Patent Application
20230029069
The present invention belongs to the field of biotechnology, and particularly relates to an enzyme having low-temperature activity and an application thereof for nucleic acid amplification reaction under an in vitro low temperature condition.
In vitro nucleic acid amplification is a very important technology in the field of modern life science. Since 1990, in vitro nucleic acid amplification technology has achieved rapid growth.
Moreover, the technical field further plays an increasingly important role in future life science field.
The early diagnosis of lots of human and animal diseases may be performed by nucleic acid technology, which relies on an effective in vitro nucleic acid amplification technology.
Polymerase chain reaction (PCR) is a classic in vitro nucleic acid amplification method. PCR has been put in use for more than 30 years since its naissance, and various kinds of nucleic acid testing methods having different functions have been derived on the basis of PCR, such as, Reverse Transcript PCR (RT-PCR), Quantitative PCR (qPCR), and nested-PCR. PCR reaction is as follows: double-stranded DNA is cracked into single strands under high temperature conditions, then cooled and annealed; a primer is paired with a template strand, and finally, the primer is extended at a condition of 72° C., and the above process is recycled and DNA shows exponential amplification. PCR reaction process needs to be done in an apparatus having a precise temperature control element, but such an apparatus is very expensive and requires operating personnel to possess very complicated professional skill. Therefore, the apparatus may be only provided in the laboratory or medical institution from some developed regions, which greatly limits the popularization and application of PCR-based molecular diagnostic technique. In consideration of the limitations in conventional PCR from instrument and equipment, electric power and other factors, in recent years, isothermal DNA amplification has been springing up quietly, such as, strand displacement amplification (SDA), helicase dependent amplification (HDA), nuclear acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), rolling circle amplification (RCA), and Recombinase Polymerase Amplification (RPA) [1]. The most widely used is LAMP and RPA, but LAMP and RPA reaction still needs to be performed under a specific temperature (LAMP: 60-65° C., RPA: 37-42° C.). Moreover, the reaction is comparatively sensitive to the change of temperature; the amplification efficiency will greatly reduce or fail to perform correct amplification not at a most suitable temperature.
In early stage, people have carried out in-depth studies on DNA duplication in vivo. Due to a simple structure, T4 bacteriophage will achieve rapid intracellular duplication of its genome DNA after invading into a bacterium. Therefore, predecessors serve T4 bacteriophage as a model organism for a large number of studies in virology and molecular genetics. In 1976, YASUO IMAE, et al., used a bacteriophage lysis solution protein for in vitro replication of T4 bacteriophage DNA [29]; in 1979, Sinha, et al., used T4 bacteriophage duplication-associated proteins (gene proteins 32,41,43,44, 62,45, and 61) to achieve efficient in vitro replication of double-stranded DNA, and the DNA extending rate is almost up to the amplification efficiency of 500 bases/s in vivo [2]. gp32 protein plays a pivotal role in DNA duplication,recombination and repair process of T4 bacteriophage, and the most important reason is that gp32 protein has a property of binding single-stranded DNA tightly [3]. In 1983, Formosa et al., immobilized gp32 protein on an agarose adsorption column to perform affinity chromatography on a bacterial lysate infected with T4 bacteriophage, finding that DNA polymerase (gp43 protein) and two important recombinant pathway proteins (uvsX and uvsYproteins) in T4 bacteriophage may specifically bind to gp32 protein [4]. It has been proved in the further study that uvsX protein has similar functions with recA in Escherichia coli, and has DNA-dependent ATPase activity, and may bind to single or double-stranded DNA under in vitro normal saline conditions, and may catalyze pairing with homologous double or single-stranded DNA fragments [5,6]. In the corresponding period, Deborah, et al.,expressed uvsX gene by cloning and recombination, and proved that in the presence of gp32 protein, uvsX protein is ATP-dependent and thus has the activity of replacing single-strand DNA into double-stranded DNA, thereby forming a D-Loop structure, and decomposes the substrate ATP into two products ADP and AMP [7A]. What is different from recA is that uvsX has an ATP catalytic hydrolysis rate 10-20 times of recA, moreover, the catalysate may be AMP+PPi and ADP+Pi, and ATP may be hydrolyzed more thoroughly, but recA catalyzes ATP to produce ADP+Pionly [7]. gp32 protein may greatly stimulate uvsX to catalyze the activity of homologous pairing of single-stranded DNA (ssDNA). Meanwhile, uvsX may further bind to uvsY tightly [7], moreover, uvsY may improve the single-stranded DNA dependent ATPase activity by enhancing the affinity between uvsX and ssDNA [8, 9]. The homologous recombination function brought by binding uvsX to ssDNA is closely associated with the duplication process of T4 DNA; after uvsX-ssDNA binds to homologous fragments, ssDNA may serve as a primer for DNA duplication [10]. The above evidences prove that gp32, uvsX and uvsY protein play a very important role in the duplication process of T4 bacteriophage DNA. It has been found in the further study that the uvsY-ssDNA complex formed by uvsY and ssDNA may cause the change of an ssDNA structure, such that ssDNA framework is more inclined to form a uvsX-SSDNA complex. Meanwhile, ATP binding makes the structure of uvsX-ssDNA more stable [11-14]. It has been found in the further study that gp32 protein and single-stranded ssDNA form a stable gp32-ssDNA complex. But under the action of uvsY, the gp32-ssDNA complex structure has an obviously reduced stability, and the ssDNA is more inclined to form a uvsX-ssDNA complex [15].
David A. Zarlinget al. used such a characteristic to perform nucleic acid amplification in a specific segment via Escherichia coliRecA protein and SSB protein and by means of a specific primer. Piepenburg made improvements based on this and replaced Escherichia coli protein into T4 bacteriophage proteins gp32, uvsX or uvsY; bsu DNA polymerase klenow fragment or sau DNA polymerase klenow fragment is selected as DNA polymerase, and the process was named RPA amplification (recombinase polymerase amplification) [22]. Gp32 protein has a similar function as the SSB protein in bacteria, and may specifically bind an ssDNA oligonucleotide primer to form a Gp32-primer complex, such that the primer maintains a single-stranded structure. Secondly, UvsY and Gp32-primer complex form a UvsY-Gp32-primer complex, and the binding affinity between Gp32 and the primer is reduced, such that UvsX competitively binds to the primer to form a UvsX-primer complex. Thirdly, under the action of ATP, the UvsX-primer complex has the characteristic of homologously pairing with the complementary sites in template strand and replaces the strand with the same base sequence, and then binds to the complementary strand to form a D-loop structure. Fourthly, under the action of DNA polymerase, 3′ terminal exposed on the primer in the D-loop structure is extended till the end of duplication. After the above process is recycled, the target DNA fragment may achieve exponential amplification.
It is reported that RPA technology may achieve amplification under the condition of 30° C., but the amplification efficiency reduces sharply. Therefore, to further reduce the reaction temperature, the present patent performs combined screening in vitro of cold-active bacteriophage protein or amino acid mutation screening directed to proteins such as Gp32, UvsX and UvsY, DNA polymerase and creatine kinase, such that the amplification reaction may be performed efficiently at an exponential rate and a lower temperature, thus shortening the amplification time. In this way, rapid amplification may achieved merely in general indoor environment temperature without any temperature-controlled equipment. In combination with a nucleic acid testing method, the present application simplifies the equipment required by the whole nucleic acid amplification and detection and achieves more convenient operation. The scope of media for the reaction is broader, and the amplification reaction may be performed not limited to a heated medium, such as, fiber paper, nylon membrane, nitrocellulose membrane and cotton fiber ball.
The host of about 90% known T4-related bacteriophage is Escherichia coli or other enteric bacilli, and the host of the rest 10% is other bacteria, such as, Aeromonas, vibrio or Synechococcus [23]. Most of them are found in domestic sewage or wastewater, and the natural host is human or other animal intestinal tract [24]. Therefore, the optimum growth temperature is similar to the host thereof, namely, 37-40° C. [25]. According to the different optimum culture temperature of forming bacteriophage plaques, the bacteriophage is classified into three categories: more than 25° C. is called high-temperature (HT) bacteriophage, 30° C. below is low-temperature (LT) bacteriophage, and the one forming bacteriophage plaques between 15° C.−42° C. is moderate temperature (MT) bacteriophage [26]. T4 bacteriophage is a kind of typical room temperature bacteriophage.
Laura Kaliniene, et al. have successively found five cold-active bacteriophages, vB_EcoM-VR5, vB_EcoM-VR7 and vB_EcoM-VR20, vB_EcoM-VR25, and vB_EcoM-VR26. Three bacteriophages vB_EcoM-VR5, vB_EcoM-VR7 and vB_EcoM-VR20 were subjected to hemolytic plaque assay respectively at the temperature of 17° C., 24° C., 30° C., 35° C., 37° C., 39° C. and 40° C. according to the method of Seeley and Primrose [27]. The result shows that temperature sensibility of the three bacteriophages is obviously different from T4 bacteriophage, and the efficiency of plating is shown in
By comparison with alignX software (as shown in
The corresponding DNA sequence is synthesized by reference to the above genome sequence, and cloned onto a pET22b expression vector with double enzyme digestion Nde I and EcoR I, and the expressed proteins are respectively named VR5X_NHlis, VR7_25X_NHlis, VR20_26X_NHlis, VR5G_NHis, VR7G_NHlis, VR25G_NHlis, VR5Y_NHlis, VR7_25_26Y_NHlis, VR20Y_NHlis, VR7_25X_CHis, VR7G_CHis, VR7_25_26Y_CHis, and the sequences are as follows:
Meanwhile, the corresponding genes uvsX, uvsY and gp32 of T4 bacteriophage are synthesized, and cloned onto an expression vector pET22b by molecular biology. The expressed amino acid sequence is as follows:
A host cell BL21(DE3) is transformed according to molecular cloning technique, and induced with IPTG for expression, then repeatedly frozen and lyzed, and purified [28] by a Ni column to obtain a high-purity protein, and the high-purity protein is subjected to amplification test.
UvsX function is similar to the RecA protein of Escherichia coli, and its homologous strand transferase displacement transferase activity is dependent on ATP. Different from RecA, uvsX decomposes ATP into two products of ADP and AMP. High-concentration ADP and AMP will produce an inhibiting effect on uvsX [31]. Therefore, the product needs to be transformed into ATP, thus reducing inhibition. The energy system is formulated by reference to Hinton, D. M, Birkenkamp-Demtroder and other methods, and ATP has a concentration of 1 mM-5 mM, phosphocreatine and myokinase [32, 33]. Myokinase may be selected from rabbit myokinase and carp myokinase. Myokinase M1 type (M1-CK) has adapted to low-temperature environment and PH value with body temperature. Wu CL, et al. have found that Gly in the 268th position of rabbit myokinase is changed into Asnmyokinase to significantly enhance the the activity of myokinase to form ATP under catalysis at low temperature. Therefore, myokinase is theoretically and preferably selected from G268N variant-type myokinase or carp myokinase [34,35].
The genes are synthesized respectively by reference to the protein sequences NCBI No. AAC96092.1 and NP_001075708.1, and respectively cloned onto a pET22b expression vector by double enzyme digestion Nde I and EcoR I; the corresponding proteins are respectively named RM-CK and Carp-M1-CK, and N terminal is fused with a 6xHis tag for the convenience of purification. Meanwhile, by reference to the above literature, the RM-CK encoding gene is mutated by means of a conventional gene site mutation technique, such that G in the position 268 free of histidine-tag) amino acid of the translated protein is mutated to N.
hpfmwnehlgyvltcpsnlgtglrggvh
Amplification reaction conditions are referring to the Sinha, N. K. method; Mg2+ concentration is 5-20 mM, K+ concentration is 20-120 mM, preferably, the concentration is 40-80 mM; dNTP concentration is 100 uM-1000 uM; preferably, the concentration is within 300 uM-600 uM.
To further improve the reaction efficiency, it attempts reducing temperature to obtain higher reaction efficiency. By synthesizing DNA directed mutation library and screening, double enzyme digestion Nde I and EcoR I are used for cloning onto a pET22b expression vector, and a plurality of protein variants having in vitro amplification activity are obtained after expression and purification; these variant proteins are respectively named VRX_Variant1, VRX_Variant2 . . . . . . numbered consecutively to VRX_Variant20. The expressed amino acid sequences are respectively as follows:
Further, the room temperature amplification reaction system is constructed as follows:
Staphylococcus aureus polymerase I klenow
TemplateCell lysis template/genome extraction/plasmid
Reaction conditions are as follows: 25 uI, amplification temperature: 20-45° C. A water bath, a thermostatic equipment or PCR instrument is taken. The reaction endpoint is monitored by agarose gel electrophoresis, Sybr green I or a specific probe. During Sybr green I monitoring, the reaction system has an increased final concentration of 0.3-0.5x Sybr green I. The reaction time may be within 20-40 min, and fluorescence is read every 30 s, and the fluorescent channel is FAM/HEX. The detection instrument may be ABI7500, FTC-3000, Bio-Rad CFX MiniOpticon System, GenDx thermostatic fluorescence detector GS8, or the like. For example, when a specific probe is used to detect the amplification system, an exonuclease III or an endonuclease IV is added to the reaction, and the reaction has a final concentration of 50-100 ng/uI, and the fluorescent-labeled probe has a final concentration of 120 nM. Probe labeling is designed and synthesize by reference to [22]. The fluorescence detection may be performed via ABI7500,FTC-3000, Bio-Rad CFX MiniOpticonSystemOpticon System, GenDx thermostatic fluorescence detector GS8, or the like.
the cold-active bacteriophage protein provided by the present invention is applied in room temperature nucleic acid amplification reaction, which may not only achieve nucleic acid amplification and detection at a lower temperature, but also may further improve detection sensitivity, capable of detecting 100 copies/uI nucleic acid.
To describe the objective, technical solution and advantages of the present invention more clearly and apparently, the present application will be further described specifically by reference to the drawings and detailed embodiments. The following examples are only used to describe the present invention, but not intended to limit the scope of the present invention.
The corresponding gene sequences were designed and synthesized respectively according to the NCBI genome sequences (Enterobacteria phage vB_EcoM_VR5, Accession: KP007359.1; vB_EcoM-VR7, Accession: HM563683.1; vB_EcoM_VR20, Accession: KP007360.1; vB_EcoM_VR25, Accession: KP007361.1; vB_EcoM_VR26, Accession: KP007362.1), and cloned onto a pET22b expression vector respectively by double enzyme digestion Nde I and EcoR I, where if a C terminal of the corresponding protein of the gene sequence was fused with 6 histidine-tag, gene+Chis was named, if an N terminal was was fused with 6 histidine-tag, gene+NHis was named; gene number was added simultaneously when the amino acid sequences were consistent among different virus strains, e.g., VR7_25_26Y_CHis, showing that the uvsY amino acid sequences of the three vB_EcoM_VR7, vB_EcoM_VR25 and vB_EcoM_VR26 were consistent, and the protein corresponding to the number was the protein with the addition of 6XHis tags on the C terminal. The expressed proteins were constructed and synthesized, including VR5X_NHis, VR7_25X_NHis, VR20_26X_NHis, VR5G_NHis, VR7G_NHis, VR25G_NHis, VR5Y_NHis, VR7_25_26Y_NHis, VR20Y_NHis, VR7_25X_CHis, VR7G_CHis, VR7_25_26Y_CHis and other corresponding plasmid vectors. A host cell BL21(DE3) was transformed according to molecular cloning technique, and induced with IPTG for expression, then repeatedly frozen and lyzed, and purified [28] by a Ni column to obtain a high-purity protein, and the high-purity protein was subjected to amplification test.
The reaction reagent and concentration thereof were as follows: 30 mMtris(hydroxymethyl) aminomethane-acetic acid buffer solution, 60 mM potassium acetate, 20 mM magnesium acetate, 2 mMdithiothreitol, 5% polyethylene glycol (molecular weight: 1450-20000), 3 mM ATP, 30 mM phosphocreatine, 90 ng/ulcreatine kinase, 200-600 ng/uI VR5X_NHis protein, 200-1000 ng/uI VR5G_NHis protein, 60 ng/uI VR5Y NHis protein, 8 Units Staphylococcus aureus polymerase I klenow fragment (exo-), 450 uMdNTP, 250 nM forward primer: peu-F:5′-GCGAACGGGTGAGTAACACGTATCCAATCT-3′ (SEQ ID NO. 39, 250 nM reverse primer: peu-R1:5′-AGCCATTACCTGCTAAAGTCATTCTTCCCAAA-3′ (SEQ ID NO. 40), and 10 ng/uI Mycoplasma pneumoniae genome DNA template, and the Sybr Green I had a final concentration of 0.4x. Reaction conditions were as follows: 20 uI, amplification temperature was 30° C. GenDx thermostatic fluorescence amplifier (specification: GS8) (http://www.gendx.cn/goods.php?id=64) was taken. The amplified result was real-timely detected by Sybr green I at the reaction endpoint. Amplification time: 30 min.
The amplified result was shown in
S1: VR5G_NHis protein, 1000 ng/uI VR5X_NHis protein, 300 ng/ul
S2: VR5G_NHis protein, 800 ng/uI VR5X_NHis protein, 400 ng/ul
S3: VR5G_NHis protein, 600ng/uI VRSX_NHis protein, 300 ng/ul
S4: VR5G_NHis protein, 400 ng/uI VR5X_NHis protein, 200 ng/ul
S5: VR5G_NHis protein, 200 ng/uI VR5X_NHis protein, 600 ng/uI
VR5Y NHis protein, 60 ng/uI, and other reagent components were consistent in this example.
The result shows that low temperature protein may be amplified directed to a specific template and be chimeric onto double strands by Sybr Green I, then a fluorescence signal was gave out to read and obtain the amplification curve by the fluorescence signal. The low temperature protein had inconsistent amplification efficiency at different concentrations in the solution.
The reaction reagent and concentration thereof were as follows: 100 mMtris(hydroxymethyl) aminomethane-acetic acid buffer solution, 120 mM potassium acetate, 15 mM magnesium acetate, 6 mMdithiothreitol, 6% polyethylene glycol (molecular weight: 1450-20000), 2 mM ATP, 40 mM phosphocreatine, 75 ng/ulcreatine kinase, 400 ng/uI VR7_25X_NHis or VR7_25X_CHis protein, 480 ng/uI VR7G_NHis or VR7G_CHis protein, 80 ng/uI VR7_25_26Y NHis or VR7_25_26Y_CHis protein, 8 Units Bacillus subtilis polymerase I klenow fragment (exo-), 450 uMdNTP, 50 ng/ulexo excision enzyme III, 250 nM forward primer ARMP-F, 250 nM reverse primer ARMP-R,120 nM fluorescent probe, about 25 ng/uI arginine mycoplasma genome DNA template, and primer and probe sequences were respectively as follows:
Reaction conditions were as follows: 50 uI, amplification temperature was 40° C.
GenDx thermostatic fluorescence amplifier (specification: GS8) was taken. The amplified result was shown in
S1/S2 reaction well: 400 ng/uI VR7_25X_NHis protein, 480 ng/uI VR7G_NHis protein; 80 ng/uI VR7_25_26Y_NHis protein.
S3/S4 reaction well: 400 ng/uI VR7_25X_CHis protein,480ng/uI VR7G_CHis protein, 80 ng/uI VR7_25_26Y_CHis protein.
S5 reaction well: 400 ng/uI VR7_25X_NHis protein, 480 ng/uI VR7G_CHis protein, 80 ng/uI VR7_25_26Y_NHis protein.
S6 reaction well: 400 ng/uI VR7_25X_CHis protein, 480 ng/uI VR7G_CHis protein, 80 ng/uI VR7_25_26Y_NHis protein.
The amplification result shows that even through the amplified fluorescence signal height value has certain differences, the detection threshold of the fluorescent amplification signal (the response time of the change of the fluorescence signal value might be monitored, TT, Threshold Time) was basically consistent. It is proved that the His protein tag has no obvious difference on the protein activity influence at the N-terminal or C-terminal of the fusion protein under the same protein concentration.
Protein sequences derived from five different virus strains were mixed to test whether the mixed protein derived from different strains could be amplified. The reaction reagent and concentration thereof were as follows: 50 mMtris(hydroxymethyl) aminomethane-acetic acid buffer solution, 80 mM potassium acetate, 20 mM magnesium acetate, 2 mMdithiothreitol, 6% polyethylene glycol (molecular weight: 1450-20000), 2 mM ATP, 30 mM phosphocreatine, 60 ng/ulcreatine kinase, 400 ng/uI VR5X_NHis, VR7_25X_NHis or VR20_26X_NHis protein, 600 ng/uI VR7G_NHis or VR25G_NHis protein, 55 ng/uI VR7_25_26Y_NHis or VR20Y_NHis protein, 8 Units Staphylococcus aureus polymerase I klenow fragment (exo-), 450 uMdNTP, 50 ng/ulexo excision enzyme III, 400 nM forward primer susF, 400 nM reverse primer susR,120 nM fluorescent probe susPB, about 15 ng/uI swine genome DNA template (or NTC as control, replaced by the same volume of ddH2O); the reaction conditions were as follows: 50 uI, amplification temperature: 36° C. GenDx thermostatic fluorescence amplifier (specification: GS8) was taken.
Primer and probe sequences were as follows:
The result was shown in
S1/S3/S5/S7 was a template with the addition of genome DNA. S2/S4/S6/S8 was NTC negative control. (
S1/S3/S5/S7 was NTC negative control. S2/S4/S6/S8 was a template with the addition of genome DNA. (
The Enterobacteria phage vB_EcoM_VR5 amplification system was used to test influences of different temperatures on amplification efficiency, and subjected to parallel comparison of amplification efficiency at low temperature with recombinase polymerase amplification (RPA). Enterobacteria phage vB_EcoM_VR5 amplification reaction reagent and concentration thereof were as follows: 20 mMtris(hydroxymethyl) aminomethane-acetic acid buffer solution, 120 mM potassium acetate, 10 mM magnesium acetate, 8 mMdithiothreitol, 5% polyethylene glycol (molecular weight: 20000), 3 mM ATP, 20 mM phosphocreatine, 30 ng/ulcreatine kinase, 350 ng/uI VR5X_NHis protein, 500 ng/uI VR5G_NHis protein, 50 ng/uI VR5Y_NHis protein, 10 Units Bacillus subtilis polymerase I klenow fragment (exo-), 450 uMdNTP, 250 nM forward primer: peu-F:5′-GCGAACGGGTGAGTAACACGTATCCAATCT-3′(SEQ ID NO. 47), 250 nM reverse primer: peu-R1:5′-AGCCATTACCTGCTAAAGTCATTCTTCCCAAA-3′(SEQ ID NO. 48), and about 100 pg/uI plasmid template carrying a segment of Mycoplasma pneumoniae 16srDNA gene sequence; the reaction conditions were as follows: 50 uI, and the amplification temperature was respectively configured into two temperatures: 20° C. and 25° C. A reagent TwistDx (www.twistdx.co.uk, Cat.No.: TALQBAS01) was used as control for the RPA technology; and products are used in strict accordance with the instruction. Three repeats were configured to each test. The reaction temperature was controlled by a water bath kettle; 1 h after reaction, the protein was inactivated immediately at a high temperature of 80° C.; the amplified product was precipitated by alcohol and then recycled, and dissolved by 20 uI TE; 10 uI recovered product was taken to detect the amplification result by gel electrophoresis, as shown in
The sequence was cloned onto a pUC57 vector, and the terminal sites were cut by an EcoR V enzyme.
It can be seen from the comparison of the reaction diagram that the amplification efficiency of the enzyme derived from low temperature species is obviously higher than that of T4 bacteriophage at low temperature of 20° C. and 25° C.
Based on the electrophoretic results of the amplification, the protein amplification efficiency derived from Enterobacteria phage vB_EcoM_VR5 bacteriophage is obviously superior to the amplification efficiency derived from T4 bacteriophage.
The reaction reagent and concentration thereof were as follows: 30 mMtris(hydroxymethyl) aminomethane-acetic acid buffer solution, 60 mM potassium acetate, 8 mM magnesium acetate, 4 mMdithiothreitol, 3% polyethylene glycol (molecular weight: 1450-20000), 3 mM ATP, 50 mM phosphocreatine, 30-50 ng/uI RM-CK/RM-CK_G268N/Carp-M1-CK, 360 ng/uI VR7_25X_NHis protein, 500 ng/uI VR7G_NHis protein, 60 ng/uI VR7_25_26Y_NHis protein, 8 Units Bacillus subtilis polymerase I klenow fragment (exo-), 450 uMdNTP, 250 nM forward primer susF, 250 nM reverse primer susR, about 10 ng/uI pork tissue genome DNA template, a probe susPB was used for detection, nfo incision enzyme IV was used, and the final concentration was 130 ng/uI. Reaction conditions were as follows: 25 uI, amplification temperature was 32° C. The reaction was performed on a GenDx GS8 fluorescence amplifier, and the fluorescence scanning interval was 60 S, and the reaction time was 40 min. The result was shown in
The test shows that in the reaction system using the enzyme of the present invention, the variant whose G is mutated into N in position 268 has amplification efficiency superior to the wild-type RM-CK.
The reaction system was as follows: 300 ng/uI VR7_25X_NHis protein, 400 ng/uI VR7G_CHis protein, 50 ng/uI VR7_25_26Y_NHis protein, 100 ng/uI polymerase (Staphylococcus aureus polymerase I klenow fragment (exo-)/Bacillus subtilis polymerase I klenow fragment (exo-)/Escherichia coli polymerase klenow fragment (exo-)/Pseudomonas fluorescens polymerase I klenow fragment (exo-); other reaction reagents and concentration thereof were the same as those in Example V, and Sybr Green I 0.4X was added additionally, and the amplification temperature was 33° C. The reaction was performed on a GenDx GS8 fluorescence amplifier, and the fluorescence scanning interval was 30 S, and the reaction time was 20 min.
The amplified result was shown in
S1/S2: Staphylococcus aureus polymerase I klenow fragment (exo-)
S3/S4: Bacillus subtilis polymerase I klenow fragment (exo-)
S5/S6: Escherichia coli polymerase klenow fragment (exo-)
S7/S8: Pseudomonas fluorescens polymerase I klenow fragment (exo-)
S1/S3/S5/S7 was a template with the addition of genome DNA. S2/S4/S6/S8 was NTC negative control.
Based on the reaction result, Escherichia coli polymerase klenow fragment (exo-) has slightly low amplification efficiency, while the other three DNA polymerases have higher amplification efficiency.
The reaction reagent and concentration thereof were as follows: 50 mMtris(hydroxymethyl) aminomethane-acetic acid buffer solution, 100 mM potassium acetate, 16 mM magnesium acetate, 2 mMdithiothreitol, 6% polyethylene glycol (molecular weight: 1450-20000), 2.5 mM ATP, 30 mM phosphocreatine, 120 ng/ulcreatine kinase, 450 ng/uI VR7_25X_NHis protein, 700 ng/uI VR7G_NHis protein, 70 ng/uI VR7_25_26Y_NHis protein, 8 Units Staphylococcus aureus polymerase I klenow fragment (exo-), 450 uMdNTP, 250 nM forward primer, 250 nM reverse primer; the template was a plasmid sequence synthesized by Grass Carp Reovirus GCRV VP7 protein gene, and respectively diluted into 10,000,000 copies/uI, 1,000,000 copies/uI, 100,000 copies/uI,10,000 copies/uI, 1000 copies/uI,100 copies/uI,and 10 copies/uI; the negative control was NTC, and 1 uI template was added to the reaction system during reaction. A probe was used for detection, exoexcision enzyme III was used, and the final concentration was 50 ng/uI. Reaction conditions were as follows: 50 uI, amplification temperature was 28° C.
The sequence carrying Grass Carp Reovirus GCRV VP7 protein gene was as follows:
The sequence was cloned onto a pUC57 vector, and the terminal sites were cut by an EcoR V enzyme.
The reaction was performed on a GenDx GS8 fluorescence amplifier, and the fluorescence scanning interval was 30 S, and the reaction time was 20 min.
S1: 10,000,000 copies/uI,
S2: 1,000,000 copies/uI,
S3: 100,000 copies/uI,
S4: 10,000 copies/uI,
S5: 1000 copies/uI,
S6: 100 copies/uI,
S7: 10 copies/uI,
S8: Negative control was NTC;
The test result (
The reaction reagent and concentration thereof were as follows: 20 mMtris(hydroxymethyl) aminomethane-acetic acid buffer solution, 120 mM potassium acetate, 10 mM magnesium acetate, 6% polyethylene glycol (molecular weight: 1450-20000), 4 mM ATP, 45 mM phosphocreatine, 90 ng/ulcreatine kinase, 450 ng/uluvsX protein from 20 different variants, 550 ng/uI VR7G_CHis protein, 60 ng/uI VR7_25_26Y_NHis protein, 120 ng/uIStaphylococcus aureus polymerase I klenow fragment (exo-), 450 uMdNTP, 400 nM forward primer ARMP-F, 400 nM reverse primer ARMP-R, and about 3000 copies/uI plasmid template carrying a segment of Mycoplasma pneumoniae 16srDNA gene sequence; Sybr Green I had a concentration of 0.5X; the reaction conditions were as follows: 50 uI, and the amplification temperature was 34° C. The reaction was performed on an MolARRAY MA-6000 fluorescent quantitative PCR amplifier, and the fluorescence scanning interval was 30 S, and the reaction time was 20 min.
The result was shown in 11 (a)-(e). In
there was no template.
In
there was no template.
In
there was no template.
In
there was no template.
In
ng/ul; there was no template.
The test result shows that the amplifiation efficiency of partial variants is obviously higher than the wild-type uvsX protein at different variant sites,such as, VRX_Variant1, VRX_Variant7, VRX_Variant11, VRX_Variant17, and VRX_Variant18. Moreover, it is presumed according to the above experiment that other variants may be also superior to the wild-type protein in combination with different gp32 and uvsY proteins.
The reaction reagent and concentration thereof were as follows: 30 mMtris(hydroxymethyl) aminomethane-acetic acid buffer solution, 60 mM potassium acetate, 8 mM magnesium acetate, 4mMdithiothreitol, 5% polyethylene glycol (molecular weight: 20000), 3 mM ATP, 50 mM phosphocreatine, 30 ng/ul RM-CK, 360 ng/ul VR7_25X_NHis protein, 500 ng/ul VR7G_NHis protein, 60 ng/ul VR7_25_26Y_NHis protein, 8 Units Bacillus subtilis polymerase I klenow fragment (exo-), 450 uMdNTP, 250 nM forward primer susF, 250 nM reverse primer susR, about 10 ng/ul pork tissue genome DNA template, a probe susPB was used for detection, and the probe susPB had a final concentration was 120 nM, and exonuclease III (exo III) had a final concentration of 70 ng/ul.Reaction conditions were as follows: 50 uI. Moreover, a reagent TwistDx (www.twistdx.co.uk, Cat.No.: TALQBASO1) was used for the RPA technology; exonuclease III (exo III) having a final concentration of 70 ng/uI was further added as control, and other amplificationconditions were consistent. The amplification temperature: 20-45° C., a temperature gradient every other 5° C. There were six groups of reaction (20, 25, 30, 35, 40, and 45° C.). The reaction was performed on a GenDx GS8 fluorescence amplifier, and the fluorescence scanning interval was 30 S, and the reaction time was 40 min.
The experiment result was shown in
The amplification result proves that different from RPA amplification reagent, the low-temperature protein system derived from VR7 has more obvious amplification effect at a condition of 20-30° C., and the RPA amplification reagent has higher amplification efficiency at 35-40° C., which is consistent with the literature report. In this test, no amplified fluorescence signal change was detected for the RPA reagent at a condition of 20° C.
The reaction reagent and concentration thereof were as follows: 100 mMtris(hydroxymethyl) aminomethane-acetic acid buffer solution, 120 mM potassium acetate, 15 mM magnesium acetate, 6mMdithiothreitol, 5% polyethylene glycol (molecular weight: 20000), 2 mM ATP, 40 mM phosphocreatine, 450 ng/uI VRX_Variant1,550 ng/uI VR5G_NHis,60 ng/uI VR5Y_NHis, 8 Units Bacillus subtilis polymerase I klenow fragment (exo-), 450 uMdNTP, and Sybr Green I 0.4X, 250 nM forward primer ARMP-F, 250 nM reverse primer ARMP-R, 120 nM fluorescent probe ARMP-PB; the primer and probe sequences were respectively as follows:
Reaction conditions were as follows: 50 uI, amplification temperature was 32° C. The sample was a cell culture fluid confirmed to be contaminated with mycoplasma; the fluorescence curve was detected after amplification.
Sample treatment: 500 μl cell supernatant (or the above cell suspension) was taken and centrifuged for 6 min at 14000 rpm; then supernatant was removed to collect precipitate (note: the supernatant may be absorbed by a sucker), and 50 I sterile water was added and vibrated evenly, heated in a 95° C. water bath for 3 min, then slightly vibrated and mixed evenly, after rapid centrifugation, a DNA template was released to the supernatant; during the reaction, 2.5 uI were taken and added to the system as a template.
The reaction was performed on a Bio-Rad Mini Opticon fluorescent quantitative PCR instrument, and the fluorescence scanning interval was 30 S, and the reaction time was 25 min.
The amplified result was shown in
In
S1: Sample No. 1
S2: Sample No. 2
S3: Sample No. 3
S4: Sample No. 4
S5: Sample No. 5 It is verified by amplification that the above samples may obtain positive amplification curves; according to different ct values, it is preliminarily presumed that No. 1 sample has more serious contamination.
| Number | Date | Country | Kind |
|---|---|---|---|
| 201910262085.3 | Apr 2019 | CN | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2019/090586 | 6/10/2019 | WO |
