Disclosure of Invention
In view of the above problems, the present invention provides a biomacromolecule hypersensitive immunoassay method based on triple extension-RNA amplification mediation, namely immune-TEBRA (triple extension-based RNAamplification). The method has the characteristics of high sensitivity, small antibody dosage and low requirement on instruments, can be used for the hypersensitive detection of biomedical indexes, and can also be used for establishing a new drug screening platform based on the monitoring of the concentration of biomarkers.
In order to solve the problems in the prior art, the invention is realized by the following technical scheme:
in a first aspect of the present invention, there is provided a biomacromolecule immunoassay method based on three times of extension-RNA amplification mediation, comprising the following steps:
1) design of related probes and primers:
(1) design of the first and second proximity probes: oligo1, 20-30nt DNA in total length, with a tag sequence ZC at one end and a complementary matching sequence (5-6 nt in length) at the other end with the end of oligo 2; oligo2, DNA with a total length of about 20-30nt, wherein one end is a T7 promoter sequence, and the other end (with a length of 5-6 nt) is complementarily paired with the end of Oligo 1;
oligo1 and Oligo2 are coupled with a substance recognizing biological macromolecules respectively to form a substance recognizing biological macromolecules-Oligo 1, a substance recognizing biological macromolecules-Oligo 2, and substances marking Oligo1 and Oligo2 are antibodies binding with biological macromolecules or biotin with affinity; because the pair of oligos is designed to be short in length (about 20-30nt), the oligo coupled with the biomacromolecule-recognizing substance can be separated from the free oligos by a simple centrifugal column chromatography after coupling;
(2) amplification primer R (named oligo 3): oligo3 has two parts, the 3 'end is complementary paired with the sequence of half of the transcribed small RNA, i.e., it hybridizes to half of the molecule at the 3' end of the transcribed small RNA by 10 or 11 nucleotides in length; the other end is a tag sequence (named as ZC1, ZC2) and a T7 promoter sequence; designing a capture probe and a detection probe according to a tag sequence for qualitative analysis of a subsequent amplification product, wherein the tag sequence is designed according to needs and has 1-2 strips and the length of 16-20 nt; the T7 promoter sequence is the T7 polymerase recognition site for subsequent transcription by T7 polymerase;
(3) stabilizing sequence 1: to increase the stability of oligo3 and the transcribed small RNA hybrid, stable sequence 1 was introduced, which binds to the tag sequence of oligo3, the complementary pairing of the T7 promoter;
(4) amplification primer F (named oligo 4): similar to the characteristics of oligo3, the cDNA has two parts, one end of which is the same as half of the molecular sequence (10-11 nucleotides) of the 5' end of the transcribed small RNA and can be combined with the cDNA sequence of the full-length transcribed small RNA in a complementary pairing way; the other end contains a tag sequence (named as ZC3), and the tag sequence can be used for coating probes or designing detection probes in the subsequent qualitative detection of an amplification product;
(5) stabilizing sequence 2: in order to increase the stability of the binding of oligo4 to the newly synthesized oligo 3-RNA-cDNA, a stabilizing sequence 2 was introduced, characterized by complementary paired binding to the tag sequence ZC 3;
2) biomacromolecule detection
(1) In a single reaction tube, a substance-oligo 1 (the substance for labeling oligo1 can be an antibody binding to the biological macromolecule, or biotin with affinity ability, etc.) for recognizing the biological macromolecule and a substance-oligo 2 (the substance for labeling oligo2 can be an antibody binding to the biological macromolecule, or biotin with affinity ability, etc.) for recognizing the biological macromolecule are simultaneously bound to the target biological macromolecule, because of the proximity (proximity), 6 nucleotide molecules at the tail of oligo1 and oligo2 are complementarily paired and bound, and then, the extension is carried out under the action of Klenow enzyme to form a dsDNA, which is the first sequence extension;
(2) the dsDNA formed in the step (1) contains a T7 promoter, and small RNA molecules with the size of 20-25 nt are transcribed under the action of T7 polymerase;
(3) and (3) combining the oligo3 with a half sequence at the end of the small RNA 3' transcribed in the step (2) to form a small RNA-oligo3 complex, wherein in order to increase the stability of the complex, the stable sequence 1 is combined to the complex by the principle of base complementary pairing, and finally the oligo3, the stable sequence 1 and the small RNA form a stable oligo 3/stable sequence 1-RNA complex by the fusion effect (stacking effect), and the complex obtains the full-length cDNA of the small RNA molecule under the action of reverse transcriptase, namely, the oligo 3-RNA-cDNA: an RNA complex, which is a second sequence extension;
(4) step (3) oligo 3-RNA-cDNA: under the action of RNaseH, RNA in the RNA complex can be degraded to form oligo 3-RNA-cDNA;
(5) complementary pairing and combination of oligo4 and oligo 3-RNA-cDNA to form oligo 3-RNA-cDNA-oligo 4 complex; to increase the stability of the complex, the stable sequence 2 is bound to the complex by the base complementary pairing principle, and finally Oligo4, the stable sequence 2, the stable sequence 1 and Oligo3 synthesized Oligo 3-RNA-cDNA form a stable complex by the fusion effect (stacking effect), i.e., Oligo 3-RNA-cDNA-Oligo 4/stable sequence 2 complex. The complex obtains double-stranded DNA containing a T7 promoter sequence, a tag sequence and the full length of a small RNA molecule under the action of reverse transcriptase, namely oligo 3-RNA-cDNA-oligo 4 double-stranded DNA, which is the third sequence extension;
(6) the sequence structure of the oligo 3-RNA-cDNA-oligo 4 double-stranded DNA formed in (5) is T7 promoter-ZC 2-ZC 1-RNA-cDNA-ZC 3, and the double-stranded DNA can be amplified by a TMA or NASBA method to obtain an RNA molecule with the sequence of ZC2-ZC 1-RNA-cDNA-ZC 3;
(7) detecting the presence, absence and/or amount of the amplified product of the RNA, thereby determining the presence, absence and/or amount of the biomacromolecule to be detected.
In another preferred example, the detection result in the step 2) and the step 7) is a qualitative or quantitative result.
In another preferred example, the method for detecting the amplification product of the RNA in step 2) (7) comprises molecular beacon, plate hybridization-signal amplification, or nucleic acid colloidal gold detection.
In another preferred example, the method for detecting the amplification product of the RNA in the step 2) (7) is plate hybridization-signal amplification detection, and particularly, a capture probe is designed according to a tag sequence (such as ZC3), and the capture probe can be combined with ZC3 in a complementary pairing manner, so that the amplified RNA molecule can be immobilized in a microplate or on other solid phase carriers; and designing a detection probe according to a tag sequence (such as ZC1 and ZC2), wherein the detection probe can be combined with the bases of ZC1 and ZC2 in a complementary pairing mode, the detection probe can be labeled with biotin, the biotin is further labeled on an amplified RNA molecule, streptavidin-HRP (Strep-HRP) and a chemiluminescent substrate can be sequentially added subsequently, and finally, the existence or quantity of an amplification product is detected by a chemiluminescent method, so that the detection condition of the biomacromolecule to be detected is judged.
The biomacromolecule mentioned above refers to substances that can recognize each other by specific interaction, such as antibodies and antigens, receptors and ligands, enzymes and substrates, lectins and polysaccharides.
The principle of the invention for detecting biomacromolecules is shown in figure 1.
Compared with the prior art, the invention has the following advantages and beneficial effects:
1. oligo1 and oligo2 were designed to be short in length, and labeled to recognize biomacromolecules, which could be easily separated from free oligos.
2. The detection sensitivity is higher due to the three times of sequence extension, and the sensitivity of the test detection of the biomacromolecule can reach the level of 0.75 pg/ml.
3. The amplification in the whole process is constant-temperature amplification, the requirement on an instrument is low, the detection can be realized by one constant-temperature device, and the popularization of the technology is facilitated.
Detailed Description
The features and advantages of the present invention will be further understood from the following detailed description taken in conjunction with the accompanying drawings. The examples provided are merely illustrative of the method of the present invention and do not limit the remainder of the disclosure in any way.
Experimental procedures without specific conditions noted in the following examples, molecular cloning is generally performed according to conventional conditions, e.g., Sa mb r ook et al: the conditions described in the laboratory Manual (N e w Y o r k: C o l d S p r i N g H a r o r laboratory Press,1989), or according to the manufacturer' S recommendations. Unless otherwise indicated, percentages and parts are percentages and parts by weight.
Example 1 activation of antibodies and proximity probes (oligo1 and oligo2)
Before the antibody is labeled with the proximity probe, the antibody and the proximity probe are subjected to corresponding activation treatment, which is specifically as follows:
1) activation treatment of antibody
(1) The antibody was dissolved in PBS buffer (pH8) and the antibody concentration was diluted to 1 mg/ml.
(2) Mu.l of antibody (1mg/ml) + 5. mu.l of TCO-PEG4-NHS (10mM) were mixed well and reacted at room temperature for 30 min.
(3) Adding Tris-HCl buffer solution (1M, Ph8.0) into the system, and stopping the reaction until the final concentration of Tris-HCl is 50-100 mM.
(4) Incubate at room temperature for 5 min.
(5) The product was passed through a column (7K pore size desalting column) to remove free TCO-PEG4-NHS and non-activated antibody, greater than 7K was eluted and collected, and less than 7K remained in the column. The resulting product is the activated antibody.
2) Activation treatment of proximity probes
(1) The proximity probes were dissolved to 100. mu.M with PBS buffer (pH 8).
(2) Mu.l of oligo (100. mu.M) + 5. mu.l of PEG4-NHS (10mM) were mixed well and reacted at room temperature for 30 min.
(3) Adding Tris-HCl buffer solution (1M, pH8.0) into the system, and stopping the reaction, wherein the addition amount is 50-100 mM of the final concentration of Tris-HCl.
(4) Incubate at room temperature for 5 min.
(5) The product was passed through a column (BioRad P-30Columns, 40,000MW limit, eluent PBS) to remove the unactivated oligo and free PEG 4-NHS. More than 40K will be collected by elution and less than 40K will remain in the column. The resulting product is the activated oligo.
Example 2 linking of proximity probes to antibodies after activation
1) Mu.l of activated oligo1 and 50. mu.l of activated antibody were dissolved in PBS buffer (pH8) to 200. mu.l and reacted at room temperature for 1 hour.
2) Purification of the labeled antibody: the purification was performed by Bio-Spin 30Tris Columns (buffer exchanged for PBS), and oligo of less than 30bp was retained in the column after column purification, thereby removing unlabeled oligo.
3) The marker was purified again using a 50K Milipore filter.
4) The final product is labeled with the antibody of the proximity probe (oligo1, oligo 2).
Example 3 detection of Vascular Endothelial Growth Factor (VEGF)
1) VEGF polyclonal antibodies (purchased from Thermo Fisher, LotNumber: P802) were labeled with oligo1 (sequence ACCCGATGGATAGGTCGGTGAA-ACGCAT) and oligo2 (sequence TAATACGACTCACTATAGGGAGA-ATGCGT) in which oligo2 carries the T7 promoter sequence and oligo1 and oligo2 can be linked by 6 base complementary pairings at the respective 3' ends.
2) Detection of VEGF
(1) Formation of double strands of antibody oligo1 and antibody oligo2
VEGF (purchased from Thermo Fisher, Lot Number: PHC9391) was diluted in a 2-fold concentration gradient and subjected to a first sequence extension as follows to give a duplex of oligo1 and oligo 2:
incubate at 37 ℃ for 40 min.
(2) RNA transcription
Transcription was performed according to the following system (transcription system purchased to Thermo Fisher):
1 hour at 37 ℃.
(3) RNA amplification
And (3) amplifying the transcribed small RNA in the step (2) to realize second and third sequence extension, wherein the design of related primers and probes is shown in the table 1.
TABLE 1 second and third sequence extension, related primer and probe design
Small RNAs were amplified according to the following system:
(2) small RNA products of medium transcription: 2 μ l
Buffer (containing oligo3 and its stabilizing sequence,
oligo4 and its stabilizing sequence): 17 μ l
1 μ l of the amplification enzyme mixture (AMV & T7 polymerase & RNaseH)
The reaction was carried out at 42 ℃ for 90min and then examined.
(4) Detecting and analyzing the product in (3) by plate hybridization
Detecting the transcribed small RNA product by a microplate hybridization method, designing a capture probe and a detection probe (a detection probe 1 and a detection probe 2) in a detection system according to the ZC sequence information of the RNA to form a detection probe-RNA product-capture probe compound, wherein the compound can be captured by a section of probe coated in a micropore and is fixed in the micropore. And sequentially adding a section of biotin-labeled probe capable of being combined with the detection probe, streptavidin-HRP enzyme and a chemiluminescent substrate into the micropores, and finally performing luminescence detection. In particular, the method comprises the following steps of,
a. immobilized hybridization of amplification products
Incubate at 42 ℃ for 60 min.
b. The well was discarded and patted dry on clean absorbent paper. Add 200. mu.L of pre-warmed hybridization wash to each well for a total of 3 washes.
c. Add 200. mu.L of blocking solution to each well and shake for 1 min at room temperature.
d. The liquid in the wells was discarded, and 100. mu.L of streptavidin-HRP enzyme conjugate was added to each well and shaken at room temperature for 30 minutes.
e. The well was discarded and patted dry on clean absorbent paper. Add 200. mu.L of pre-warmed hybridization wash to each well for a total of 3 washes.
f. Preparing a substrate solution, wherein a substrate A, a substrate B and a substrate diluent (Tris buffer solution, pH8.5) are mixed according to the proportion of 1: 1: 8 and mixing uniformly.
g. 95 μ L of substrate solution was added to each well and after 5 minutes of incubation, the Relative Light Units (RLU) were measured on a chemiluminescence detector.
h. The experimental results are as follows:
| content of VEGF | Dilution ratio | RLU value |
| 125pg/ml | 1:1600 | 3506542 |
| 62.5pg/ml | 1:3200 | 1813211 |
| 31pg/ml | 1:6400 | 1023212 |
| 15.5pg/ml | 1:12800 | 609832 |
| 7.5pg/ml | 1:25600 | 423216 |
| 3.5pg/ml | 1:51200 | 205432 |
| 1.5pg/ml | 1:102400 | 108844 |
| 0.75pg/ml | 1:204800 | 66543 |
| 0.36pg/ml | 1:409600 | 44332 |
| Blank | / | 10355 |
The detection result shows that the detection sensitivity can reach the level of 0.75pg/ml when the detection method detects VEGF.
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