen Company, and the carboxyl magnetic beads and the coupling reagent are purchased from the company Bangs Laboratories. Diphtheria toxin coupled to magnetic beads procedure is referred to the manufacturer's instructions. The protein concentration change in the diphtheria toxin solution before and after coupling is measured by the protein concentration BCA method, and the coupling efficiency of the magnetic beads is calculated to be 83%; diphtheria toxin magnetic beads were dispersed in PBS buffer and stored at 4 ℃.
(3) 1nmol of ssDNA random library was dissolved in 500. Mu.L of selection buffer (50 mM Tris-HCl,100mM NaCl,1mM MgCl) 2 5mM KCl, pH 7.4) and then heat-shockedAnd (5) performing living treatment. The method for heat activation treatment comprises the following steps: after denaturation at 95℃for 5min, the mixture was immediately placed in an ice-water bath for 10min and then at room temperature for 10min.
(4) The ssDNA library after step (3) was incubated with the diphtheria toxin beads (diphtheria toxin loading 20 ng) obtained in step (2) for 1h at room temperature with yeast tRNA (molar amount 5 times that of ssDNA library).
(5) Magnetically separating the diphtheria toxin magnetic beads after the step (4), and washing off unbound, weakly bound and nonspecifically bound ssDNA on the surfaces of the diphtheria toxin magnetic beads by using a selection buffer containing 0.2% BSA; then the diphtheria toxin beads were treated with 200. Mu.L ddH 2 O is resuspended, and after 5min of hot water bath at 100 ℃, the mixture is placed in a magnetic rack for 1-2min, and supernatant is collected to obtain ssDNA which is specifically combined with diphtheria toxin magnetic beads, namely ssDNA enrichment library.
(6) And (3) PCR amplification: adding the ssDNA enriched library obtained in step (5) to 1mL PCRmix; after vortex shaking and mixing, 50 mu L of each tube is subpackaged for PCR amplification, and the amplification conditions are as follows: pre-denaturing at 94 deg.c for 5 min; denaturation at 94℃for 30S, annealing at 63℃for 30S, elongation at 72℃for 30S,15-25 cycles.
Wherein 1mL of PCRmix contains: 100. Mu.L of 10 XPCR buffer; pfu enzyme 3. Mu.L; dNTP 20. Mu.L; primer DTup:5'-FAM-GTCGCATGGAAGGAGCGACG-3' and primer DTdown: 3 mu L each of 5'-Biotin-ACTTGGACCGCCGGTCCCG-3'; the primer DTup and the primer DTdown are both consigned to be synthesized by the engineering and bioengineering Co.Ltd.
(7) Purification of PCR products: PCR products, labeled with biotin and fluorescent groups FAM at both ends, were purified using a small fragment purification kit (the small fragment purification kit was purchased from Biotechnology Co., ltd.), the purified dsDNA was incubated with streptavidin beads (purchased from Invitrogen-Dynal Co.) at 37℃for 20min, and after washing the dsDNA-binding streptavidin beads three times with wash buffer (5 mM Tris-HCl, pH 7.5,1M NaCl, 500. Mu.M EDTA), dsDNA was melted by incubation with 50. Mu.L NaOH solution (0.1M) for 30min at 37 ℃; the FAM-labeled secondary ssDNA library was obtained by ethanol precipitation of the supernatant, which was isolated with a magnetic rack, and dissolved in selection buffer as the secondary library for the next round of screening.
(8) The screening process was performed for a total of 12 rounds. From the second round, the secondary libraries were used in an amount of 30pmol each.
Embodiment two: acquisition and analysis of the nucleic acid aptamer DT01 sequence:
(1) After 12 rounds of screening, the enriched ssDNA library was collected and the beijing xinnaobao medical examination was committed to all companies to analyze the library sequence using high throughput sequencing technology, the analysis process was: PCR amplifying the enriched library and adding sequencing adapter and Index portions; selecting a purified library by gel electrophoresis; measuring the concentration and purity of the DNA by using the Nanodrop one for quality control analysis; using IlluminaNovaSeq TM 6000 platform, using single-chain library as template to make bridge PCR amplification, sequencing primer annealing and sequencing while synthesizing; and comparing and enriching the sequencing result.
(2) According to the enrichment degree of the aptamer in the library, ssDNA with high enrichment degree is selected as a candidate aptamer, wherein the aptamer DT01 accounts for 12.4% of the enrichment library, and the sequence of the aptamer DT01 is shown as SEQ ID NO. 1.
(3) Analysis using a UNAFold network platform at 25℃with 100mM Na + ,1mM Mg 2+ Under the conditions of the aptamer DT01 sequence. The secondary structure schematic diagram of the sequence of the aptamer DT01 is shown in FIG. 1.
Embodiment III: specificity analysis of aptamer DT 01:
(1) FAM-labeled aptamer DT01 was synthesized chemically in vitro and dissolved in selection buffer.
(2) Referring to step (2) of example one, BSA (purchased from Sigma), pertussis Toxin (PTX, purchased from UK The Native Antigen Company) and Staphylococcus aureus enterotoxin B (SEB, purchased from Toxin Technology Co. U.S.A.) were coupled to carboxyl magnetic beads to prepare BSA magnetic beads, PTX magnetic beads and SEB magnetic beads, respectively.
(3) Mixing 200 mu L of the aptamer DT01 solution obtained in the step (1) with the BSA magnetic beads, the PTX magnetic beads, the SEB magnetic beads and the diphtheria toxin magnetic beads prepared in the step (2), incubating for 1h in a cassette at room temperature, and taking blank magnetic beads as blank control.
(4) Washing the magnetic beads of step (3) with 0.1% PBST for 3 times, and eluting the nucleic acid aptamer bound to the magnetic beads by boiling with 200. Mu.L selection buffer at 100℃for 5 min.
(5) The fluorescence intensities of the initial solution and the eluent are measured by a fluorescence quantitative analyzer, and the fluorescence binding rate = (initial fluorescence intensity-elution fluorescence intensity)/initial fluorescence intensity×100% is calculated, and the calculated value represents the binding rate of the aptamer DT01 and the target molecule.
As shown in FIG. 2, the binding rate of the aptamer DT01 and diphtheria toxin is obviously higher than that of the aptamer DT01 and BSA, PTX, SEB, which indicates that the aptamer DT01 and diphtheria toxin have better specificity.
Embodiment four: affinity analysis of aptamer DT01
(1) Mixing FAM-labeled aptamer DT01 solutions with different concentrations with diphtheria toxin magnetic beads, and incubating in a cassette at room temperature for 1h.
(2) Referring to the step (4) and the step (5) in the third embodiment, the fluorescence binding rate of the nucleic acid aptamer DT01 solution with different concentrations and the diphtheria toxin magnetic beads is obtained and calculated through experiments.
(3) And drawing a saturation binding curve of the nucleic acid aptamer DT01 binding to the diphtheria toxin by using the calculated value of the fluorescence binding rate, and calculating the dissociation constant of the nucleic acid aptamer DT01 binding to the diphtheria toxin by nonlinear regression analysis.
As shown in FIG. 3, the saturation binding curve of the aptamer DT01 is obtained, and the dissociation constant of the aptamer DT01 is 23.7pM (95% IC:15.94-35.15 pM) calculated, which shows that the aptamer DT01 has strong binding capacity to diphtheria toxin, and the dissociation constant is in the picomolar level.
Fifth embodiment: research on toxicity of nucleic acid aptamer DT01 against diphtheria toxin
(1) Determining the diphtheria toxin test dose: diphtheria toxin test dose is determined according to the standard method recommended by the national institutes of health, the main method being as follows: guinea pigs weighing around 250g (purchased from the 900 st hospital animal center) were purchased, and after 1d adaptation to the test environment, were grouped according to diphtheria toxin dose, 5 Diphtheria Antitoxin (DAT) per group, 1IU of diphtheria antitoxin (DT) was mixed with different doses of Diphtheria Toxin (DT) to prepare a mixture (designated DAT-DT), and incubated at room temperature for at least 1h. DAT-DT was subcutaneously injected at 0d per animal in a volume of 3.0mL. The physical condition and mortality of guinea pigs were observed, and the dose of diphtheria toxin, which all dead guinea pigs within 96 hours, was taken as the test dose. The lowest lethal dose was observed to be chosen as the test dose, namely ≡4fl (4.0156 fL).
(2) Method for studying the toxic effects of the aptamer DT01 against diphtheria toxin:
A. preparation of polyethylene glycol aptamer DT 01: the method comprises the steps of synthesizing a nucleic acid aptamer DT01 with amino modification at the 5 'end and dT modification at the 3' end by the IQ bioengineering Co-Ltd; and then, carrying out polyethylene glycol treatment on the modified nucleic acid aptamer DT01 by using 40-kDa polyethylene glycol (PEG), thus obtaining the polyethylene glycol nucleic acid aptamer DT01 (PEG-DT 01), wherein the polyethylene glycol treatment process is entrusted to completion of Beijing key Kai technology Co., ltd, and the PEG-DT01 is homozygous by HPLC for later use.
B. Animal model experiment of aptamer DT 01: guinea pigs weighing around 250g (purchased from the 900 st hospital animal center) were purchased, and after 1d adaptation to the test environment, 5 animals per group were grouped according to doses of diphtheria antitoxin and aptamer, and different doses of pegylated aptamer DT01 (PEG-DT 01), diphtheria Antitoxin (DAT) were mixed with 4fL Diphtheria Toxin (DT) to prepare mixtures (designated PEG-DT01-DT and DAT-DT, respectively) and incubated at room temperature for at least 1h. PEG-DT01-DT and DAT-DT were subcutaneously injected at 0d per animal, in a volume of 3.0mL. The physical condition and mortality of guinea pigs were observed, and the observation time was extended from standard 96h to 30d to allow greater discrimination of dose effects and assessment of signs of toxin-induced end organ damage occurring 30d after toxin exposure. Animals were observed daily for signs of diphtheria toxin poisoning, and body weight was measured weekly as a measure of overall health. Establishing a digital scoring system for clinical symptoms: asymptomatic = 0; sloppy fur = 1; comatose = 2; dehydration = 3; dragging one or two hind legs = 4; moribund = 5; death=6. Animals that are dying or animals that have a weight loss of 20% from baseline are euthanized.
(3) Results of studies on antagonism of diphtheria toxin toxic effects by aptamer DT 01: as shown in Table 1, in the animal model receiving DAT-DT injections, all guinea pigs receiving DAT doses of 1.25IU or less died, and the lower the DAT dose, the earlier the guinea pigs died; all guinea pigs receiving a DAT dose of > 1.75IU survived. Survival was variable in guinea pigs receiving DAT doses of 1.5IU-1.6 IU. In the animal model receiving PEG-DT01-DT injection, all guinea pigs receiving the PEG-DT01 dosage of 16 μg or less die, and the lower the dosage, the earlier the guinea pigs die; all guinea pigs receiving a PEG-DT01 dose of > 48 μg survived. Survival was variable in guinea pigs receiving PEG-DT01 doses of 16-48 μg, suggesting that the aptamer DT01 has a similar effect as diphtheria antitoxin. In addition, clinical symptoms of the tested guinea pigs are observed, and when the dosage of PEG-DT01 is more than or equal to 64 mug, the clinical manifestation fraction of all the guinea pigs is less than or equal to 3, which indicates that the aptamer DT01 can be used as an antagonist to effectively neutralize the toxic effect of diphtheria toxin and relieve the clinical symptoms of diphtheria toxin poisoning.
TABLE 1 protection of diphtheria toxin lethal guinea pig model by aptamer DT01 and diphtheria antitoxin
The foregoing is merely a preferred embodiment of the present invention, and it should be noted that changes, modifications and adaptations to those skilled in the art may be made without departing from the spirit of the present invention and are intended to be comprehended within the scope of the present invention.
Sequence listing
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