CN110343753B - Nucleotide molecule sequencing method of phosphate modified fluorophore - Google Patents
Nucleotide molecule sequencing method of phosphate modified fluorophore Download PDFInfo
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Abstract
The invention relates to a polynucleotide sequencing method, in particular to a method for sequencing mixed nucleotide molecules modified by phosphate with fluorophores. In the invention, each round of sequencing uses a set of reaction solution, each set of reaction solution at least comprises two reaction solutions, each reaction solution comprises at least one of A, G, C, T nucleotide molecules, or each reaction solution comprises at least one of A, G, C, U nucleotide molecules; at least one of the reaction solutions contains two or three different nucleotide molecules.
Description
Technical Field
The invention relates to a high-throughput sequencing method, and belongs to the field of gene sequencing.
Background introduction
High throughput sequencers are a technology that has developed at a rapid pace in recent years. Compared with the traditional Sanger sequencing, the high-throughput sequencing has the greatest advantage that massive sequence information can be read simultaneously. Although the accuracy is not as good as that of the traditional sequencing method, information beyond the sequence itself, such as gene expression amount and copy number variation, can be obtained due to massive data analysis.
Currently, the mainstream sequencers use the SBS (sequencing by synthesis sequencing) method, such as solexa/illumina, 454, iontorent, etc. These sequencers are structurally similar and include fluidic systems, optical systems, and chip systems. The sequencing reaction takes place on-chip. The sequencing process is also similar, and comprises the following steps: and introducing the reaction liquid into the chip to perform SBS reaction, collecting signals, washing and performing the next round. Such a periodic process. With the increase of the cycle, continuous single-base non-degenerate sequence information (e.g., ACTGACTG) is measured. However, high throughput sequencers do not completely eliminate sequencing errors. Sequencing errors may result from: occasional errors or cumulative errors in response, errors in signal acquisition, errors in signal correction, and the like. In the conventional sequencer, these chemical or optical errors, software errors, or noises cannot be recognized at a single read site. Elimination can only be achieved by deep sequencing, using multiple reads of the same sequence at different sites. More accurate read-out is an important direction in the development of high-throughput sequencing. However, the prior art has no innovation in sequencing logic because the optimization of the accuracy mostly focuses on the optimization of the chemical reaction itself and the subsequent image signal processing.
The invention relates to a polynucleotide sequencing method, in particular to a method for sequencing mixed nucleotide molecules modified by phosphate with fluorophores. Meanwhile, the invention relates to a method for sequencing a fluorophore with fluorescence switching property. Fluorophore sequencing of the fluorescence switching nature uses a terminal phosphate-labeled nucleotide substrate. Substrates for fluorophores of the fluorescence switching nature are of the general formula: a fluorophore having fluorescence switching properties is modified at the end or in the middle of the 5' polyphosphate. It is characterized in that the terminal phosphate or the middle phosphate of deoxyribonucleotides (including A, C, G, T, U and other nucleotides) of 4, 5, 6 or more phosphates is modified with a fluorescence-switched fluorophore, and the base and 3' hydroxyl are not labeled. This fluorophore when modified on the phosphate will have an absorption spectrum and/or emission spectrum that is different from that when the phosphate is cleaved off. Sequencing is again a continuous, similar cycle (cycle) component. Each period comprises the steps of sample introduction, reaction and signal acquisition, and cleaning of unreacted reactant molecules. In the previously reported method, substrate molecules of one base are introduced each time, and if incorrect pairing occurs, no reaction occurs; if correctly paired, the polymerase attaches the substrate molecule to the 3' tail and releases the polyphosphate-modified fluorescent molecule and the fluorescence spectrum changes. If successive pairings with homopolymers are possible, there is a fold change in the spectrum. In practical applications, fluorophores with fluorescence-switching properties, which are labeled without absorption on the terminal phosphate and with a high quantum yield in the released state, tend to be used as modifying labels for substrate molecules, such as methyl fluorescein, halogenated methyl fluorescein, DDAO, resorufin, fluorescent molecules as referred to in CN104844674, and the like. The four substrate molecules may be labeled with different fluorescent molecules. In the sequencing process, ACGTACGT … or any circulating or non-circulating sample injection process is used for sample injection, and the sequencing reaction is carried out on the reaction solution containing the substrate molecules in a limited period. The DNA sequence was obtained from the extension information obtained for each cycle.
Disclosure of Invention
The invention relates to a method for sequencing by using nucleotide molecules with fluorescence switching fluorophores, which is characterized in that the nucleotide substrate molecules modified with fluorescence switching fluorophores at the tail ends of 5' polyphosphoric acid or middle phosphoric acid are used for sequencing; the fluorescence switching property means that the fluorescence signal intensity after sequencing is obviously increased compared with that before sequencing reaction; using a set of reaction solution groups for each round of sequencing, wherein each set of reaction solution group comprises at least two reaction solutions, each reaction solution comprises at least one of A, G, C, T nucleotide molecules, or each reaction solution comprises at least one of A, G, C, U nucleotide molecules; firstly, fixing a nucleotide sequence fragment to be detected in a reaction chamber, and introducing one reaction solution in a set of reaction solution groups; detecting and recording fluorescence information; introducing one reaction solution each time, sequentially introducing other reaction solutions in the same reaction solution group, and detecting and recording fluorescence information each time; wherein, in the reaction liquid group, at least one reaction liquid comprises two or three different nucleotide molecules; in the sequencing, an enzyme is used to release a fluorophore on a nucleotide substrate of the fluorophore having a fluorescence switching property, thereby causing fluorescence switching.
The invention relates to a method for sequencing by using nucleotide molecules with fluorescence switching fluorophores, which is characterized in that the nucleotide substrate molecules modified with fluorescence switching fluorophores at the tail ends of 5' polyphosphoric acid or middle phosphoric acid are used for sequencing; the fluorescence switching property means that the fluorescence signal intensity after sequencing is obviously increased compared with that before sequencing reaction; each round of sequencing uses a set of reaction solution group, each set of reaction solution group at least comprises two reaction solutions, each reaction solution comprises any one of A, G, C, T nucleotide molecules, or each reaction solution comprises any one of A, G, C, U nucleotide molecules; firstly, fixing a nucleotide sequence fragment to be detected in a reaction chamber, and introducing one reaction solution in a set of reaction solution groups; detecting and recording fluorescence information; and introducing one reaction solution each time, sequentially introducing other reaction solutions in the same reaction solution group, and detecting and recording fluorescence information each time.
The invention relates to a method for sequencing by using nucleotide molecules with fluorescence switching fluorophores, which is characterized in that the nucleotide substrate molecules modified with fluorescence switching fluorophores at the tail ends of 5' polyphosphoric acid or middle phosphoric acid are used for sequencing; the fluorescence switching property refers to that the fluorescence signal intensity after sequencing is obviously increased compared with that before sequencing reaction; each round of sequencing uses a reaction solution group, wherein the reaction solution comprises A, G, C, T four nucleotide molecules, or the reaction solution comprises A, G, C, U four nucleotide molecules; fixing the nucleotide sequence fragment to be detected in a reaction chamber, and introducing a reaction solution; and detecting and recording fluorescence information.
In addition, according to a preferred embodiment of the present invention, the method further comprises removing the residual reaction solution and the fluorescent molecules by using a washing solution, and then performing the next round of sequencing reaction.
According to the preferred technical scheme of the invention, the reaction solution can be fed at a low temperature, then heated to the enzyme reaction temperature, and then the fluorescence signal is detected.
According to the preferred technical scheme of the invention, after the reaction liquid is introduced, the reaction chamber is closed, and then the fluorescence information is detected and recorded.
According to the preferred technical scheme of the invention, after the reaction liquid is introduced, the space outside the reaction chamber is filled with oil, so that the reaction chamber is isolated and closed.
According to a preferred embodiment of the present invention, the nucleotide substrate molecule of a polyphosphoric acid refers to a nucleotide having 4 to 8 phosphate molecules;
according to the preferred technical scheme of the invention, the nucleotide substrate molecule modified with the fluorophore can be marked by a fluorophore according to different bases to perform monochromatic sequencing; multicolor sequencing can also be performed with different fluorophore labels.
According to a preferred embodiment of the invention, the step of releasing the fluorophore on the nucleotide substrate of the fluorophore having fluorescence-switching properties is carried out using an enzyme comprising DNA polymerase and/or alkaline phosphatase.
According to the preferred technical scheme of the invention, the two bases on the nucleotide sequence to be detected refer to any two bases in A, G, C, T or any two bases in A, G, C, U; wherein base C is either methylated C or unmethylated C.
According to a preferred embodiment of the present invention, the reaction solution contains the enzyme, that is, when the reaction solution is introduced into the reaction region where the gene fragment to be detected is located, the enzyme contained therein releases the fluorophore on the nucleotide substrate having the fluorophore with the fluorescence switching property.
According to a preferred embodiment of the present invention, the reaction solution and the enzyme are not added simultaneously; firstly, introducing a reaction solution in a set of reaction solution group, and introducing an enzyme solution; then the second reaction solution in the same set of reaction solution is introduced, and the enzyme solution is introduced.
According to the preferred technical scheme of the invention, one set of reaction liquid groups can be used for carrying out one round of sequencing, two sets of reaction liquid groups can be used for carrying out two rounds of sequencing, and three sets of reaction liquid groups can be used for carrying out three rounds of sequencing.
According to a preferred embodiment of the present invention, a degenerate coding result is obtained by performing one round of sequencing with a set of reaction sets.
According to the preferred technical scheme of the invention, two sets of reaction solution groups are used for carrying out two rounds of sequencing to obtain base sequence information.
According to the preferred technical scheme of the invention, three sets of reaction liquid are used for three rounds of sequencing, and on the basis of two rounds of sequencing results, the mutual information among the three rounds of sequencing is utilized for error checking.
According to a preferred embodiment of the present invention, the fluorophore having fluorescence switching property refers to a fluorophore having a structure of methyl fluorescein, halogenated methyl fluorescein, DDAO, resorufin, etc.
According to a preferred embodiment of the present invention, the use of an enzyme to release a fluorophore on a nucleotide substrate of a fluorophore having a fluorescence-switching property preferably means that a polyphosphate-substituted fluorophore is first released using a DNA polymerase and then the substituted polyphosphate is cleaved using a phosphatase to release the fluorophore.
According to a preferred embodiment of the present invention, when the reaction solution contains two or more nucleotides with different bases, the reaction solution can be simply split into two or more reaction solutions, each of which contains one or more nucleotides; at least one of the reaction solutions contains nucleotides of two or three different bases.
A method of high throughput sequencing using any of the methods described above, wherein the sequencing reaction is performed on a chip having a plurality of reaction chambers, and the nucleotide sequence fragments to be detected are immobilized in the reaction chambers.
The invention relates to a polynucleotide sequencing method, in particular to a method for sequencing mixed nucleotide molecules modified by phosphate with fluorophores. Compared with a sequencing method of non-phosphate modified mixed nucleotide, the method has the advantages of convenient hydrolysis, no introduction of other groups after the reaction is finished, contribution to extension of the sequencing reaction and simple sequencing reaction. Furthermore, the present invention combines fluorescence-switched sequencing with polynucleotide sequencing, which has unexpected effects. For example, sequencing fluorescence-switched polynucleotides provides data redundancy and verification features, which further improves the accuracy of the sequencing data, and sequencing with unclosed 3-termini also makes the sequencing reaction not require real-time information acquisition, which further improves the accuracy of the signals. Independently of the sequencing chemistry principle itself, it can be matched to different sequencing chemistries. Furthermore, the fluorescence switching property of 2+2 (two bases at a time) has obvious advantages compared with other polynucleotide sequencing methods, and the method is relatively easy to analyze data and provides characteristics of data redundancy and verification. The special signal acquisition mode and acquisition efficiency of the method make the method have great application prospect in the gene sequencing direction. Fluorescence-switched multi-base sequencing reduces the error rate and makes the reaction simpler compared to non-fluorescence-switched polynucleotide sequencing. The fluorescence switching polynucleotide method has the sequencing accuracy of 99.99 percent, the reading length exceeding ILLUMINA sequencing can reach more than 300nt, and the cost of raw materials is low. It adopts the method of reaction first and then scanning, and has no limitation of flux. The monograph reaction time is short, and the rapid detection can be realized. By adopting the strategy of fluorescence switching and mixed sequencing of multiple nucleotide molecules, the sequencing read length of each reaction cycle and the information content of each reaction cycle can be prolonged. For example, the read length of the illumina sequencing per reaction cycle is 1nt (1 base), and the information content is 2 bits. 2+2 (two different basic nucleotide molecules are entered each time, two reaction liquids are totally used) monochrome sequencing, the read length of each reaction period is 2nt, and the information amount is 2 bit. 2+2 two-color sequencing, each reaction cycle of the read length of 2nt, information content is about 3.4 bit.
The words used in the specification are words of art that are basically common to the art, and for further clarity, the words used in the specification are explained further below.
Fluorescence generating, fluorescence generating fluorophore: some fluorophores have the property that when a substituent is changed, the fluorescence spectrum (absorption and reflection spectrum) changes, known as fluorescence switching.
When under certain excitation and acquisition (emission) conditions, the intensity of the acquired signal rises, termed fluorescence occurs.
Nucleotides and nucleotide tags: the nucleotide molecule comprises a ribose skeleton, a base molecule at the glycosidic position, and a polyphosphoric acid chain connected with a hydroxyl at the 5-position of the ribose skeleton. The 2C of the ribose ring may be linked to a hydroxyl group (to form a ribonucleotide) or to only H (to be referred to as a deoxyribonucleotide). The base molecule may be the main base of 4: ACGT, and uracil, and modified bases such as methylation, hydroxymethylation, and the like. The number of phosphate backbones can be 1 to 8. The micelle may be modified at multiple positions. At the 3C hydroxyl of the ribose backbone, at the phosphate. The position of the modification may be one or more. For example, the fluorophore is modified at the phosphate and the ethynyl group is modified at the 3C.
An unmodified polyphosphate nucleotide substrate at 3C (greater than three phosphates) retains the active hydroxyl group at the 3 position during the polymerase chain reaction. The polymerase reaction continues until the paired bases are missing or a 3C non-hydroxyl-containing nucleotide molecule is bound, as long as the next bases can still pair.
A fluorescence-generating nucleotide: the phosphate end is labeled with a nucleotide molecule of a fluorescence-generating fluorophore that can be switched by the phosphohydrolysis process, referred to as a fluorescence-generating nucleotide for short. The length of the phosphate chain may be 4-8.
Not important: the phosphate may be terminal, or pendant. The number of the marks may be 1 or more. The plurality of labels may be the same or different.
More precisely, nucleotides which are fluorescent for the polymerase, and which may also be fluorescent, are not labeled at the phosphate position, nor are fluorescent for the polymerase.
The nucleotide molecule may be a ribonucleotide, a deoxyribonucleotide, or a (deoxy) ribonucleotide modified at the 3' C
Fluorescence-generating nucleotide polymerase reaction: the fluorogenic nucleotide polymerase reaction uses fluorogenic nucleotides, nucleic acid polymerase (DNA polymerase), phosphatase, together with a nucleic acid substrate. The DNA polymerase first polymerizes the fluorogenic nucleotide into the nucleic acid substrate, releasing the phosphorylated fluorogenic fluorophore, which is then further hydrolyzed by a phosphatase to remove the phosphate, releasing the fluorogenic fluorophore with a changed fluorescence state.
Fluorescence generation sequencing: the information of the polymerase reaction can be obtained by using the fluorescence-generated nucleotide polymerase reaction and detecting the fluorescence change (light intensity and spectrum) of the fluorescence-generated fluorophore.
Fluorescence generation sequencing reaction solution: comprises a fluorescence generating nucleotide, a nucleic acid polymerase (DNA polymerase) and a phosphatase.
The fluorogenic nucleotide may be one or more. The nucleotide species may be one or more. The plurality of substrates may be labeled with the same or different fluorogenic substrates, respectively.
A set of fluorescence generation sequencing reaction solution: comprises more than 2 fluorescence generation sequencing reaction liquids. For example, four reaction solutions containing A, C, G and T at specific concentrations. Or two reaction solutions containing specific concentrations (AC), (GT).
One cycle of fluorescence sequencing reaction: a sequencing reaction solution was used to perform a fluorescence-generating polymerase reaction, and a fluorescent signal was detected.
One round of fluorogenic sequencing reaction: and (3) using a set of fluorescence generation sequencing reaction solution, and sequentially carrying out sequencing reaction cycles by using members of the set of fluorescence generation sequencing reaction solution according to a determined sequence.
One set of fluorogenic sequencing reactions: comprising one or more cycles of fluorogenic sequencing.
Single base resolution sequencing: one way to achieve this is (2+2 monochrome sets), where the first reaction is mixed with two bases (e.g., AC) and the second reaction is mixed with two other bases (e.g., GT), and the two reactions are sequenced alternately. In this case, the number of bases extended per cycle becomes large. After N rounds of sequencing, the extension base was 2N nt. The carried information is 2N bit. The sequencing is completed by 3 combinations, namely AC/GT, AG/CT and AT/CG; or according to standard degenerate nucleotide (marker) marks written as M/K, R/Y, W/S. The three combinations can be sequenced separately, or re-sequenced after completing another set of sequencing. The ith base on the DNA sequence is detected and must be paired by polymerase in a unique cycle in both sets of sequencing and release the signal. In each set of sequencing, there are two possible sampling periods for detecting the base, so that there are 4 possible cases of 2x 2. Corresponds exactly to 4 bases. Sequencing combination sequencing does not affect the inference of bases.
In a further embodiment, a third set of different reaction solution combinations is used for sequencing after a second set of different sequencing. The ith base on the DNA sequence is detected and must be paired by polymerase in a unique cycle of the three sets of sequencing and release the signal. In each set of sequencing, there are two possible sampling periods for detecting the base, so that there are 8 possible cases of 2x 2x 2. Only 4 of them are justified, the other four are unreasonable. In true fluorescence-switched sequencing, insertion or deletion errors are likely to occur in the sequencing. For a certain base, if a sequencing error occurs in one of 3 sets of sequencing, the sequence cannot be correctly deduced, and it can be concluded that a sequencing error occurs in one or more of 3 sets of sequencing.
Such errors can be corrected. Because when a sequencing error in a single set of data is corrected, a large number of subsequent errors are corrected together.
Another embodiment, two rounds of 2+2, the first reaction solution is mixed with two bases and carries a different fluorescent label (e.g., A-X/C-Y), and the second reaction solution is mixed with two other bases (e.g., G-X/T-Y). In this case, the number of extended bases per cycle was increased to 2nt on average. The carried information is 3.4 bits.
Detailed Description
To further illustrate the present invention, the following specific embodiments are now set forth. The specific parameters, steps, etc. involved are conventional in the art. The detailed description and examples do not limit the scope of the invention.
Example 1.
2+2 sequencing, single color: 3 sets of reaction liquid are prepared, each set comprises two bottles, each bottle comprises two bases marked with fluorescent groups, and the fluorescent groups are X. Two reaction vials in one set contained exactly the entire 4 bases. 6 bottles of solution were not repeated.
| First bottle | Second bottle | |
| First set | AX+CX | GX+TX |
| Second cover | AX+GX | CX+TX |
| Third set | AX+TX | CX+GX |
The complete sequencing process comprises three rounds, which are performed sequentially. The three sets of reagents were used for each round of sequencing. Otherwise, the reaction conditions were identical (identical using the same sequencing primers).
Each round of sequencing contained:
1. hybridizing sequencing primer on prepared DNA array
2. The sequencing process is started. The process of 2.1-2.4 is repeated for a limited number of times.
2.1 into the first vial of reagent. Reacting and collecting fluorescence signals.
2.2 washing of all residual reaction solution and fluorescent molecules produced in flowcell
2.3 into a second vial of reagent. Reacting and collecting fluorescence signals.
2.2 Wash all residual reaction solution and resulting fluorescent molecules in flowcell
3. The extended sequencing primer was unwound.
At this point, the next round of experiment can be performed.
Preparing a reaction solution:
preparing a washing solution of a sequencing reaction solution, which is called washing solution for short, and comprises the following components:
20mM Tris-HCl pH 8.8
10mM(NH4)2SO4
50mM KCl
2mM MgSO4
0.1％
20
preparing a mother solution (mother solution for short) of a sequencing reaction solution, which comprises the following components:
20mM Tris-HCl pH 8.8
10mM(NH4)2SO4
50mM KCl
2mM MgSO4
0.1％
20
8000unit/mL Bst polymerase
100unit/mL CIP
three groups of sequencing reaction solutions were prepared, and six bottles were used. Respectively as follows:
1A, mother liquor +20uM dA4P-TG +20uM dC4P-TG
1B, mother liquor +20uM dG4P-TG +20uM dG4P-TG
2A, mother liquor +20uM dA4P-TG +20uM dG4P-TG
2B, mother liquor +20uM dC4P-TG +20uM dG4P-TG
3A, mother liquor +20uM dA4P-TG +20uM dT4P-TG
3B, mother liquor +20uM dC4P-TG +20uM dG4P-TG
The prepared reaction solution and mother solution are placed in a 4c refrigerator or ice for standby.
Hybridization sequencing primer:
the sequencing chip is injected with sequencing primer solution (10uM dissolved in 1X SSC buffer), heated to 90 ℃, and cooled to 40 ℃ at the speed of 5 ℃ per min. The sequencing primer solution was washed away with a wash solution.
Performing first sequencing:
the sequencing chip was placed on a sequencer.
Sequencing was performed using the first set of reaction solutions. The following procedure was followed.
1, introducing 10mL of washing liquid to wash the chip
2, cooling the chip to 4 DEG C
3, 100uL of the reaction solution 1A was introduced
4, heating the chip to 65 DEG C
5, waiting for 1min
Fluorescence images were taken with 473nm laser excitation.
7, introducing 10mL of washing liquid to wash the chip
8, cooling the chip to 4 DEG C
9, 100uL of the reaction solution 1B was introduced
10, heating the chip to 65 DEG C
11, waiting for 1min
12, a fluorescence image was taken by excitation with a 473nm laser.
The steps 1-12 were repeated 50 times to obtain 100 fluorescence signals.
Example 2.
On the basis of example 1, a second sequencing was carried out:
and cooling the chip to room temperature. 200uL of 0.1M NaOH solution was passed in. All DNA duplexes extended in the first sequencing were denatured. Then 10mL of wash solution was introduced to thoroughly wash the remaining NaOH and denatured single-stranded DNA.
The sequencing primer was hybridized again according to the previous protocol.
Sequencing was performed using the second set of reaction solutions. The following procedure was followed:
1, introducing 10mL of washing liquid to wash the chip
2, cooling the chip to 4 DEG C
3, 100uL of the reaction solution 2A was introduced
4, heating the chip to 65 DEG C
5, waiting for 1min
Fluorescence images were taken with 473nm laser excitation.
7, introducing 10mL of washing liquid to wash the chip
8, cooling the chip to 4 DEG C
9, 100uL of the reaction solution 2B was introduced
10, heating the chip to 65 DEG C
11, waiting for 1min
Fluorescence images were taken with 473nm laser excitation.
The steps 1-12 were repeated 50 times to obtain 100 fluorescence signals.
Example 3.
On the basis of example 2, a third sequencing was performed
And cooling the chip to room temperature. 200uL of 0.1M NaOH solution was passed in. All DNA duplexes extended in the first sequencing were denatured. Then 10mL of wash solution was introduced to thoroughly wash the remaining NaOH and denatured single-stranded DNA.
The sequencing primer was hybridized again according to the protocol described above.
Sequencing was performed using the third set of reaction solutions. The following procedure was followed.
1, introducing 10mL of washing liquid to wash the chip
2, cooling the chip to 4 DEG C
3, 100uL of the reaction solution 3A was introduced
4, heating the chip to 65 DEG C
5, waiting for 1min
Fluorescence images were taken with 473nm laser excitation.
7, introducing 10mL of washing liquid to wash the chip
8, cooling the chip to 4 DEG C
9, 100uL of the reaction solution 3B was introduced
10, heating the chip to 65 DEG C
11, waiting for 1min
12, a fluorescence image was taken by excitation with a 473nm laser.
The steps 1-12 were repeated 50 times to obtain 100 fluorescence signals.
End of sequencing
Example 4
3 sets of reaction solution are prepared, each set has two bottles, and each bottle has two basic groups. The two bases are labeled with different fluorescent chromophores to allow discrimination, and the emission wavelengths are different.
In this example, two chromophoric groups are used for all bases: x and Y. Two reaction vials in one set contained exactly the entire 4 bases. 6 bottles of solution were not repeated.
The complete sequencing process comprises three rounds, which are performed sequentially. The three sets of reagents were used for each round of sequencing. Otherwise it is identical.
Each round of sequencing contained:
1 hybridizing a sequencing primer on the prepared DNA array
2 start the sequencing process. The process of 2.1-2.4 is repeated for a limited number of times.
2.1 into the first vial of reagent. The fluorescence signals of two wavelengths are reacted and collected.
2.2 washing of all residual reaction solution and fluorescent molecules produced in flowcell
2.3 into a second vial of reagent. The fluorescence signals of two wavelengths are reacted and collected.
2.2 Wash all residual reaction solution and resulting fluorescent molecules in flowcell
3 unwinding the extended sequencing primer.
At this point, the next round of experiment can be performed.
Comparative example 1:
this example relates to 4 3-terminal blocked nucleotide molecules that prevent the polymerase from extending the nucleotide molecule continuously as a substrate, and the blocked group can be cleaved under specific conditions to generate a hydroxyl group. Each nucleotide molecule is labeled with a different fluorescent moiety that does not contain a fluorophore with fluorescence-switching properties and can be cleaved under specific conditions. The fluorescent molecules are marked as W, X, Y, Z. The substrate molecules are W-A, X-C, Y-G and Z-T.
A first reagent: and (5) carrying out main sequencing reaction liquid. Comprises 4 kinds of 3-end blocked fluorescent-labeled nucleotide molecules and polymerase capable of recognizing the substrate.
And a second reagent: and (5) cleaning the liquid.
And (3) reagent III: removing the sealing liquid. Comprising a reagent that cleaves the 3-terminal blocking group and the fluorophore.
When sequencing, a sequencing primer is hybridized on the template strand.
Mixing the first reagent with the hybridized template and generating polymerase reaction. And washing the unreacted sequencing solution by using a reagent II after the reaction. And collecting the fluorescent signal and judging the extended base type. Then, the third reagent is introduced to cut off all the 3-terminal blocking groups and the fluorescent groups. After cleaning, the next round of reaction was carried out.
This sequencing method does not possess the characteristics of data redundancy and verification.
Comparative example 2.
Nucleotide sequencing using non-fluorescent switching properties. This example is similar to example 1. Except that the fluorescent label is not on the phosphate. This example relates to 4 nucleotide molecules, all of which are free to be extended by a polymerase under complementary pairing conditions. Each nucleotide molecule is labeled at its base with the same fluorescent molecular group that contains non-fluorescent switching properties and can be cleaved under specific conditions. 3 sets of reaction solution were prepared, each set of two bottles containing exactly 4 bases. 6 bottles of solution were not repeated.
| First bottle | Second bottle | |
| First set | AX+CX | GX+TX |
| Second cover | AX+GX | CX+TX |
| Third set | AX+TX | CX+GX |
The complete sequencing process comprises three rounds, which are performed sequentially. The three sets of reagents were used for each round of sequencing. Otherwise, the reaction conditions were identical (identical using the same sequencing primers).
Each round of sequencing contained:
1. hybridizing sequencing primer on prepared DNA array
2. The sequencing process is started. The process of 2.1-2.4 is repeated for a limited number of times.
2.1 introduce the first vial of reagent. And (4) reacting.
2.2 Wash all residual reaction solution and resulting fluorescent molecules in flowcell
2.3 fluorescent signals are collected.
2.4 introduction of a cleavage reagent to cleave the fluorescent marker group.
2.1 introduce a second vial of reagent. And (4) reacting.
2.2 Wash all residual reaction solution and resulting fluorescent molecules in flowcell
2.3 fluorescent signals are collected.
2.4 introduction of a cleavage reagent to cleave the fluorescent marker group.
3. The extended sequencing primer was unwound.
At this point, the next round of experiment can be performed. The three rounds of sequencing were completed.
With substrates of non-fluorescent switching properties, cleavage reagents need to be introduced and the sequencing step is extended. And leaves molecular scars on the resulting double stranded DNA, preventing further extension.
The specific examples given in this detailed description of the invention are intended to be illustrative of the invention and are not intended to be limiting.
Claims (11)
1. A method for sequencing a nucleotide molecule using a fluorophore having fluorescence switching properties,
sequencing the nucleotide substrate molecules by modifying the 5' polyphosphate end or the middle phosphate with a fluorophore with fluorescence switching properties;
the fluorescence switching property means that the fluorescence signal intensity after sequencing is obviously increased compared with that before sequencing reaction;
using a set of reaction solution groups for each round of sequencing, wherein each set of reaction solution group at least comprises two reaction solutions, each reaction solution comprises at least one of A, G, C, T nucleotide molecules, or each reaction solution comprises at least one of A, G, C, U nucleotide molecules;
firstly, fixing a nucleotide sequence fragment to be detected in a reaction chamber, and introducing one reaction solution in a set of reaction solution groups;
detecting and recording fluorescence information;
introducing one reaction solution each time, sequentially introducing other reaction solutions in the same reaction solution group, and detecting and recording fluorescence information each time;
wherein, in the reaction liquid group, at least one reaction liquid comprises two or three different nucleotide molecules;
in the sequencing, an enzyme is used to release the fluorophore on the nucleotide substrate of the fluorophore having the fluorescence switching property, thereby causing the fluorescence switching.
2. The sequencing method of claim 1,
further comprises the steps of removing residual reaction liquid and fluorescent molecules by using a cleaning solution, and then carrying out the next round of sequencing reaction.
3. The sequencing method of claim 1,
entering the reaction solution at a low temperature, heating to the enzyme reaction temperature, and detecting a fluorescence signal.
4. The method of claim 1,
and (3) after the reaction liquid is introduced, sealing the reaction chamber, and then detecting and recording fluorescence information.
5. The method of claim 1,
after the reaction liquid is introduced, the space outside the reaction chamber is filled with oil, thereby isolating and sealing the reaction chamber.
6. The sequencing method according to any one of claims 1 to 5,
the nucleotide substrate molecule of polyphosphoric acid refers to a nucleotide having 4-8 phosphate molecules.
7. The sequencing method according to any one of claims 1 to 5,
the nucleotide substrate molecule modified with the fluorophore can be marked by a fluorophore according to different bases to carry out monochromatic sequencing; multicolor sequencing can also be performed with different fluorophore labels.
8. The sequencing method according to any one of claims 1 to 5,
the step of releasing a fluorophore having a fluorescence-switching property on a nucleotide substrate using an enzyme includes a DNA polymerase and a basic phosphatase.
9. The sequencing method according to any one of claims 1 to 5,
the reaction solution contains the enzyme, namely when the reaction solution is introduced into a reaction area where the gene fragment to be detected is located, the contained enzyme releases a fluorophore on a nucleotide substrate of the fluorophore with fluorescence switching property.
10. The method of claim 9,
the liberation of the fluorophore on the nucleotide substrate of the fluorophore having a fluorescence switching property using the enzyme means that the polyphosphate-substituted fluorophore is first liberated using a DNA polymerase, and then the substituted polyphosphate is cleaved using a phosphatase, thereby liberating the fluorophore.
11. A method of high throughput sequencing using the method of any one of claims 1 to 10,
the sequencing reaction is carried out on a chip, a plurality of reaction chambers are arranged on the chip, and the nucleotide sequence fragments to be detected are fixed in the reaction chambers.
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| Publication number | Publication date |
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| CN108060069A (en) | 2018-05-22 |
| CN108070526A (en) | 2018-05-25 |
| CN108070525B (en) | 2024-03-29 |
| CN108060069B (en) | 2024-03-29 |
| CN106755292B (en) | 2019-06-18 |
| CN106755292A (en) | 2017-05-31 |
| CN108070525A (en) | 2018-05-25 |
| CN110343753A (en) | 2019-10-18 |
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