Orginal Article |
|
|
|
|
The Research Progress of Gene Cloning and Assembly |
SHENG Xiao-jing,QI Xiao-xue,XU Lei,QI Zhi-qing(),DIAO Yong() |
Insititute of Molecular Medicine, School of MEDIcine, Huaqiao University, Quanzhou 362021, China |
|
|
Abstract With the development of sequencing technology, the number of known DNA sequences increase exponentially. In order to explore their biological functions more quickly, some new techniques have been developed. Most of these techniques require to construct plasmids in vitro, but the purification process of recombinant enzymes is complicated, transport and preservation are very difficult, which leads to high cost. Recently, researchers have developed simple and low-cost ways to assemble DNA in vivo. The research status, principle, advantages and disadvantages of all kinds of methods are reviewed and the trend is prospected in combination with practical work, hoping to provide a reference for the further research.
|
Received: 11 May 2019
Published: 27 March 2020
|
|
Corresponding Authors:
Zhi-qing QI,Yong DIAO
E-mail: zqqi@hotmail.com;diaoyong@hqu.edu.cn
|
|
|
[1] |
Liu C J, Jiang H, Wu L , et al. OEPR cloning: an efficient and seamless cloning strategy for large- and multi-fragments. Sci Rep, 2017,7:44648.
|
|
|
[2] |
Trehan A, Kielbus M, Czapinski J , et al. REPLACR-mutagenesis, a one-step method for site-directed mutagenesis by recombineering. Sci Rep, 2016,6:19121.
|
|
|
[3] |
Garcia-Nafria J, Watson J F, Greger I H . IVA cloning: A single-tube universal cloning system exploiting bacterial in vivo assembly. Sci Rep, 2016,6:27459.
|
|
|
[4] |
Beyer H M, Gonschorek P, Samodelov S L , et al. AQUA cloning: a versatile and simple enzyme-free cloning approach. PLoS One, 2015,10(9):e137652.
|
|
|
[5] |
Koskela E V, Frey A D . Homologous recombinatorial cloning without the creation of single-stranded ends: exonuclease and ligation-independent cloning (ELIC). Mol Biotechnol, 2015,57(3):233-240.
|
|
|
[6] |
Cao P, Wang L, Zhou G , et al. Rapid assembly of multiple DNA fragments through direct transformation of PCR products into E. coli and Lactobacillus. Plasmid, 2014,76:40-46.
|
|
|
[7] |
Oliner J D, Kinzler K W, Vogelstein B . In vivo cloning of PCR products in E. coli. Nucleic Acids Res, 1993,21(22):5192-5197.
|
|
|
[8] |
Bubeck P, Winkler M, Bautsch W . Rapid cloning by homologous recombination in vivo. Nucleic Acids Res, 1993,21(15):3601-3602.
|
|
|
[9] |
Kostylev M, Otwell A E, Richardson R E , et al. Cloning should be simple: Escherichia coli DH5alpha-mediated assembly of multiple DNA fragments with short end homologies. PLoS One, 2015,10(9):e137466.
|
|
|
[10] |
Jacobus A P, Gross J . Optimal cloning of PCR fragments by homologous recombination in Escherichia coli. PLoS One, 2015,10(3):e119221.
|
|
|
[11] |
Hartley J L, Temple G F, Brasch M A . DNA cloning using in vitro site-specific recombination. Genome Res, 2000,10(11):1788-1795.
|
|
|
[12] |
Zhang Y, Werling U, Edelmann W . SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res, 2012,40(8):e55.
|
|
|
[13] |
Zhang Y, Buchholz F, Muyrers J P , et al. A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet, 1998,20(2):123-128.
|
|
|
[14] |
Wang H, Li Z, Jia R , et al. ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes. Nucleic Acids Research, 2018,46(5):e28.
|
|
|
[15] |
Jiang W, Zhao X, Gabrieli T , et al. Cas9-assisted targeting of chromosome segments CATCH enables one-step targeted cloning of large gene clusters. Nat Commun, 2015,6:8101.
|
|
|
[16] |
Bland M J, Ducos-Galand M, Val M E , et al. An att site-based recombination reporter system for genome engineering and synthetic DNA assembly. BMC Biotechnol, 2017,17(1):62.
|
|
|
[17] |
Reece-Hoyes J S, Walhout A . Gateway recombinational cloning. Cold Spring Harb Protoc, 2018,1:94912.
|
|
|
[18] |
Weller S K, Sawitzke J A . Recombination promoted by DNA viruses: phage lambda to herpes simplex virus. Annu Rev Microbiol, 2014,68(1):237-258.
|
|
|
[19] |
Ivanov E L, Sugawara N, Fishman-Lobell J , et al. Genetic requirements for the single-strand annealing pathway of double-strand break repair in Saccharomyces cerevisiae. Genetics, 1996,142(3):693-704.
|
|
|
[20] |
Zhang Y, Werling U, Edelmann W . Seamless ligation cloning extract (SLiCE) cloning method. Methods Mol Biol, 2014,1116:235-244.
|
|
|
[21] |
Motohashi K . A simple and efficient seamless DNA cloning method using SLiCE from Escherichia coli laboratory strains and its application to SLiP site-directed mutagenesis. BMC Biotechnol, 2015,15:47.
|
|
|
[22] |
Okegawa Y, Motohashi K . A simple and ultra-low cost homemade seamless ligation cloning extract (SLiCE) as an alternative to a commercially available seamless DNA cloning kit. Biochem Biophys Rep, 2015,4:148-151.
|
|
|
[23] |
Motohashi K . Seamless ligation cloning extract (SLiCE) method using cell lysates from laboratory Escherichia coli strains and its application to SLiP site-directed mutagenesis. Methods Mol Biol, 2017,1498:349-357.
|
|
|
[24] |
Messerschmidt K, Hochrein L, Dehm D , et al. Characterizing seamless ligation cloning extract for synthetic biological applications. Anal Biochem, 2016,509:24-32.
|
|
|
[25] |
Garneau J E, Dupuis M E, Villion M , et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature, 2010,468(7320):67-71.
|
|
|
[26] |
Gabrieli T, Sharim H, Fridman D , et al. Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH). Nucleic Acids Res, 2018,46(14):e87.
|
|
|
[27] |
Sternberg S H, Redding S, Jinek M , et al. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 2014,507(7490):62-67.
|
|
|
[28] |
Lovett S T, Hurley R L, Sutera V J , et al. Crossing over between regions of limited homology in Escherichia coli. RecA-dependent and RecA-independent pathways. Genetics, 2002,160(3):851-859.
|
|
|
[29] |
Muyrers J P, Zhang Y, Buchholz F , et al. RecE/RecT and Redalpha/Redbeta initiate double-stranded break repair by specifically interacting with their respective partners. Genes Dev, 2000,14(15):1971-1982.
|
|
|
[30] |
Lu D, Danilowicz C, Tashjian T F , et al. Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology. J Biol Chem, 2019,294(21):8606-8616.
|
|
|
[31] |
Fu J, Bian X, Hu S , et al. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nature Biotechnology, 2012,30(5):440-446.
|
|
|
[32] |
Wang H, Li Z, Jia R , et al. RecET direct cloning and Redαβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression. Nature Protocols, 2016,11(7):1175-1190.
|
|
|
[33] |
Ma Z, Wang P G . RecET Direct cloning of polysaccharide gene cluster from gram-negative bacteria. Methods Mol Biol, 2019,1954:15-23.
|
|
|
[34] |
Benoit R M, Ostermeier C, Geiser M , et al. Seamless insert-plasmid assembly at high efficiency and low cost. PLoS One, 2016,11(4):e153158.
|
|
|
[35] |
Motohashi K . Evaluation of the efficiency and utility of recombinant enzyme-free seamless DNA cloning methods. Biochem Biophys Rep, 2017,9:310-315.
|
|
|
[36] |
Huang F, Spangler J R, Huang A Y . In vivo cloning of up to 16 kb plasmids in E. coli is as simple as PCR. PLoS One, 2017,12(8):e183974.
|
|
|
[37] |
华侨大学. 一种利用DNA非特异性结合蛋白HU蛋白构建克隆载体的方法:中国(福建), CN201510602398.0. 2019-02-22.[2019-12-15]. http://www.cnipa.gov.cn/.
|
|
|
[37] |
Qi Z Q, Qi X X, Hou D , et al. A method of constructing cloning vector using DNA nonspecific binding protein HU. Chinese: CN105200074B. 2019-02-22.[2019-12-15]. http://www.cnipa.gov.cn/.
|
|
|
[38] |
Ohtsuka M, Kimura M, Tanaka M , et al. Recombinant DNA technologies for construction of precisely designed transgene constructs. Curr Pharm Biotechnol, 2009,10(2):244-251.
|
|
|
[39] |
Okegawa Y, Motohashi K . Evaluation of seamless ligation cloning extract preparation methods from an Escherichia coli laboratory strain. Anal Biochem, 2015,486:51-53.
|
|
|
[40] |
Wang B, Hu Q, Zhang Y , et al. A RecET-assisted CRISPR-Cas9 genome editing in Corynebacterium glutamicum. Microb Cell Fact, 2018,17(1):63.
|
|
|
[41] |
Taylor G M, Mordaka P M, Heap J T . Start-stop assembly: a functionally scarless DNA assembly system optimized for metabolic engineering. Nucleic Acids Res, 2018,47(3):e17.
|
|
|
[42] |
Lin D, O’Callaghan C A . MetClo: methylase-assisted hierarchical DNA assembly using a single type IIS restriction enzyme. Nucleic Acids Res, 2018,46(19):e113.
|
|
|
[43] |
van Dolleweerd C J, Kessans S A, an de Bittner K C , et al. MIDAS: A modular DNA assembly system for synthetic biology. ACS Synth Biol, 2018,7(4):1018-1029.
|
|
|
[44] |
Ding S, Gu Z, Yan R , et al. A novel mode of DNA assembly at electrode and its application to protein quantification. Anal Chim Acta, 2018,1029:24-29.
|
|
|
[45] |
Casini A, Storch M, Baldwin G S , et al. Bricks and blueprints: methods and standards for DNA assembly. Nat Rev Mol Cell Biol, 2015,16(9):568-576.
|
|
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|