无限制克隆技术研究进展及其应用

无限制克隆(restriction-free cloning,RFC)是近年来建立起来的一种简单通用的DNA克隆技术,它可以精确地将目的片段插入到质粒内任意位置,是一种不受酶切位点、连接酶效率、目的基因长度或载体序列等条件限制的新型DNA重组技术.与其他多种克隆方法相比,RFC技术拥有不可替代的优势.本文在总结国内外RFC技术研究的基础上,系统阐述了RFC技术的原理、特点和在克隆方面的研究进展,并探讨其在分子生物学和合成生物学等领域的应用价值.     

DNA克隆和组装技术研究进展

DNA克隆和组装技术是重要的分子生物学工具。近年来,随着合成生物学的飞速发展,对大片段DNA元件的快速有效组装就显得尤为关键。同时,各种DNA克隆和组装技术也竞相发展起来。通过对基于非典型酶切连接、PCR、同源重组、单链退火拼接等原理发展起来的各种DNA克隆和组装技术进行综述,为合成生物学的进一步发展提供有效的操作工具。     

镜像克隆系统:DNA重组技术的新进展

镜像克隆系统是近几年新发展起来的一种DNA重组技术,它突破了传统重组限制酶切及连接的繁琐和费时,利用重组酶使外源基因快速、方便地进行亚克隆和表达。本阐述了镜像克隆系统的结构、作用原理及特点。     

大肠杆菌重组工程

源于噬菌体的大肠杆菌同源重组系统不需要限制性内切酶和DNA连接酶就可以进行DNA克隆和亚克隆,还能快速地改造质粒、细菌人工染色体及细菌基因组染色体,是基因工程技术的一大突破,被称为重组基因工程或重组工程。该技术操作简单,效率较高,可望为功能基因组学研究提供一个有力的工具。     

体内直接克隆大片段DNA的研究进展

基因组序列的功能分析以及代谢途径的构建改造等都需要克隆目的DNA。获得大片段DNA序列的方法有构建和筛选基因文库,PCR扩增,体外大片段DNA合成和组装等,但体内重组直接克隆的方法在操作、克隆长片段和应用等方面更具优势。介绍了Red/ET重组介导的大片段DNA体内直接克隆的主要方法及其应用。     

通路克隆系统:DNA重组技术的新进展

近几年新发展了一种载体间DNA片段相互灵活转化的多功能系统 ,即通路克隆系统(gatewaycloningsystem)。它是一种位点特异的DNA重组技术 ,包括PCR产物的定向克隆 ,DNA片断高效、广泛的亚克隆 ,氨基或羧基末端的融合蛋白表达等。重点阐述了该系统的作用原理、特点及其应用。     

现代生物学基因研究进展——从遗传因子到超级基因（2）

3基因的反向生物学阶段 近20年来,由于重组DNA技术的完善和应用,人们已经改变了从表型到基因型的传统研究基因的途径,而是直接从克隆目的基因出发,研究基因的功能及其与表型之间的关系,使基因的研究进入了反向生物学阶段。     

基因克隆及组装技术的研究进展 *

随着测序技术的发展,已知的DNA序列数量呈指数性增加,为了能更快的探索其未知的生物功能,一些简化组装流程的DNA克隆及组装新技术争相发展起来。其中大部分需要在菌体外构建重组体,但重组酶纯化过程复杂,运送和保存方法要求严格,致使成本较高。最近研究者开发了一些在菌体内进行DNA组装的简易、低成本的新方法。主要对各类基因克隆及组装方法的研究现状、原理和优缺点等进行综述,并结合实际的工作内容展望了未来的发展趋势,希望能为进一步研究开发新技术提供参考。     

噬菌体重组酶介导的DNA同源重组工程

来源于噬菌体的遗传操作工具在基因工程中具有非常重要的地位,例如位点特异性重组酶、柯斯质粒DNA文库及同源重组酶等。其中,来源于lambda噬菌体的同源重组酶Redα/Redβ和来源于Rac原噬菌体的同源重组酶RecE/RecT能够高效地介导35–50 bp短同源臂之间的重组。基于噬菌体同源重组酶Redα/Redβ和RecE/RecT开发的DNA同源重组工程（Recombineering）能够对靶标DNA分子进行快速、精准、高效的修饰,不受限制性内切酶识别位点和DNA分子大小限制,已发展成为一种新型的基因工程技术。本文主要综述了噬菌体同源重组酶及其作用机制、在大肠杆菌及其他细菌中的应用和开发,以及在微生物次级代谢产物的挖掘、动植物转基因、病毒基因组克隆和修饰等方面的应用。原位激活沉默基因簇需要宿主特异性的DNA同源重组工程进行启动子和调控元件的修饰;异源表达次级代谢产物的首要步骤一般是通过RecET直接克隆大的DNA片段;动植物转基因复杂载体的构建效率在有了Red同源重组系统以后有了革命性的发展;RecET直接克隆和Red同源重组介导的感染性克隆构建和修饰方法,不仅有利于病毒基因组功能研究,同时也为载体疫苗开发提供了最优方案。     

一种可转移的重组工程系统 pYM-Red 的建立

重组工程是近几年发展的新型遗传工程技术. 以 PCR 扩增的线性低拷贝质粒 pACYC184 为载体,用 Gap-repair 方法从大肠杆菌 DY330 染色体上直接体内亚克隆了包括 Red 重组酶基因在内的长约 6.7 kb 的基因序列,构建了 pYM-Red 重组质粒. 在宿主菌 W3110 体内进行了染色体上 galk 基因的敲除,验证了 Red 重组酶的生物功能,并确定了影响 pYM-Red 重组效率的诱导时间和线性 DNA 片段用量. 在 42℃诱导 10 min 和线性 DNA 打靶分子浓度为 300 ng 时, pYM-Red 的重组效率可达到大约每 4 000 个电转存活细胞中有 1 个重组阳性克隆,分别比 pKD46 和 pBR322-Red 系统高 5~6 倍.     

Retroviral vectors for homologous recombination provide efficient cloning and expression in mammalian cells

Homologous recombination technologies enable high-throughput cloning and the seamless insertion of any DNA fragment into expression vectors. Additionally, retroviral vectors offer a fast and efficient method for transducing and expressing genes in mammalian cells, including lymphocytes. However, homologous recombination cannot be used to insert DNA fragments into retroviral vectors; retroviral vectors contain two homologous regions, the 5′- and 3′-long terminal repeats, between which homologous recombination occurs preferentially. In this study, we have modified a retroviral vector to enable the cloning of DNA fragments through homologous recombination. To this end, we inserted a bacterial selection marker in a region adjacent to the gene insertion site. We used the modified retroviral vector and homologous recombination to clone T-cell receptors (TCRs) from single Epstein Barr virus-specific human T cells in a high-throughput and comprehensive manner and to efficiently evaluate their function by transducing the TCRs into a murine T-cell line through retroviral infection. In conclusion, the modified retroviral vectors, in combination with the homologous recombination method, are powerful tools for the high-throughput cloning of cDNAs and their efficient functional analysis.     

Protoplasts as tools for plant genome modifications

We present here the application of protoplast technology in the selection and recovery of rare, spontaneous plant genome alterations. Using protoplasts as a cell cloning system allowed the detection and molecular characterization of intrachromosomal recombination events between genomic repeats. The mechanism, frequencies and the induction of intrachromosomal recombination are discussed as well as its application for genome mutagenesis.     

A simple and ultra-low cost homemade seamless ligation cloning extract (SLiCE) as an alternative to a commercially available seamless DNA cloning kit

The seamless ligation cloning extract (SLiCE) method is a novel seamless DNA cloning tool that utilizes homologous recombination activities in Escherichia coli cell lysates to assemble DNA fragments into a vector. Several laboratory E. coli strains can be used as a source for the SLiCE extract; therefore, the SLiCE-method is highly cost-effective.The SLiCE has sufficient cloning ability to support conventional DNA cloning, and can simultaneously incorporate two unpurified DNA fragments into vector. Recently, many seamless DNA cloning kits have become commercially available; these are generally very convenient, but expensive. In this study, we evaluated the cloning efficiencies between a simple and highly cost-effective SLiCE-method and a commercial kit under various molar ratios of insert DNA fragments to vector DNA. This assessment identified that the SLiCE from a laboratory E. coli strain yielded 30?85% of the colony formation rate of a commercially available seamless DNA cloning kit. The cloning efficiencies of both methods were highly effective, exhibiting over 80% success rate under all conditions examined. These results suggest that SLiCE from a laboratory E. coli strain can efficiently function as an effective alternative to commercially available seamless DNA cloning kits.     

Evaluation of the efficiency and utility of recombinant enzyme-free seamless DNA cloning methods

Simple and low-cost recombinant enzyme-free seamless DNA cloning methods have recently become available. In vivo Escherichia coli cloning (iVEC) can directly transform a mixture of insert and vector DNA fragments into E. coli, which are ligated by endogenous homologous recombination activity in the cells. Seamless ligation cloning extract (SLiCE) cloning uses the endogenous recombination activity of E. coli cellular extracts in vitro to ligate insert and vector DNA fragments. An evaluation of the efficiency and utility of these methods is important in deciding the adoption of a seamless cloning method as a useful tool. In this study, both seamless cloning methods incorporated inserting DNA fragments into linearized DNA vectors through short (15–39 bp) end homology regions. However, colony formation was 30–60-fold higher with SLiCE cloning in end homology regions between 15 and 29 bp than with the iVEC method using DH5α competent cells. E. coli AQ3625 strains, which harbor a sbcA gene mutation that activates the RecE homologous recombination pathway, can be used to efficiently ligate insert and vector DNA fragments with short-end homology regions in vivo. Using AQ3625 competent cells in the iVEC method improved the rate of colony formation, but the efficiency and accuracy of SLiCE cloning were still higher. In addition, the efficiency of seamless cloning methods depends on the intrinsic competency of E. coli cells. The competency of chemically competent AQ3625 cells was lower than that of competent DH5α cells, in all cases of chemically competent cell preparations using the three different methods. Moreover, SLiCE cloning permits the use of both homemade and commercially available competent cells because it can use general E. coli recA^? strains such as DH5α as host cells for transformation. Therefore, between the two methods, SLiCE cloning provides both higher efficiency and better utility than the iVEC method for seamless DNA plasmid engineering.