WO2025137872A1 - Terminal deoxyribonucleoside transferase mutant, preparation method therefor and use thereof - Google Patents
Terminal deoxyribonucleoside transferase mutant, preparation method therefor and use thereof Download PDFInfo
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- the present application belongs to the field of genetic engineering technology and relates to a terminal deoxyribonucleoside transferase mutant and a preparation method and application thereof.
- Phosphoramidite synthesis is the mainstream method for synthesizing short-chain DNA, which can reliably provide short DNA chains of ⁇ 200 nucleotides.
- Phosphoramidite synthesis mainly completes a single base addition cycle through four steps of deprotection, coupling, capping and oxidation. The steps are cumbersome, and there are problems such as long single cycle time (6-8 minutes), high consumption of chemical reagents, and high cost. In addition, a large amount of toxic and flammable organic reagents are used in the reaction process, which causes great pollution.
- the synthesis of nucleotide sequences >200bp by phosphoramidite synthesis is still a heavy burden. For this reason, researchers have tried to develop alternative technologies such as Gibbs assembly to produce longer DNA chains.
- Terminal deoxynucleotidyl transferase is a DNA polymerase that is widely used and has obvious advantages in enzymatic de novo DNA synthesis technology.
- TdT can indiscriminately extend four natural nucleotides (A, T, C, G) to the 3' end of the starting chain without a template.
- A, T, C, G natural nucleotides
- TdT extends oligonucleotides in a promiscuous manner in the 5' to 3' direction of the starting chain. Since any of the four nucleotides will participate in each step of the reaction, it will eventually lead to the simultaneous formation of oligonucleotide sequences of different lengths and codes.
- an effective solution is to control the incorporation of nucleotides through a "reversible termination" mechanism: in the pentose sugar of the nucleotide, the incorporation of nucleotides is controlled by a "reversible termination” mechanism.
- a reversibly removable protecting group "Protecting Group, PG” is added to the 3rd position of the nucleotide to ensure that each reaction step is terminated after extending one nucleotide, and in the subsequent reaction, PG can be removed and restored to a hydroxyl group to extend the next required nucleotide ( Figure 1).
- This DNA de novo synthesis strategy catalyzed by TdT only requires two steps of coupling and deprotection to complete a single base addition cycle. Compared with the phosphoramidite synthesis method, it greatly improves the possible limit of single-cycle efficiency, and the entire reaction is completed in the aqueous phase, with the characteristics of mild reaction conditions and greener.
- CN114921436A discloses a terminal deoxynucleotidyl transferase mutant with improved thermal stability, by mutating the sites of the amino acid sequence of the wild-type terminal deoxynucleotidyl transferase as shown in SEQ ID NO.1 to obtain a mutant with six mutations: N135P, S138H, Q229D, K232D, L234R, and V366M.
- the present application provides a terminal deoxyribonucleoside transferase mutant and a preparation method and application thereof, in order to solve the problems of low efficiency, reaction energy consumption, high pollution, etc. in synthesizing DNA by the traditional phosphoramidite synthesis method, as well as the low catalytic efficiency of wild terminal deoxyribonucleoside transferase.
- the activities of the GeTdT mutants shown in the figure for the four nucleotides with azidomethyl modification at the 3' end are better than those of the wild type, among which the conversion rates of the mutants E459R, E459R/R460Q, E459R/R460K, E459R/R460E, E459R/R460H, E459R/R460N and E459R/R460D are greatly improved compared with the wild type.
- the oligonucleotide substrate 5'-ROX-Oligo(dT) 98 was extended by one base under the action of terminal deoxyribonucleoside transferase to obtain the product 5'-ROX-Oligo(dT) 99 -3'-O-Azidomethyl.
- the reaction system for determining the conversion rate of the GeTdT wild type and its mutants is shown in Table 3. After the reaction system is mixed, the reaction is reacted at 37°C for 10 minutes. After the reaction is completed, the reaction is terminated by heating at 95°C for 10 minutes.
- Oligo(dT) 18 an oligonucleotide substrate, was extended by one base under the action of terminal deoxyribonucleoside transferase to obtain the product Oligo(dT) 19 -3'-O-PG.
- the reaction system for the terminal transfer activity test of the wild-type GeTdT enzyme and its mutants is shown in Table 5. After the reaction system is mixed, it is reacted at 37°C for 10 minutes. After the reaction is completed, it is heated at 95°C for 10 minutes to terminate the reaction.
- the reaction products of GeTdT wild type and its mutants were semi-quantitatively analyzed by urea polyacrylamide gel electrophoresis (20% denaturing gel). The results are shown in FIG5 .
- NC represents Oligo(dT) 18 ; Lanes 1-3 represent: 1, WT; 2, E459R; 3, E459R/R460E.
- the 5 ⁇ reaction buffer used in this application is formulated as: 0.5M Na-Cacodylate, 5mM CoCl 2 , pH 7.2.
- the present application obtains advantageous TdT mutants by molecularly modifying natural TdT, thereby greatly improving the catalytic efficiency of modified nucleic acid monomers and achieving efficient single-base addition efficiency.
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Abstract
Description
本申请属于基因工程技术领域,涉及一种末端脱氧核糖核苷转移酶突变体及其制备方法和应用。The present application belongs to the field of genetic engineering technology and relates to a terminal deoxyribonucleoside transferase mutant and a preparation method and application thereof.
在高通量测序和基因编辑技术的推动下,合成生物学迅速崛起,DNA合成也已经成为一个新兴的行业。DNA的合成需求在许多研究和商业活动领域都在不断地增加。如果DNA合成能够大规模、低成本地被提供,这将会推动工程生物学、治疗、数据存储和纳米技术等技术的快速发展。DNA结构被发现后,随着固相合成技术的进步,DNA的从头合成技术已经实现了实质性的里程碑。目前从头合成寡核苷酸的方法主要有两种:化学合成法(亚磷酰胺合成法)和生物合成法(酶促合成法)。亚磷酰胺合成法是当前合成短链DNA的主流方法,能够可靠地提供<200核苷酸的短DNA链。亚磷酰胺合成法主要通过脱保护、偶联、加帽以及氧化四步来完成一个单碱基添加循环,其步骤繁琐,存在单个循环耗时较长(6-8分钟)、化学试剂消耗较多、成本较高的问题,且反应过程中大量使用有毒、易燃的有机试剂,污染较大。目前通过亚磷酰胺合成法合成>200bp的核苷酸序列仍然是负担较重的,为此研究者们尝试开发吉布斯组装等替代技术来产生更长的DNA链。Driven by high-throughput sequencing and gene editing technologies, synthetic biology has risen rapidly, and DNA synthesis has become an emerging industry. The demand for DNA synthesis is increasing in many fields of research and commercial activities. If DNA synthesis can be provided on a large scale and at low cost, it will promote the rapid development of technologies such as engineering biology, treatment, data storage and nanotechnology. After the discovery of the DNA structure, with the advancement of solid-phase synthesis technology, the de novo synthesis technology of DNA has achieved substantial milestones. At present, there are two main methods for synthesizing oligonucleotides from scratch: chemical synthesis (phosphoramidite synthesis) and biosynthesis (enzymatic synthesis). Phosphoramidite synthesis is the mainstream method for synthesizing short-chain DNA, which can reliably provide short DNA chains of <200 nucleotides. Phosphoramidite synthesis mainly completes a single base addition cycle through four steps of deprotection, coupling, capping and oxidation. The steps are cumbersome, and there are problems such as long single cycle time (6-8 minutes), high consumption of chemical reagents, and high cost. In addition, a large amount of toxic and flammable organic reagents are used in the reaction process, which causes great pollution. Currently, the synthesis of nucleotide sequences >200bp by phosphoramidite synthesis is still a heavy burden. For this reason, researchers have tried to develop alternative technologies such as Gibbs assembly to produce longer DNA chains.
酶促法从头合成DNA是一种很有应用前景的技术,自20世纪50年代以来一直受到人们的关注。末端脱氧核苷酸转移酶(Terminal deoxynucleotidyl Transferase,TdT)是酶促法从头合成DNA技术中应用较多且优势较明显的DNA聚合酶。TdT能够在没有模板的情况下将四种天然核苷酸(A、T、C、G)无差别的延伸到起始链的3’端。研究表明,TdT能够在1秒内延伸数个核苷酸,并且可以将合成的DNA延长到几千碱基,优越的合成长度和速度远远超出了商业上可获得的亚磷酰胺合成法技术的范围。然而TdT是以混杂的方式在起始链的5’到3’的方向上延长寡核苷酸的,由于每步反应四个核苷酸中的任何一个都会参与,最终导致同时形成不同长度和编码的寡核苷酸序列。针对这个问题,一个有效的解决方案是通过“可逆终止”机制控制核苷酸的掺入:在核苷酸五碳糖 的3号位添加一个可逆去除的保护基团“Protecting Group,PG”,确保每个反应步骤延伸一个核苷酸后即被终止,并且在随后的反应中PG可被切除恢复成羟基,进而延伸下一个所需的核苷酸(图1)。这种由TdT催化的DNA从头合成策略,只需要偶联、脱保护两步反应即可完成一个单碱基添加循环,相比亚磷酰胺合成法极大地提高了单循环效率的可能极限值,并且反应全程在水相中完成,具有反应条件温和、更加绿色等特点。如何实现高效的单碱基添加效率是TdT主导的酶促法从头合成DNA方案的关键。由于方案中采用的是带PG修饰的非天然核苷酸单体,天然TdT对其活性太低,导致合成效率低下,因此需要通过分子改造来提高TdT对修饰核苷酸单体的聚合活性。如CN114921436A公开了一种热稳定性提高的末端脱氧核苷酸转移酶突变体,对如SEQ ID NO.1所示的野生型末端脱氧核苷酸转移酶的氨基酸序列的位点进行突变,获得N135P、S138H、Q229D、K232D、L234R、V366M六位点突变的突变体。Enzymatic de novo DNA synthesis is a promising technology that has attracted attention since the 1950s. Terminal deoxynucleotidyl transferase (TdT) is a DNA polymerase that is widely used and has obvious advantages in enzymatic de novo DNA synthesis technology. TdT can indiscriminately extend four natural nucleotides (A, T, C, G) to the 3' end of the starting chain without a template. Studies have shown that TdT can extend several nucleotides within 1 second and can extend the synthesized DNA to several thousand bases. The superior synthesis length and speed far exceed the range of commercially available phosphoramidite synthesis technology. However, TdT extends oligonucleotides in a promiscuous manner in the 5' to 3' direction of the starting chain. Since any of the four nucleotides will participate in each step of the reaction, it will eventually lead to the simultaneous formation of oligonucleotide sequences of different lengths and codes. To address this problem, an effective solution is to control the incorporation of nucleotides through a "reversible termination" mechanism: in the pentose sugar of the nucleotide, the incorporation of nucleotides is controlled by a "reversible termination" mechanism. A reversibly removable protecting group "Protecting Group, PG" is added to the 3rd position of the nucleotide to ensure that each reaction step is terminated after extending one nucleotide, and in the subsequent reaction, PG can be removed and restored to a hydroxyl group to extend the next required nucleotide (Figure 1). This DNA de novo synthesis strategy catalyzed by TdT only requires two steps of coupling and deprotection to complete a single base addition cycle. Compared with the phosphoramidite synthesis method, it greatly improves the possible limit of single-cycle efficiency, and the entire reaction is completed in the aqueous phase, with the characteristics of mild reaction conditions and greener. How to achieve efficient single-base addition efficiency is the key to the TdT-dominated enzymatic de novo DNA synthesis scheme. Since the scheme uses non-natural nucleotide monomers modified with PG, the activity of natural TdT on it is too low, resulting in low synthesis efficiency. Therefore, it is necessary to improve the polymerization activity of TdT on modified nucleotide monomers through molecular modification. For example, CN114921436A discloses a terminal deoxynucleotidyl transferase mutant with improved thermal stability, by mutating the sites of the amino acid sequence of the wild-type terminal deoxynucleotidyl transferase as shown in SEQ ID NO.1 to obtain a mutant with six mutations: N135P, S138H, Q229D, K232D, L234R, and V366M.
综上所述,挖掘设计高聚合活性的末端脱氧核苷酸转移酶,对于核酸合成领域具有重要意义。In summary, the discovery and design of terminal deoxynucleotidyl transferases with high polymerization activity is of great significance in the field of nucleic acid synthesis.
发明内容Summary of the invention
本申请提供一种末端脱氧核糖核苷转移酶突变体及其制备方法和应用,以期解决传统亚磷酰胺合成法合成DNA具有效率低、反应耗能、污染大等问题,以及野生末端脱氧核糖核苷转移酶催化效率低等问题。The present application provides a terminal deoxyribonucleoside transferase mutant and a preparation method and application thereof, in order to solve the problems of low efficiency, reaction energy consumption, high pollution, etc. in synthesizing DNA by the traditional phosphoramidite synthesis method, as well as the low catalytic efficiency of wild terminal deoxyribonucleoside transferase.
第一方面,本申请提供一种末端脱氧核糖核苷转移酶突变体,所述末端脱氧核糖核苷转移酶突变体的氨基酸序列包括以下序列中任意一种:In a first aspect, the present application provides a terminal deoxyribonucleoside transferase mutant, wherein the amino acid sequence of the terminal deoxyribonucleoside transferase mutant comprises any one of the following sequences:
(1)在SEQ ID NO:2所示序列基础上发生如下突变:E459R、E459K、E459Q、E459V、R460Q、R460K、R460E、R460H、R460N、R460D、R460S、R460L、R460M、R460W、R460F、R460Y、R460C或R460G中任意一种或至少两种的序列;或,(1) the following mutations occur based on the sequence shown in SEQ ID NO:2: any one or at least two of the following sequences: E459R, E459K, E459Q, E459V, R460Q, R460K, R460E, R460H, R460N, R460D, R460S, R460L, R460M, R460W, R460F, R460Y, R460C or R460G; or,
(2)由如(1)所述序列经取代、缺失或添加一个或至少两个氨基酸残基获得,且与(1)所述序列功能相同或相似的序列;或,(2) a sequence obtained by substituting, deleting or adding one or at least two amino acid residues of the sequence described in (1), and having the same or similar function as the sequence described in (1); or
(3)与(1)或(2)所述序列具有至少90%序列同源性,且与(1)所述序列功能相同或相似的序列。(3) A sequence having at least 90% sequence homology with the sequence described in (1) or (2) and having the same or similar functions as the sequence described in (1).
本申请中,对来源壁虎(Gecko)的末端脱氧核糖核苷转移酶GeTdT进行 分子改造,通过分子改造来对活性口袋进行极性以及空间大小的调整,使其能够很好的容纳非天然核苷酸,从而提高其对修饰核苷酸单体的聚合活性,极大的提高了对修饰核酸单体的催化效率,实现高效的单碱基添加效率,能够在没有模板的情况下将多种3’-O-阻断修饰dNTPs底物添加到寡聚核苷酸单链的3’-OH端,为酶促法从头合成核酸提供新型、有效的工具酶。In this application, the terminal deoxyribonucleoside transferase GeTdT from Gecko was used to Molecular modification is used to adjust the polarity and spatial size of the active pocket so that it can accommodate non-natural nucleotides well, thereby improving its polymerization activity for modified nucleotide monomers, greatly improving the catalytic efficiency for modified nucleic acid monomers, and achieving efficient single-base addition efficiency. It can add a variety of 3'-O-blocked modified dNTPs substrates to the 3'-OH end of the oligonucleotide single chain without a template, providing a new and effective tool enzyme for the enzymatic synthesis of nucleic acids from scratch.
本申请中,在野生型末端脱氧核糖核苷转移酶中引入特定突变,能够提高其对修饰核苷酸单体的聚合活性,可以理解,在所述末端脱氧核糖核苷转移酶突变体基础上,本领域技术人员能够利用本领域通用技术手段进行取代、缺失或添加一个或至少两个氨基酸残基获得功能相同或相似的其他序列。
In the present application, the introduction of specific mutations into the wild-type terminal deoxyribonucleoside transferase can improve its polymerization activity for modified nucleotide monomers. It can be understood that based on the terminal deoxyribonucleoside transferase mutant, those skilled in the art can use the general technical means in the art to replace, delete or add one or at least two amino acid residues to obtain other sequences with the same or similar functions.
本申请中,术语“同源性”可以用肉眼或计算机软件(比如Ausubel et al.eds.(2007)在Current Protocols in Molecular Biology中所述的软件程序)进行评价。当被比较的序列中的位置被相同的碱基或氨基酸占据时,则分子在该位置是同一的。两个或多个序列之间的同源性可以用百分比(%)表示,其可以用来评价相关序列之间的同源性。多聚核苷酸序列或氨基酸序列与另一序列有具有一定百分比(例如90%、95%、98%或者99%)的“序列同源性”是指当序列比对时,所比较的两个序列中该百分比的碱基或氨基酸相同。In this application, the term "homology" can be evaluated by the naked eye or by computer software (such as the software program described in Current Protocols in Molecular Biology by Ausubel et al. eds. (2007). When a position in the compared sequences is occupied by the same base or amino acid, the molecules are identical at that position. The homology between two or more sequences can be expressed as a percentage (%), which can be used to evaluate the homology between related sequences. A polynucleotide sequence or amino acid sequence has a certain percentage (for example, 90%, 95%, 98% or 99%) of "sequence homology" with another sequence means that when the sequences are aligned, the percentage of bases or amino acids in the two compared sequences are the same.
本申请中,涉及到E459的单点、E459与R460两位点的组合突变,优选地,(1)所述突变可包括E459R和R460Q组合突变(可写为E459R/R460Q)、E459R和R460K组合突变、E459R和R460E组合突变、E459R和R460H组合突变、E459R和R460N组合突变、E459R和R460D组合突变、E459R和R460S组合 突变、E459R和R460L组合突变、E459R和R460M组合突变、E459R和R460W组合突变、E459R和R460F组合突变、E459R和R460Y组合突变、E459R和R460C组合突变或E459R和R460G组合突变中任意一种。In the present application, single-site mutation of E459 and combined mutation of two sites of E459 and R460 are involved. Preferably, (1) the mutation may include combined mutation of E459R and R460Q (which can be written as E459R/R460Q), combined mutation of E459R and R460K, combined mutation of E459R and R460E, combined mutation of E459R and R460H, combined mutation of E459R and R460N, combined mutation of E459R and R460D, combined mutation of E459R and R460S. mutation, E459R and R460L combined mutation, E459R and R460M combined mutation, E459R and R460W combined mutation, E459R and R460F combined mutation, E459R and R460Y combined mutation, E459R and R460C combined mutation or E459R and R460G combined mutation.
第二方面,本申请提供一种核酸分子,所述核酸分子编码第一方面所述的糖基转移酶突变体。In a second aspect, the present application provides a nucleic acid molecule encoding the glycosyltransferase mutant described in the first aspect.
第三方面,本申请提供一种重组载体,所述重组载体含有第二方面所述的核酸分子。In a third aspect, the present application provides a recombinant vector, wherein the recombinant vector contains the nucleic acid molecule described in the second aspect.
第四方面,本申请提供一种重组细胞,所述重组细胞含有第三方面所述的重组载体。In a fourth aspect, the present application provides a recombinant cell, wherein the recombinant cell contains the recombinant vector described in the third aspect.
第五方面,本申请提供第一方面所述的末端脱氧核糖核苷转移酶突变体的制备方法,所述制备方法包括:In a fifth aspect, the present application provides a method for preparing the terminal deoxyribonucleoside transferase mutant according to the first aspect, the preparation method comprising:
将编码第一方面所述的末端脱氧核糖核苷转移酶突变体的核酸分子插入表达载体,得到重组载体,将所述重组载体导入宿主细胞,或,直接将所述核酸分子整合在宿主细胞的基因组上,获得基因工程菌,进行培养和分离纯化,得到所述末端脱氧核糖核苷转移酶突变体。Inserting a nucleic acid molecule encoding the terminal deoxyribonucleoside transferase mutant described in the first aspect into an expression vector to obtain a recombinant vector, and introducing the recombinant vector into a host cell, or directly integrating the nucleic acid molecule into the genome of the host cell to obtain a genetically engineered bacterium, and culturing and separating and purifying the terminal deoxyribonucleoside transferase mutant.
第六方面,本申请提供第一方面所述的末端脱氧核糖核苷转移酶突变体在制备用于核酸合成的产品中的应用。In a sixth aspect, the present application provides the use of the terminal deoxyribonucleoside transferase mutant described in the first aspect in the preparation of a product for nucleic acid synthesis.
第七方面,本申请提供一种用于核酸合成的产品,所述产品包括第一方面所述的末端脱氧核糖核苷转移酶突变体。In a seventh aspect, the present application provides a product for nucleic acid synthesis, wherein the product comprises the terminal deoxyribonucleoside transferase mutant described in the first aspect.
第八方面,本申请提供第一方面所述的末端脱氧核糖核苷转移酶突变体在核酸合成中的应用。In an eighth aspect, the present application provides the use of the terminal deoxyribonucleoside transferase mutant described in the first aspect in nucleic acid synthesis.
第九方面,本申请提供一种合成核酸的方法,所述方法包括:In a ninth aspect, the present application provides a method for synthesizing nucleic acid, the method comprising:
利用第一方面所述的末端脱氧核糖核苷转移酶突变体催化dNTPs连接到寡聚核苷酸单链的3’-OH端。The terminal deoxyribonucleoside transferase mutant described in the first aspect is used to catalyze the connection of dNTPs to the 3'-OH end of the oligonucleotide single chain.
优选地,所述dNTPs包括3’-O-阻断修饰的dNTPs,阻断修饰包括如保护基团“Protecting Group,PG”。Preferably, the dNTPs include 3’-O-blocking modified dNTPs, and the blocking modification includes a protecting group such as “Protecting Group, PG”.
与现有技术相比,本申请具有以下有益效果:Compared with the prior art, this application has the following beneficial effects:
本申请对野生型末端脱氧核糖核苷转移酶进行分子改造,提高其对修饰核苷酸单体的聚合活性,极大的提高了对修饰核酸单体的催化效率,实现高效的单碱基添加效率,能够在没有模板的情况下将多种3’-O-阻断修饰dNTPs底物添 加到寡聚核苷酸单链的3’-OH端,为酶促法从头合成核酸提供新型、有效的工具酶。The present invention molecularly modifies the wild-type terminal deoxyribonucleoside transferase to improve its polymerization activity for modified nucleotide monomers, greatly improves the catalytic efficiency for modified nucleic acid monomers, achieves efficient single-base addition efficiency, and is able to add a variety of 3'-O-blocked modified dNTPs substrates to the nucleotides without a template. Adding to the 3'-OH end of a single-stranded oligonucleotide provides a new and effective tool enzyme for enzymatic de novo synthesis of nucleic acids.
图1为末端脱氧核糖核苷转移酶主导的酶法合成方案流程图。FIG1 is a flow chart of the terminal deoxyribonucleoside transferase-dominated enzymatic synthesis scheme.
图2为GeTdT突变体纯化蛋白的SDS-PAGE图。FIG. 2 is an SDS-PAGE image of the purified protein of the GeTdT mutant.
图3末端脱氧核糖核苷转移酶产物的Urea-PAGE图。Figure 3 Urea-PAGE of terminal deoxyribonucleoside transferase products.
图4为GeTdT野生型及其E459R和E459R/R460Q突变体转化产物的毛细管电泳图。FIG4 is a capillary electrophoresis diagram of the transformation products of GeTdT wild type and its E459R and E459R/R460Q mutants.
图5为末端脱氧核糖核苷转移酶产物的Urea-PAGE图。FIG5 is a Urea-PAGE image of the terminal deoxyribonucleoside transferase product.
为进一步阐述本申请所采取的技术手段及其效果,以下结合实施例和附图对本申请作进一步地说明。可以理解的是,此处所描述的具体实施方式仅仅用于解释本申请,而非对本申请的限定。To further illustrate the technical means and effects adopted by the present application, the present application is further described below in conjunction with the embodiments and drawings. It is understood that the specific implementation methods described herein are only used to explain the present application, rather than to limit the present application.
实施例中未注明具体技术或条件者,按照本领域内的文献所描述的技术或条件,或者按照产品说明书进行。所用试剂或仪器未注明生产厂商者,均为可通过正规渠道购买获得的常规产品。If no specific techniques or conditions are specified in the examples, the techniques or conditions described in the literature in the field or the product instructions are used. If no manufacturer is specified for the reagents or instruments used, they are all conventional products that can be purchased through regular channels.
本申请具体实施例中采用整体方案为:设计引物进行定点突变→通过大肠杆菌表达系统获得TdT突变体的粗蛋白液→镍离子亲和层析获得纯化的TdT突变体蛋白→对蛋白进行活性测试→尿素聚丙烯酰胺凝胶(Urea-PAGE)和毛细管电泳(CE)分析产物。The overall scheme adopted in the specific embodiments of the present application is: design primers for site-directed mutagenesis → obtain the crude protein solution of TdT mutant through Escherichia coli expression system → obtain purified TdT mutant protein by nickel ion affinity chromatography → test the activity of protein → analyze the product by urea polyacrylamide gel (Urea-PAGE) and capillary electrophoresis (CE).
实施例1Example 1
末端脱氧核糖核苷转移酶GeTdT突变体的构建。Construction of terminal deoxyribonucleoside transferase GeTdT mutant.
改造对象是来源壁虎(Gecko)的末端脱氧核糖核苷转移酶GeTdT,其核苷酸序列如SEQ ID NO.1所示、氨基酸序列如SEQ ID NO.2所示,根据序列分别设计并合成含有E459R、E459K、E459Q、E459V、E459R/(“/”表示和)R460Q、E459R/R460K、E459R/R460E、E459R/R460H、E459R/R460N、E459R/R460D、E459R/R460S、E459R/R460L、E459R/R460M、E459R/R460W、E459R/R460F、E459R/R460Y、E459R/R460C、E459R/R460G突变的引物,对GeTdT进行定点突变。以携带编码GeTdT部分肽链(SEQ ID NO.2中的氨基酸G144到A512, 即后续所述的野生型GeTdT)基因的重组表达质粒pGS-21a/GeTdT(G144—A512)为模板,利用如表1所示的相应突变引物对通过快速PCR技术在特点位点引入突变,并通过Sanger测序确认GeTdT突变体的编码基因是否正确。重组表达质粒pGS-21a/GeTdT(G144—A512)表达的完整肽链序列如SEQ ID NO.3所示。The object of transformation is the terminal deoxyribonucleoside transferase GeTdT from Gecko, whose nucleotide sequence is shown in SEQ ID NO.1 and amino acid sequence is shown in SEQ ID As shown in NO.2, primers containing E459R, E459K, E459Q, E459V, E459R/("/" indicates sum)R460Q, E459R/R460K, E459R/R460E, E459R/R460H, E459R/R460N, E459R/R460D, E459R/R460S, E459R/R460L, E459R/R460M, E459R/R460W, E459R/R460F, E459R/R460Y, E459R/R460C, and E459R/R460G mutations were designed and synthesized according to the sequence, and site-directed mutagenesis of GeTdT was performed. To carry the partial peptide chain encoding GeTdT (amino acids G144 to A512 in SEQ ID NO.2, That is, the recombinant expression plasmid pGS-21a/GeTdT (G144—A512) of the wild-type GeTdT gene described later was used as a template, and the mutation was introduced into the characteristic site by rapid PCR technology using the corresponding mutation primer pair shown in Table 1, and the coding gene of the GeTdT mutant was confirmed to be correct by Sanger sequencing. The complete peptide chain sequence expressed by the recombinant expression plasmid pGS-21a/GeTdT (G144—A512) is shown in SEQ ID NO.3.
表1构建GeTdT突变体的对应引物
Table 1 Corresponding primers for constructing GeTdT mutants
PCR反应体系均为:10μL的5×PS buffer,4μL的dNTPs Mix(2.5mmol/L),lμL正向引物(10μmol/L),1μL反向引物(10μmol/L),1μL模板DNA,0.5μL的Primer Star HS(Takara,5U/μL),加入蒸馏水至50μL。The PCR reaction system was: 10 μL of 5×PS buffer, 4 μL of dNTPs Mix (2.5 mmol/L), 1 μL of forward primer (10 μmol/L), 1 μL of reverse primer (10 μmol/L), 1 μL of template DNA, 0.5 μL of Primer Star HS (Takara, 5 U/μL), and distilled water was added to 50 μL.
PCR扩增程序设定为:首先94℃预变性5min;然后进入21个循环(98℃变性10s,55℃退火5s,72℃延伸7min 50s);最后72℃延伸7min,4℃保温。PCR产物用1%琼脂糖凝胶电泳进行检测。The PCR amplification program was set as follows: first, pre-denaturation at 94°C for 5 min; then 21 cycles (denaturation at 98°C for 10 s, annealing at 55°C for 5 s, extension at 72°C for 7 min 50 s); finally, extension at 72°C for 7 min, and insulation at 4°C. PCR products were detected by 1% agarose gel electrophoresis.
在凝胶电泳验证正确的PCR产物中加入Dpn I,37℃水浴2h,降解模板,之后分别转化到大肠杆菌JM109感受态细胞(购买自天根生化科技有限公司)中。将转化产物涂布于含有100mg/L氨苄青霉素的LB固体培养基,37℃培养11h,挑取克隆接种于LB液体培养基,37℃培养9h。菌液进行Sanger测序以验证突变位点是否正确引入。将测序正确的克隆进行质粒提取,并转化到表达宿主大肠杆菌BL21(DE3)感受态细胞(购买自天根生化科技有限公司)中,得到能够表达18种突变体及GeTdT野生型蛋白的19种重组大肠杆菌菌株。
Dpn I was added to the PCR product verified by gel electrophoresis, and the template was degraded by water bath at 37°C for 2 hours, and then transformed into Escherichia coli JM109 competent cells (purchased from Tiangen Biochemical Technology Co., Ltd.). The transformation product was spread on LB solid medium containing 100 mg/L ampicillin, cultured at 37°C for 11 hours, and the clones were picked and inoculated into LB liquid medium and cultured at 37°C for 9 hours. The bacterial solution was subjected to Sanger sequencing to verify whether the mutation site was correctly introduced. The clones with correct sequencing were subjected to plasmid extraction and transformed into the expression host Escherichia coli BL21 (DE3) competent cells (purchased from Tiangen Biochemical Technology Co., Ltd.), and 19 recombinant Escherichia coli strains capable of expressing 18 mutants and GeTdT wild-type proteins were obtained.
需要说明的是,由于密码子简并性原则,翻译氨基酸序列的核苷酸序列并不是唯一恒定的序列,任何可以编码相同氨基酸序列的核苷酸序列都是本专利范围内的核酸序列。
It should be noted that due to the principle of codon degeneracy, the nucleotide sequence for translating an amino acid sequence is not a unique constant sequence, and any nucleotide sequence that can encode the same amino acid sequence is a nucleic acid sequence within the scope of this patent.
实施例2Example 2
末端脱氧核糖核苷转移酶GeTdT及其突变体的表达和纯化。Expression and purification of terminal deoxyribonucleoside transferase GeTdT and its mutants.
将实施例1中得到的19种重组大肠杆菌分别接种于LB培养基中,在37℃下培养8h后,以发酵培养基体积5%的接种量转接至300mL TB发酵培养基中。先放至37℃、200rpm恒温培养3h,在菌体OD600为0.5~0.7时添加IPTG至1μM终浓度并转至25℃、200rpm诱导发酵24h。发酵结束后,将发酵液经高压匀浆破碎(破碎条件为4℃、80MPa)后离心(12000rpm、30min、4℃),上清即为重组菌所产的末端脱氧核糖核苷转移酶突变体粗酶液。The 19 recombinant E. coli obtained in Example 1 were inoculated into LB medium respectively, and after culturing at 37°C for 8h, they were transferred to 300mL TB fermentation medium with an inoculation amount of 5% of the volume of the fermentation medium. First, they were placed at 37°C and 200rpm for constant temperature culture for 3h. When the bacterial OD 600 was 0.5-0.7, IPTG was added to a final concentration of 1μM and the culture was induced at 25°C and 200rpm for 24h. After the fermentation was completed, the fermentation broth was crushed by high-pressure homogenization (crushing conditions were 4°C and 80MPa) and then centrifuged (12000rpm, 30min, 4°C), and the supernatant was the crude enzyme solution of the terminal deoxyribonucleoside transferase mutant produced by the recombinant bacteria.
将上步准备好的酶液样品进行蛋白纯化,具体如下:采用镍离子亲和层析对末端脱氧核糖核苷转移酶蛋白进行纯化。将末端脱氧核糖核苷转移酶突变体粗酶液分别加载到镍离子亲和层析柱上(镍柱)。使用梯度洗脱法纯化重组蛋白:用纯化缓冲液A和纯化缓冲液B配制成洗脱液1(含0%缓冲液B)、洗脱液2(含5%缓冲液B)、洗脱液3(含10%缓冲液B)、洗脱液4(含20%缓冲液B)、洗脱液5(含50%缓冲液B)和洗脱液6(含100%缓冲液B),然后按咪唑浓度由低到高的顺序用洗脱液逐步洗脱镍柱上结合的蛋白。纯化过程中所有的洗脱液均预冷至4℃以确保重组蛋白保持生物活性。使用能截留30kDa蛋白的超滤管对含纯化目的蛋白的洗脱液4进行超滤浓缩,并用2×酶储缓冲液置换纯化洗脱液。最后在得到的浓缩蛋白中加入等体积的甘油,混匀后储存于-20℃低温下。纯化重组蛋白的纯度通过SDS-PAGE进行分析,图2中M表示蛋白标准品;泳道1-19分别代表:1,WT(野生型);2,E459R;3,E459K;4,E459Q;5,E459V;6,E459R/R460Q;7,E459R/R460K;8,E459R/R460E;9,E459R/R460H;10,E459R/R460N;11,E459R/R460D;12,E459R/R460S;13,E459R/R460L;14, E459R/R460M;15,E459R/R460W;16,E459R/R460F;17,E459R/R460Y;18,E459R/R460C;19,E459R/R460G,表明获得了较纯的蛋白。The enzyme solution sample prepared in the previous step was subjected to protein purification, as follows: the terminal deoxyribonucleoside transferase protein was purified by nickel ion affinity chromatography. The crude enzyme solution of the terminal deoxyribonucleoside transferase mutant was loaded onto a nickel ion affinity chromatography column (nickel column) respectively. The recombinant protein was purified by gradient elution method: purification buffer A and purification buffer B were used to prepare eluent 1 (containing 0% buffer B), eluent 2 (containing 5% buffer B), eluent 3 (containing 10% buffer B), eluent 4 (containing 20% buffer B), eluent 5 (containing 50% buffer B) and eluent 6 (containing 100% buffer B), and then the protein bound to the nickel column was gradually eluted with the eluents in the order of imidazole concentration from low to high. During the purification process, all eluents were precooled to 4°C to ensure that the recombinant protein maintained biological activity. The eluent 4 containing the purified target protein was ultrafiltered and concentrated using an ultrafiltration tube that could retain 30 kDa protein, and the purified eluent was replaced with 2× enzyme storage buffer. Finally, an equal volume of glycerol was added to the concentrated protein, mixed and stored at -20°C. The purity of the purified recombinant protein was analyzed by SDS-PAGE. In Figure 2, M represents protein standard; lanes 1-19 represent: 1, WT (wild type); 2, E459R; 3, E459K; 4, E459Q; 5, E459V; 6, E459R/R460Q; 7, E459R/R460K; 8, E459R/R460E; 9, E459R/R460H; 10, E459R/R460N; 11, E459R/R460D; 12, E459R/R460S; 13, E459R/R460L; 14, E459R/R460M; 15, E459R/R460W; 16, E459R/R460F; 17, E459R/R460Y; 18, E459R/R460C; 19, E459R/R460G, indicating that a relatively pure protein was obtained.
纯化缓冲液A(pH8.0):20mM Tris-HCl、500mM NaCl、10mM咪唑。Purification buffer A (pH 8.0): 20 mM Tris-HCl, 500 mM NaCl, 10 mM imidazole.
纯化缓冲液B(pH8.0):20mM Tris-HCl、500mM NaCl、500mM咪唑。Purification buffer B (pH 8.0): 20 mM Tris-HCl, 500 mM NaCl, 500 mM imidazole.
2×酶储缓冲液(pH7.2):40mM Tris-HCl、400mM NaCl、5%甘油。2× enzyme storage buffer (pH 7.2): 40 mM Tris-HCl, 400 mM NaCl, 5% glycerol.
实施例3Example 3
末端脱氧核糖核苷转移酶GeTdT及其突变体的活性半定量分析。Semi-quantitative analysis of the activity of terminal deoxyribonucleoside transferase GeTdT and its mutants.
使用聚合度为18的单链Oligo(dT)18(SEQ ID NO.40)作为寡核苷酸底物,使用3’端带叠氮甲基修饰的四种核苷酸(3’-O-Azidomethyl-dATP、3’-O-Azidomethyl-dTTP、3’-O-Azidomethyl-dCTP、3’-O-Azidomethyl-dGTP)为核酸单体底物(结构如图3所示),对纯化得到的野生型GeTdT及其突变体进行末端转移活性的测定。寡核苷酸底物Oligo(dT)18在末端脱氧核糖核苷转移酶的作用下延伸一个碱基,得到产物Oligo(dT)18-dNTP-3’-O-Azidomethyl。野生型GeTdT酶及其突变体的活性测试反应体系如表2,反应体系混匀后于37℃反应10min,反应结束后95℃加热10min终止反应。采用尿素聚丙烯酰胺凝胶电泳(20%变性胶)对GeTdT野生型及其突变体的反应产物进行半定量分析,结果如图3。所用的5×Reaction buffer配方为:0.5M Na-Cacodylate,5mM CoCl2,pH 7.2。Using single-stranded Oligo(dT) 18 (SEQ ID NO.40) with a polymerization degree of 18 as an oligonucleotide substrate, and using four nucleotides with azidomethyl modification at the 3' end (3'-O-Azidomethyl-dATP, 3'-O-Azidomethyl-dTTP, 3'-O-Azidomethyl-dCTP, 3'-O-Azidomethyl-dGTP) as nucleic acid monomer substrates (structures shown in Figure 3), the terminal transfer activity of the purified wild-type GeTdT and its mutants was determined. Oligo(dT) 18, an oligonucleotide substrate, was extended by one base under the action of terminal deoxyribonucleoside transferase to obtain the product Oligo(dT) 18- dNTP-3'-O-Azidomethyl. The reaction system for the activity test of the wild-type GeTdT enzyme and its mutants is shown in Table 2. After the reaction system is mixed, it is reacted at 37°C for 10 minutes. After the reaction is completed, it is heated at 95°C for 10 minutes to terminate the reaction. Urea polyacrylamide gel electrophoresis (20% denaturing gel) was used to semi-quantitatively analyze the reaction products of GeTdT wild type and its mutants, and the results are shown in Figure 3. The formula of the 5× reaction buffer used was: 0.5M Na-Cacodylate, 5mM CoCl 2 , pH 7.2.
表2野生型GeTdT酶及其突变体的活性测试反应体系
Table 2 Activity test reaction system of wild-type GeTdT enzyme and its mutants
图3中,产物由GeTdT及其突变体转化3’端带叠氮甲基修饰的四种核苷酸单体底物(3’-O-Azidomethyl-dATP、3’-O-Azidomethyl-dTTP、3’-O-Azidomethyl-dCTP、3’-O-Azidomethyl-dGTP)获得;NC表示Oligo(dT)18;PC表示Oligo(dT)19;泳道1-19分别代表:1,WT(野生型);2,E459R;3,E459K;4,E459Q;5,E459V;6,E459R/R460Q;7,E459R/R460K;8,E459R/R460E;9, E459R/R460H;10,E459R/R460N;11,E459R/R460D;12,E459R/R460S;13,E459R/R460L;14,E459R/R460M;15,E459R/R460W;16,E459R/R460F;17,E459R/R460Y;18,E459R/R460C;19,E459R/R460G。图中所示GeTdT突变体对3’端带叠氮甲基修饰的四种核苷酸的活性均好于野生型,其中突变体E459R、E459R/R460Q、E459R/R460K、E459R/R460E、E459R/R460H、E459R/R460N及E459R/R460D的转化率相比野生型大大提高。In Figure 3, the products were obtained by transforming four nucleotide monomer substrates with azidomethyl modification at the 3' end (3'-O-Azidomethyl-dATP, 3'-O-Azidomethyl-dTTP, 3'-O-Azidomethyl-dCTP, 3'-O-Azidomethyl-dGTP) by GeTdT and its mutants; NC represents Oligo(dT) 18 ; PC represents Oligo(dT) 19 ; Lanes 1-19 represent: 1, WT (wild type); 2, E459R; 3, E459K; 4, E459Q; 5, E459V; 6, E459R/R460Q; 7, E459R/R460K; 8, E459R/R460E; 9, E459R/R460H; 10, E459R/R460N; 11, E459R/R460D; 12, E459R/R460S; 13, E459R/R460L; 14, E459R/ R460M; 15, E459R/R460W; 16, E459R/R460F; 17, E459R/R460Y; 18, E459R/R460C; 19, E459R/R460G. The activities of the GeTdT mutants shown in the figure for the four nucleotides with azidomethyl modification at the 3' end are better than those of the wild type, among which the conversion rates of the mutants E459R, E459R/R460Q, E459R/R460K, E459R/R460E, E459R/R460H, E459R/R460N and E459R/R460D are greatly improved compared with the wild type.
实施例4Example 4
末端脱氧核糖核苷转移酶GeTdT及其突变体的转化率测定。Conversion rate determination of terminal deoxyribonucleoside transferase GeTdT and its mutants.
使用聚合度为98的单链5’端修饰ROX荧光基团的5’-ROX-Oligo(dT)98(SEQ ID NO.41)作为寡核苷酸底物,使用3’端带叠氮甲基修饰的3’-O-Azidomethyl-dTTP为核酸单体底物,对纯化得到的GeTdT野生型及其突变体进行末端转移活性的测定并利用毛细管电泳法对反应产物的转化率进行定量测定。寡核苷酸底物5’-ROX-Oligo(dT)98在末端脱氧核糖核苷转移酶的作用下延伸一个碱基,得到产物5’-ROX-Oligo(dT)99-3’-O-Azidomethyl。GeTdT野生型及其突变体的转化率测定反应体系如表3,反应体系混匀后于37℃反应10min,反应结束后95℃加热10min终止反应。Using 5'-ROX-Oligo(dT) 98 (SEQ ID NO.41) with a single-stranded 5' end modified with ROX fluorescent group with a polymerization degree of 98 as an oligonucleotide substrate, and 3'-O-Azidomethyl-dTTP with an azidomethyl modification at the 3' end as a nucleic acid monomer substrate, the terminal transfer activity of the purified GeTdT wild type and its mutants was determined, and the conversion rate of the reaction product was quantitatively determined by capillary electrophoresis. The oligonucleotide substrate 5'-ROX-Oligo(dT) 98 was extended by one base under the action of terminal deoxyribonucleoside transferase to obtain the product 5'-ROX-Oligo(dT) 99 -3'-O-Azidomethyl. The reaction system for determining the conversion rate of the GeTdT wild type and its mutants is shown in Table 3. After the reaction system is mixed, the reaction is reacted at 37°C for 10 minutes. After the reaction is completed, the reaction is terminated by heating at 95°C for 10 minutes.
表3野生型GeTdT酶及其突变体的转化率测定反应体系
Table 3. Reaction system for determining the conversion rate of wild-type GeTdT enzyme and its mutants
采用毛细管电泳法进行末端脱氧核糖核苷转移酶反应产物转化率测定:反应产物用ddH2O稀释200倍后取1μL作为样品,与9μL混有内标的HiDi formamide混匀,采用Applied Biosystems 3730xl基因分析仪分析所得片段长度。反应产物转化率可表征反应活性,计算公式为:转化率=片段99峰面积/(片段98峰面积+片段99峰面积)。GeTdT野生型及突变体活性测试结果如表4和图4所示,98代表底物5’-ROX-Oligo(dT)98的峰,99代表产物5’-ROX-Oligo(dT)99-3’-O-Azidomethyl的峰。 The conversion rate of the terminal deoxyribonucleoside transferase reaction product was determined by capillary electrophoresis: the reaction product was diluted 200 times with ddH 2 O, 1 μL was taken as a sample, and mixed with 9 μL of HiDi formamide mixed with internal standard, and the fragment length was analyzed by Applied Biosystems 3730xl Genetic Analyzer. The conversion rate of the reaction product can characterize the reaction activity, and the calculation formula is: conversion rate = fragment 99 peak area/(fragment 98 peak area + fragment 99 peak area). The activity test results of GeTdT wild type and mutant are shown in Table 4 and Figure 4, 98 represents the peak of substrate 5'-ROX-Oligo(dT) 98 , and 99 represents the peak of product 5'-ROX-Oligo(dT) 99 -3'-O-Azidomethyl.
表4野生型GeTdT酶及其突变体的活性测试结果
Table 4 Activity test results of wild-type GeTdT enzyme and its mutants
由结果可知,表中所列GeTdT突变体对3’-O-Azidomethyl-dTTP的活性均好于野生型,转化率都从野生型的45%提高到50%以上,其中以突变体E459R、E459R/R460Q、E459R/R460K、E459R/R460E、E459R/R460H、E459R/R460N及E459R/R460D为较优突变体,转化率大于90%。The results show that the activities of the GeTdT mutants listed in the table towards 3’-O-Azidomethyl-dTTP are better than those of the wild type, and the conversion rates are increased from 45% of the wild type to more than 50%. Among them, the mutants E459R, E459R/R460Q, E459R/R460K, E459R/R460E, E459R/R460H, E459R/R460N and E459R/R460D are better mutants, with conversion rates greater than 90%.
实施例5Example 5
末端脱氧核糖核苷转移酶GeTdT及其突变体对不同3’-O-阻断修饰dTTPs的活性测试。Activity testing of terminal deoxyribonucleoside transferase GeTdT and its mutants towards different 3’-O-blocked modified dTTPs.
使用聚合度为18的单链Oligo(dT)18(SEQ ID NO.40)作为寡核苷酸底物,使用3’端带不同保护基团(PG)修饰的四种核苷酸(3’-O-Amide-dTTP、3’-O-Allyl-dTTP、3’-O-Methy-dTTP、3’-O-Oxime-dTTP)为核酸单体底物(结构如图5所示),对纯化得到的野生型GeTdT及其突变体进行末端转移活性的测定。寡核苷酸底物Oligo(dT)18在末端脱氧核糖核苷转移酶的作用下延伸一个碱基,得到产物Oligo(dT)19-3’-O-PG。野生型GeTdT酶及其突变体的末端转移活性测试反应体系如表5,反应体系混匀后于37℃反应10min,反应结束后95℃加热10min终止反应。采用尿素聚丙烯酰胺凝胶电泳(20%变性胶)对GeTdT野生型及其突变体的反应产物进行半定量分析,结果如图5所示,产物由GeTdT及其突变体转化四种3’端带不同保护基团(Amide、Allyl、Methy和Oxime)修饰的核苷酸单体底物获得。NC表示Oligo(dT)18;泳道1-3分别代表:1,WT;2,E459R;3,E459R/R460E。本申请中所用的5×Reaction buffer配方为:0.5M Na-Cacodylate,5mM CoCl2,pH 7.2。Using single-stranded Oligo(dT) 18 (SEQ ID NO.40) with a degree of polymerization of 18 as an oligonucleotide substrate, and using four nucleotides (3'-O-Amide-dTTP, 3'-O-Allyl-dTTP, 3'-O-Methy-dTTP, 3'-O-Oxime-dTTP) with different protective groups (PG) modified at the 3' end as nucleic acid monomer substrates (structures shown in Figure 5), the terminal transfer activity of the purified wild-type GeTdT and its mutants was determined. Oligo(dT) 18 , an oligonucleotide substrate, was extended by one base under the action of terminal deoxyribonucleoside transferase to obtain the product Oligo(dT) 19 -3'-O-PG. The reaction system for the terminal transfer activity test of the wild-type GeTdT enzyme and its mutants is shown in Table 5. After the reaction system is mixed, it is reacted at 37°C for 10 minutes. After the reaction is completed, it is heated at 95°C for 10 minutes to terminate the reaction. The reaction products of GeTdT wild type and its mutants were semi-quantitatively analyzed by urea polyacrylamide gel electrophoresis (20% denaturing gel). The results are shown in FIG5 . The products were obtained by GeTdT and its mutants transforming four nucleotide monomer substrates with different 3'-end protective groups (Amide, Allyl, Methy and Oxime). NC represents Oligo(dT) 18 ; Lanes 1-3 represent: 1, WT; 2, E459R; 3, E459R/R460E. The 5× reaction buffer used in this application is formulated as: 0.5M Na-Cacodylate, 5mM CoCl 2 , pH 7.2.
表5野生型GeTdT酶及其突变体的末端转移活性测试反应体系
Table 5. Terminal transfer activity test reaction system of wild-type GeTdT enzyme and its mutants
由结果可知,图5中所示GeTdT突变体对3’端带不同保护基团修饰的四种核苷酸的活性均优于野生型。The results show that the activity of the GeTdT mutant shown in Figure 5 towards the four nucleotides modified with different protecting groups at the 3' end is better than that of the wild type.
综上所述,本申请通过对天然TdT进行分子改造,获得优势TdT突变体,极大的提高了对修饰核酸单体的催化效率,实现高效的单碱基添加效率。In summary, the present application obtains advantageous TdT mutants by molecularly modifying natural TdT, thereby greatly improving the catalytic efficiency of modified nucleic acid monomers and achieving efficient single-base addition efficiency.
申请人声明,本申请通过上述实施例来说明本申请的详细方法,但本申请并不局限于上述详细方法,即不意味着本申请必须依赖上述详细方法才能实施。所属技术领域的技术人员应该明了,对本申请的任何改进,对本申请产品各原料的等效替换及辅助成分的添加、具体方式的选择等,均落在本申请的保护范围和公开范围之内。 The applicant declares that the present application uses the above-mentioned embodiments to illustrate the detailed methods of the present application, but the present application is not limited to the above-mentioned detailed methods, that is, it does not mean that the present application must rely on the above-mentioned detailed methods to be implemented. The technicians in the relevant technical field should understand that any improvement to the present application, the equivalent replacement of the raw materials of the product of the present application, the addition of auxiliary components, the selection of specific methods, etc., all fall within the scope of protection and disclosure of the present application.
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Non-Patent Citations (4)
| Title |
|---|
| "Wanfang Dissertations of China", 27 May 2021, article TANG MENGTONG: "The Study on the Regulation of TdT Enzymatic DNA Polymerization", XP093329885, DOI: 10.27356/d.cnki.gtjdu.2021.002500 * |
| DATABASE PROTEIN 26 February 2023 (2023-02-26), XP093329940, Database accession no. XP_053243387.1 * |
| GUO MIAO, WANG YINA, TANG YUYUE, CHEN ZIJING, HOU JINFENG, DAI JINGLI, WANG YUDONG, WANG LIANGYAN, XU HONG, TIAN BING, HUA YUEJIN,: "Mechanism of genome instability mediated by human DNA polymerase mu misincorporation", NATURE COMMUNICATIONS, NATURE PUBLISHING GROUP, UK, vol. 12, no. 1, UK, XP093329943, ISSN: 2041-1723, DOI: 10.1038/s41467-021-24096-7 * |
| TROSHCHYNSKY, A. ET AL.: "Functional Analyses of Polymorphic Variants of Human Terminal Deoxynucleotidyl Transferase", GENES AND IMMUNITY, vol. 16, 4 June 2015 (2015-06-04), XP036971149, DOI: 10.1038/gene.2015.19 * |
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