CN109055363A - A kind of magnetic bead reagent and screening technique suitable for screening overlength nucleic acids - Google Patents
A kind of magnetic bead reagent and screening technique suitable for screening overlength nucleic acids Download PDFInfo
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Abstract
The present invention relates to technical field of molecular biology, more specifically, it is related to a kind of magnetic bead reagent and screening technique suitable for screening overlength nucleic acids, the reagent include concentration be 20~800ng/ μ L oxidation silicone hydroxyl magnetic bead, concentration be 5~50mmol/L Tris-HCL, concentration be 1~60mol/L sodium chloride, concentration be 0.1~20mol/L sodium laurate, concentration be 0.1~10mol/L guanidine hydrochloride, concentration for 0.1~100mol/L NaN3, concentration of volume percent be 1%~25% polyethylene glycol and pH=8 concentration be 0.1~10mmol/L EDTA.The reagent builds library process for high-flux sequence in the prior art, the problem of large fragment DNA poor recovery effect, it is designed and optimizes by the buffer to magnetic bead, realize the separation screening that large fragment is carried out using magnetic bead, long segment single-molecule sequencing technology especially suitable for PacBio and Nanopore etc., the fragment length that sequencing data can greatly be promoted, obtains better sequencing result.
Description
Technical field
The present invention relates to technical field of molecular biology, are suitable for screening overlength nucleic acids more particularly, to one kind
Magnetic bead reagent and screening technique.
Background technique
High throughput sequencing technologies, i.e., next-generation sequencing technologies (next generation sequencing) can be once to several
100000 to millions of DNA moleculars carry out sequencing and quantization, provide one for basic biomedical research and clinical detection
A powerful tool, and the scientific research and clinical conversion of genomics are pushed, it has been established in the foundation stone status of accurate medicine.
And a measuring samples also need to do before going on high-throughput DNA sequencing machine sequencing a large amount of work, committed step therein
It is exactly library construction.Library construction include nucleic acid fragment, repair reaction, plus A reaction, connection reaction, segment screening with purifying,
The processes such as PCR amplification, PCR product purifying, library quality inspection, these processes need to do the work of a large amount of nucleic acid purification and segment screening
Make.
Nucleic acid purification and the method for segment screening have glue absorption method, centrifugal column method etc. at present.But there is operation in these methods
It is cumbersome, it is time-consuming, or need gel electrophoresis or need to be centrifuged, it cannot achieve high-throughput, automatic operation.Paramagnetic particle method can overcome above
The disadvantage, paramagnetic particle method are using super-paramagnetism nano magnetic bead Specific adsorption and desorption core in two different solution environmentals
The characteristic of acid cooperates equipment for magnetic separation, reagent system and nucleic acid fragment selective purification process is pointedly designed, to reach
To the purpose for fast implementing nucleic acid samples purifying and segment screening.Paramagnetic particle method nucleic acid purification process safety is nontoxic, easy to operate, can
Selective purification is carried out to nucleic acid fragment, and automation, high throughput can be realized based on magnetic speciality.
Why magnetic bead can be because of its pan coating glass fibre in conjunction with nucleic acid.Siliceous film silica magnetic bead tool
There are superparamagnetism kernel and silica shells, a large amount of silicone hydroxyl of surface modification.The silicone hydroxyl of magnetic bead surfaces can be with solution
In nucleic acid specifically bound by hydrogen bond and electrostatic interaction, under high salt conditions in conjunction with nucleic acid, and in low-salt environment
Under be eluted, thus directly can be rapidly separated nucleic acid from complicated biosystem.
The foundation structure of the magnetic bead of Nano grade is generally divided into 3 layers in the prior art, the core of innermost layer be polystyrene,
Second layer coated magnetic substance-ferroso-ferric oxide (Fe3O4), outermost surface is the high molecular material institute modified by functional group
It constitutes, wherein functional group exercises the work in conjunction with nucleic acid.The packet of magnetic bead middle layer matrix, functional group's type of modification, matrix
It will affect the fundamental property and its characterization of adsorption of magnetic bead by technique, modified with functional group technique.And what magnetic bead Buffer was formulated changes
Change also will affect its adsorption effect, as lubricant will affect the residual of magnetic bead;The PEG imbibition power of different molecular weight is not yet
Together.Existing market magnetic bead is many kinds of, is mainly used for the extraction or 1KB small fragment screening below of nucleic acid, for large fragment
DNA, there is no an ideal recovery schemes.
Summary of the invention
For the technical problems in the prior art, the invention proposes a kind of suitable for screening overlength nucleic acids
Magnetic bead solution and screening technique, this method build library process, large fragment DNA recovering effect for high-flux sequence in the prior art
The problem of difference, is designed and is optimized by the buffer to magnetic bead, realizes the separation screening that large fragment is carried out using magnetic bead, special
Not Shi Yongyu PacBio and Nanopore etc. long segment single-molecule sequencing technology, can greatly promote the segment of sequencing data
Length obtains better sequencing result.
To achieve the above object, the present invention is achieved by the following technical solutions:
The first purpose of this invention is to propose a kind of magnetic bead reagent suitable for screening overlength nucleic acids, the examination
Agent include concentration be 20~800ng/ μ L oxidation silicone hydroxyl magnetic bead, concentration be 5~50mmol/L Tris-HCL, concentration 1
The guanidine hydrochloride that sodium laurate that the sodium chloride of~60mol/L, concentration are 0.1~20mol/L, concentration are 0.1~10mol/L is dense
Degree is the NaN of 0.1~100mol/L3, concentration of volume percent be 1%~25% polyethylene glycol and pH=8 concentration be 0.1~
10mmol/L EDTA。
Further, the reagent include concentration be 350ng/ μ L oxidation silicone hydroxyl magnetic bead, concentration be 10mmol/L's
The hydrochloric acid that sodium laurate that sodium chloride that Tris-HCL, concentration are 1.6mol/L, concentration are 10mol/L, concentration are 5.6mol/L
Guanidine, concentration are the NaN of 25mol/L3, concentration of volume percent be 11% polyethylene glycol and pH=8 concentration be 1mmol/L
EDTA。
Further, the molecular weight of the polyethylene glycol is 8000 dalton.
It further, further include three or four base ammonium bromide of magnesium chloride and cetyl in the reagent, the magnesium chloride
Final concentration of 5mmol/L-9.5mmol/L, the final concentration of 0.5mmol/L- of three or the four base ammonium bromide of cetyl
3.5mmol/L。
Second object of the present invention is to propose a kind of extracts kit that overlength segment is calculated, and the kit includes
The magnetic bead reagent described in any of the above embodiments for being suitable for screening overlength nucleic acids.
Third object of the present invention is to propose a kind of screening technique of overlength nucleic acids, and the method uses right
It is required that the magnetic bead reagent for being suitable for screening overlength nucleic acids of any one of 1-4 includes the following steps: come what is realized
(1) it will be suitable for screening the magnetic bead reagent equilibrium at room temperature 30min of overlength nucleic acids;
(2) Balanced magnetic bead reagent in step (1) is added into the reaction tube for filling connection reaction product, flicks mixed
It is even, it mixes combine 10min at room temperature;
(3) sample is placed on magnetic frame 2min and clarified to supernatant by brief centrifugation;
(4) supernatant is abandoned, ABB cleaning is added, EP pipe, sufficiently washing magnetic bead are slowly rotated on magnetic frame, 30s is stood, abandons
Supernatant;
(5) brief centrifugation abandons supernatant to the greatest extent, drying at room temperature;
(6) eluent is added, mixes 10min;It is placed on magnetic frame and is stored at room temperature 1-3min, supernatant screens after purification
The segment containing overlength nucleic acid.
Further, the volume of magnetic bead reagent is added to determine for the clip size desirably recycled in the step (2);
The volume of the magnetic bead reagent is 0.85x~1.1x.
Compared with prior art, the beneficial effects of the present invention are:
(1) the magnetic bead reagent proposed by the present invention for being suitable for screening overlength nucleic acids, the reagent is in the prior art
The problem of high-flux sequence builds library process, large fragment DNA poor recovery effect, is designed and excellent by the buffer to magnetic bead
Change, realize using magnetic bead carry out large fragment separation screening, single point of long segment especially suitable for Pa cBio and Nanopore etc.
Sub- sequencing technologies can greatly promote the fragment length of sequencing data, obtain better sequencing result.
(2) magnetic bead reagent key of the invention is each component by specific proportion combination, and wherein Tris-Hcl is buffered
Liquid can guarantee the stability of DNA;The sodium ion of sodium chloride plays the role of cationic bridge, can neutralize phosphatase nucleic acid skeleton
On negative electrical charge, promote phosphatase nucleic acid group to be effectively combined the surface of hydroxyl magnetic bead;The molecular weight of polyethylene glycol is preferably
8000, enhance (the mainly effect of the leading nanometer magnetic bead absorption nucleic acid of sodium chloride of high salt concentration in nucleic acid purification reagent;Salt
Sour guanidine can greatly shorten the time of suction-operated, and the magnesium ion of magnesium chloride plays certain stablizing to entire buffer solution system and makees
With, and recovery of nucleic acid can be improved in three or four base ammonium bromide of cetyl.The present invention passes through the proportion of each component of assay optimization
Nucleic acid screening of the magnetic bead reagent of formation for during building library purifies, the screening compared to the bluepippin that official is recommended,
This method only needs the time within 30min, and segment screening operation can be completed, and cost only needs 10% left side of bluepippin
It is right.Meanwhile this method can provide the recovery efficiency of sample, general bluepippin screening recovery efficiency is used 30%
The magnetic bead of this patent is screened, and recovery efficiency can be promoted to 60% or more.
Detailed description of the invention
Fig. 1 is the agarose gel electrophoresis figure that purification result is screened when adding the magnetic bead reagent of different volumes in embodiment 5
Spectrum.
Specific embodiment
It shows that example illustrates certain embodiments of the present invention, and should not be construed as limiting model of the invention
It encloses.Present disclosure can be improved from material, method and reaction condition simultaneously, all these improvement should all
It falls within spirit and scope of the invention.Unless otherwise specified, technological means used in embodiment is art technology
Conventional means known to personnel.
The magnetic bead reagent that the invention proposes a kind of suitable for screening overlength nucleic acids, the reagent include that concentration is 20
The chlorination that Tris-HCL that the oxidation silicone hydroxyl magnetic bead of~800ng/ μ L, concentration are 5~50mmol/L, concentration are 1~60mol/L
The guanidine hydrochloride that sodium laurate that sodium, concentration are 0.1~20mol/L, concentration are 0.1~10mol/L, concentration are 0.1~100mol/
The NaN of L3, concentration of volume percent be 1%~25% polyethylene glycol and pH=8 concentration be 0.1~10mmol/L EDTA.It is excellent
Selection of land, the reagent include concentration be 350ng/ μ L oxidation silicone hydroxyl magnetic bead, concentration be 10mmol/L Tris-HCL, concentration
For the sodium chloride of 1.6mol/L, concentration be 10mol/L sodium laurate, concentration be 5.6mol/L guanidine hydrochloride, concentration is
The NaN of 25mol/L3, concentration of volume percent be 11% polyethylene glycol and pH=8 concentration be 1mmol/L EDTA.Further
It is preferred that the molecular weight of the polyethylene glycol is 8000 dalton.It further include three or four base of magnesium chloride and cetyl in the reagent
Ammonium bromide, the final concentration of 5mmol/L-9.5mmol/L of the magnesium chloride, the final concentration of three or the four base ammonium bromide of cetyl
For 0.5mmol/L-3.5mmol/L.
It includes following step that overlength nucleic acids are screened using the above-mentioned magnetic bead reagent for being suitable for screening overlength nucleic acids
It is rapid:
(1) it will be suitable for screening the magnetic bead reagent equilibrium at room temperature 30min of overlength nucleic acids;
(2) Balanced magnetic bead reagent in step (1) is added into the reaction tube for filling connection reaction product, flicks mixed
It is even, it mixes combine 10min at room temperature;
(3) sample is placed on magnetic frame 2min and clarified to supernatant by brief centrifugation;
(4) supernatant is abandoned, ABB cleaning is added, EP pipe, sufficiently washing magnetic bead are slowly rotated on magnetic frame, 30s is stood, abandons
Supernatant;
(5) brief centrifugation abandons supernatant to the greatest extent, drying at room temperature;
(6) eluent is added, mixes 10min;It is placed on magnetic frame and is stored at room temperature 1-3min, supernatant screens after purification
The segment containing overlength nucleic acid.
The volume of magnetic bead reagent is added to determine for the clip size wherein desirably recycled in step (2);The magnetic bead
The volume of reagent is 0.85x~1.1x, shown in table specific as follows:
Table 1
Magnetic bead and sample of nucleic acid volume ratio | Recyclable nucleic acid fragment size |
1.1x | >1kb |
1.05x | >1kb |
1x | >1kb |
0.95x | >2kb |
0.9x | >4kb |
0.85x | >5kb |
0.8x | >6kb |
0.75x | >23kb |
Embodiment 1
The magnetic bead reagent of the screening overlength nucleic acids of the present embodiment includes the oxidation silicone hydroxyl magnetic that concentration is 20ng/ μ L
Sodium laurate that sodium chloride that Tris-HCL that pearl, concentration are 5mmol/L, concentration are 1mol/L, concentration are 0.1mol/L, concentration
For the guanidine hydrochloride of 0.1mol/L, concentration is the NaN of 0.5mol/L3, concentration of volume percent be 1% polyethylene glycol and pH=8
Concentration is 0.1mmol/L EDTA.Wherein the molecular weight of polyethylene glycol is 8000 dalton;Oxidation silicone hydroxyl magnetic bead derives from
The XP magnetic bead of Beckman, with sterile water wash magnetic bead, the residual for completely removing the original Buffer of magnetic bead obtains the oxygen of the present embodiment
SiClx hydroxyl magnetic bead.
Embodiment 2
The magnetic bead reagent of the screening overlength nucleic acids of the present embodiment includes the oxidation silicone hydroxyl magnetic that concentration is 350ng/ μ L
It is sodium laurate that sodium chloride that Tris-HCL that pearl, concentration are 10mmol/L, concentration are 1.6mol/L, concentration are 10mol/L, dense
Degree is the guanidine hydrochloride of 5.6mol/L, and concentration is the NaN of 25mol/L3, concentration of volume percent be 11% polyethylene glycol, pH=8
Concentration is three or four base of cetyl of 1mmol/L EDTA, the magnesium chloride of final concentration of 5mmol/L and final concentration of 0.5mmol/L
Ammonium bromide.Wherein the molecular weight of polyethylene glycol is 8000 dalton;The XP magnetic bead that silicone hydroxyl magnetic bead derives from Beckman is aoxidized,
With sterile water wash magnetic bead, the residual for completely removing the original Buffer of magnetic bead obtains the oxidation silicone hydroxyl magnetic bead of the present embodiment.
Embodiment 3
The magnetic bead reagent of the screening overlength nucleic acids of the present embodiment includes the oxidation silicone hydroxyl magnetic that concentration is 800ng/ μ L
It is sodium laurate that sodium chloride that Tris-HCL that pearl, concentration are 50mmol/L, concentration are 60mol/L, concentration are 20mol/L, dense
Degree is the guanidine hydrochloride of 10mol/L, and concentration is the NaN of 100mol/L3, concentration of volume percent be 25% polyethylene glycol, pH=8
Concentration is the cetyl three of 10mmol/L EDTA, the magnesium chloride of final concentration of 9.5mmol/L and final concentration of 3.5mmol/L
Four base ammonium bromides.Wherein the molecular weight of polyethylene glycol is 8000 dalton;Oxidation silicone hydroxyl magnetic bead derives from the magnetic bead that Novi praises,
With sterile water wash magnetic bead, the residual for completely removing the original Buffer of magnetic bead obtains the oxidation silicone hydroxyl magnetic bead of the present embodiment.
Embodiment 4
Respectively by embodiment 1-3 magnetic bead reagent,The magnetic bead that XP magnetic bead and Novi praise is for building library mistake
Cheng Zhong, the screening purifying of connection product, detailed process is as follows:
It repairs the end of 1.DNA sample
Reaction is repaired in the end for taking 5 parts of equivalent samples to carry out DNA sample respectively, and reaction system is as follows:
Table 2
Flick mixing, brief centrifugation, 20 DEG C of incubation 30min, 65 DEG C of incubation 5min are placed on ice.
2. product purification is repaired in end
It usesXP magnetic bead purifies five parts of ends respectively and repairs product, the specific steps are as follows:
A) willXP magnetic bead equilibrium at room temperature 30min;
B) product will be repaired and is transferred to 1.5mL low adsorption pipe, the magnetic bead (about 60 μ L) of 1X volume is added, flicks mixing, is placed in
It is mixed on four-dimension rotation blending instrument and combines 10min;
Sample is placed on magnetic frame 2min and clarified to supernatant by c) brief centrifugation;
D) supernatant is abandoned, 75% ethyl alcohol of 1mL is added, stands 30s, abandons supernatant;
E) repeated washing is primary;
F) brief centrifugation abandons supernatant to the greatest extent, drying at room temperature 30s;
G) 32 μ L water are added, flick mixing, is placed on four-dimensional rotation blending instrument and mixes 10min;
H) it is placed in 2min on magnetic frame, shifts 31 μ L supernatants into the new PCR pipe of 0.2mL.
3. jointing
The product that five parts are purified carries out following reaction system:
Table 3
It is placed on four-dimensional rotation blending instrument and mixes 3min, brief centrifugation, 16 DEG C of reaction 30min.
4. the segment of connection product is screened
(1) two parts of connection connection products are taken, are respectively adoptedThe magnetic bead that XP magnetic bead and Novi praise is according to official
The normal process of recommendation carries out segment screening, specific as follows:
A) willThe magnetic bead equilibrium at room temperature 30min that XP magnetic bead or Novi praise;
B) connection product is transferred to 1.5mL low adsorption pipe, the magnetic bead (about 45 μ L) of 0.45X volume is added, flicks mixing, sets
10min is combined in mixing on four-dimension rotation blending instrument;
Sample is placed on magnetic frame 2min and clarified to supernatant by c) brief centrifugation;
D) supernatant is abandoned, the Adapter Bead Binding Buffer (ABB) of 140 μ L is added, is slowly revolved on magnetic frame
Turn EP pipe 3~5 weeks, sufficiently washing magnetic bead, stands 30s, abandon supernatant;
E) it is primary to reuse ABB cleaning;
F) brief centrifugation abandons supernatant to the greatest extent, drying at room temperature 30s;
G) the Elution Buffer (ELB) of 16 μ L is added, flicks mixing, is placed on four-dimensional rotation blending instrument and mixes
10min;
H) it is placed in 2min on magnetic frame, 15.5 μ L supernatants of transfer obtain sequencing library to the new EP pipe of 1.5mL.
(2) three parts of connection connection products are taken, the magnetic bead reagent being respectively adopted in embodiment 1-3 purifies connection as follows
Product, the specific steps are as follows:
A) by LFB magnetic bead equilibrium at room temperature 30min;
B) connection product is transferred to 1.5mL low adsorption pipe, the LFB magnetic bead (about 85 μ L) of 0.85X volume is added, flicks mixed
It is even, it is placed on four-dimensional rotation blending instrument and mixes in conjunction with 10min;
Sample is placed on magnetic frame 2min and clarified to supernatant by c) brief centrifugation;
D) supernatant is abandoned, the Adapter Bead Binding Buffer (ABB) of 140 μ L is added, is slowly revolved on magnetic frame
Turn EP pipe 3~5 weeks, sufficiently washing magnetic bead, stands 30s, abandon supernatant;
E) it is primary to reuse ABB cleaning;
F) brief centrifugation abandons supernatant to the greatest extent, drying at room temperature 30s;
G) the Elution Buffer (ELB) of 16 μ L is added, flicks mixing, is placed on four-dimensional rotation blending instrument and mixes
10min;
H) it is placed in 2min on magnetic frame, 15.5 μ L supernatants is shifted into the new EP pipe of 1.5mL, obtains sequencing library.
5. machine is sequenced on
Upper machine sequencing is carried out according to Nanopore official standard operating process, the sequencing result in two libraries is compared as follows:
Table 4
, it is apparent that it can be the case where not reducing data output using magnetic bead reagent of the invention from comparison sheet
Under, the average length of sequencing data is promoted to 9.6kb by 5.9kb, the N50 length of sequencing data is promoted to by 16.8kb
25.6kb.After carrying out large fragment screening using LFB magnetic bead, higher proportion of lengthy motion picture segment data can be obtained.
Embodiment 5
When carrying out nucleic acid screening using magnetic bead reagent of the invention, the clip size that desirably recycles determines addition magnetic
The volume of pearl reagent.The present embodiment test magnetic bead reagent addition volume be respectively 1.1x, 1.05x, 1x, 0.95x, 0.9x,
When 0.85x, 0.8x, 0.75x, the size of segment is recycled.The agarose gel electrophoretogram for screening purification result is as shown in Figure 1.
The foregoing is only a preferred embodiment of the present invention, but scope of protection of the present invention is not limited thereto,
Anyone skilled in the art in the technical scope disclosed by the present invention, according to the technique and scheme of the present invention and its
Inventive concept is subject to equivalent substitution or change, should be covered by the protection scope of the present invention.
Claims (7)
1. a kind of magnetic bead reagent suitable for screening overlength nucleic acids, which is characterized in that the reagent include concentration be 20~
The chlorination that Tris-HCL that the oxidation silicone hydroxyl magnetic bead of 800ng/ μ L, concentration are 5~50mmol/L, concentration are 1~60mol/L
The guanidine hydrochloride that sodium laurate that sodium, concentration are 0.1~20mol/L, concentration are 0.1~10mol/L, concentration are 0.1~100mol/
The NaN of L3, concentration of volume percent be 1%~25% polyethylene glycol and pH=8 concentration be 0.1~10mmol/L EDTA.
2. a kind of magnetic bead reagent suitable for screening overlength nucleic acids according to claim 1, which is characterized in that described
Reagent include concentration be 350ng/ μ L oxidation silicone hydroxyl magnetic bead, concentration be 10mmol/L Tris-HCL, concentration 1.6mol/
The guanidine hydrochloride that sodium laurate that the sodium chloride of L, concentration are 10mol/L, concentration are 5.6mol/L, concentration are the NaN of 25mol/L3、
The polyethylene glycol and pH=8 concentration that concentration of volume percent is 11% are 1mmol/L EDTA.
3. a kind of magnetic bead reagent suitable for screening overlength nucleic acids according to claim 1 or 2, which is characterized in that
The molecular weight of the polyethylene glycol is 8000 dalton.
4. a kind of magnetic bead reagent suitable for screening overlength nucleic acids according to claim 1 or 2, which is characterized in that
It further include three or four base ammonium bromide of magnesium chloride and cetyl, the final concentration of 5mmol/L- of the magnesium chloride in the reagent
9.5mmol/L, the final concentration of 0.5mmol/L-3.5mmol/L of three or the four base ammonium bromide of cetyl.
5. the extracts kit that a kind of overlength segment is calculated, which is characterized in that the kit includes any one of claim 1-4
The magnetic bead reagent for being suitable for screening overlength nucleic acids.
6. a kind of screening technique of overlength nucleic acids, which is characterized in that the method is using any one of claim 1-4's
Magnetic bead reagent suitable for screening overlength nucleic acids includes the following steps: come what is realized
(1) it will be suitable for screening the magnetic bead reagent equilibrium at room temperature 30min of overlength nucleic acids;
(2) Balanced magnetic bead reagent in step (1) is added into the reaction tube for filling connection reaction product, flicks mixing, room
Lower mix of temperature combines 10min;
(3) sample is placed on magnetic frame 2min and clarified to supernatant by brief centrifugation;
(4) supernatant is abandoned, ABB cleaning is added, EP pipe, sufficiently washing magnetic bead are slowly rotated on magnetic frame, 30s is stood, abandons supernatant;
(5) brief centrifugation abandons supernatant to the greatest extent, drying at room temperature;
(6) eluent is added, mixes 10min;It is placed on magnetic frame and is stored at room temperature 1-3min, supernatant is to screen containing after purification
The nucleic acid of overlength segment.
7. a kind of screening technique of overlength nucleic acids according to claim 6, which is characterized in that in the step (2)
The volume of magnetic bead reagent is added to determine for the clip size desirably recycled;The volume of the magnetic bead reagent be 0.85x~
1.1x。
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