期刊论文详细信息
Journal of Biological Engineering
Amplified insert assembly: an optimized approach to standard assembly of BioBrickTM genetic circuits
Tom L Richard1  Michael A Speer1 
[1] Department of Agricultural and Biological Engineering, The Pennsylvania State University, 249 Agricultural Engineering Bldg., University Park, PA 16802, USA
关键词: DpnI;    assembly;    vector;    insert;    amplification;    PCR;    Synthetic biology;    BioBrick;   
Others  :  813551
DOI  :  10.1186/1754-1611-5-17
 received in 2011-05-03, accepted in 2011-12-16,  发布年份 2011
PDF
【 摘 要 】

A modified BioBrick™ assembly method was developed with higher fidelity than current protocols. The method utilizes a PCR reaction with a standard primer set to amplify the inserted part. Background colonies are reduced by a combination of dephosphorylation and digestion with DpnI restriction endonuclease to reduce vector and insert background respectively. The molar ratio of the insert to vector in the ligation was also optimized, with the accuracy of the transformed construct approaching 100%.

【 授权许可】

   
2011 Speer and Richard; licensee BioMed Central Ltd.

【 预 览 】
附件列表
Files Size Format View
20140710005154208.pdf 1197KB PDF download
Figure 5. 121KB Image download
Figure 4. 66KB Image download
Figure 3. 69KB Image download
Figure 2. 58KB Image download
Figure 1. 34KB Image download
【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

【 参考文献 】
  • [1]Lobban PE, Kaiser AD: Enzymatic End-to-End Joining of DNA Molecules. Journal of Molecular Biology 1973, 78:453.
  • [2]Mertz JE, Davis RW: Cleavage of DNA by Ri Restriction Endonuclease Generates Cohesive Ends. Proceedings of the National Academy of Sciences of the United States of America 1972, 69:3370.
  • [3]Jackson DA, Berg P, Symons RH: Biochemical Method for Inserting New Genetic Information into DNA of Simian Virus 40-Circular Sv40 DNA Molecules Containing Lambda Phage Genes and Galactose Operon of Escherichia-Coli. Proceedings of the National Academy of Sciences of the United States of America 1972, 69:2904.
  • [4]Cohen SN, Chang ACY, Boyer HW, Helling RB: Construction of Biologically Functional Bacterial Plasmids in-Vitro. Proceedings of the National Academy of Sciences of the United States of America 1973, 70:3240-3244.
  • [5]Gayle RB, Auger EA, Gough GR, Gilham PT, Bennett GN: Formation of Mboii Vectors and Cassettes Using Asymmetric Mboii Linkers. Gene 1987, 54:221-228.
  • [6]Rebatchouk D, Daraselia N, Narita JO: NOMAD: A versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design. Proceedings of the National Academy of Sciences of the United States of America 1996, 93:10891-10896.
  • [7]Stahl S, Sjolander A, Hansson M, Nygren PA, Uhlen M: A General Strategy for Polymerization, Assembly and Expression of Epitope-Carrying Peptides Applied to the Plasmodium-Falciparum Antigen Pf155/Resa. Gene 1990, 89:187-193.
  • [8]Knight TF: Idempotent Vector Design for Standard Assembly of BioBricks. MIT Synthetic Biology Working Group Technical Reports 2003
  • [9]Endy D: Foundations for engineering biology. Nature 2005, 438:449-453.
  • [10]Che A: BioBricks++ Assembly Scheme. IT Synthetic Biology Working Group Technical Reports 2004 2004.
  • [11]Phillips IE, Silver PA: A New Biobrick Assembly Strategy Designed for Facile Protein Engineering. Dspace 2006.
  • [12]Anderson JC, Dueber J, Leguia M, Wu G, Goler J, Arkin A, Keasling J: BglBricks: A flexible standard for biological part assembly. 4:1:1.
  • [13]Canton B, Labno A, Endy D: Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology 2008, 26:787-793.
  • [14]Shetty R, Lizarazo M, Rettberg R, Knight TF: Assembly of BioBrick standard biological parts using three antibiotic assembly. Methods in Enzymology 2011, 498:311-326.
  • [15]Shetty RP, Endy D, Knight TF: Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering 2008, 2:5. BioMed Central Full Text
  • [16]Van Reeth T, Dreze PL, Szpirer J, Szpirer C, Gabant P: Positive selection vectors to generate fused genes for the expression of His-tagged proteins. Biotechniques 1998, 25:898-904.
  • [17]Bernard P: Positive selection of recombinant DNA by CcdB. Biotechniques 1996, 21:320-323.
  • [18]Quandt J, Hynes MF: Versatile Suicide Vectors Which Allow Direct Selection for Gene Replacement in Gram-Negative Bacteria. Gene 1993, 127:15-21.
  • [19]Sambrook J, Russell DW, Cold Spring Harbor L: Molecular cloning: a laboratory manual/Joseph Sambrook, David W. Russell. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory; 2001.
  • [20]Sleight SC, Bartley BA, Lieviant JA, Sauro HM: In-Fusion BioBrick assembly and re-engineering. Nucleic Acids Research 2010, 38:2624-2636.
  • [21]Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA, Smith HO: Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods 2009, 6:343-U341.
  • [22]Horton RM, Hunt HD, Ho SN, Pullen JK, Pease LR: Engineering Hybrid Genes without the Use of Restriction Enzymes-Gene-Splicing by Overlap Extension. Gene 1989, 77:61-68.
  • [23]Geier GE, Modrich P: Recognition Sequence of the Dam Methylase of Escherichia-Coli-K12 and Mode of Cleavage of Dpn-I Endonuclease. Journal of Biological Chemistry 1979, 254:1408-1413.
  • [24]Bergerat A, Kriebardis A, Guschlbauer W: Preferential Site-Specific Hemimethylation of Gatc Sites in Pbr322 DNA by Dam Methyltransferase from Escherichia-Coli. Journal of Biological Chemistry 1989, 264:4064-4070.
  • [25]Zabin I: Beta-Galactosidase Alpha-Complementation-a Model of Protein-Protein Interaction. Molecular and Cellular Biochemistry 1982, 49:87-96.
  • [26]Campbell RE, Tour O, Palmer AE, Steinbach PA, Baird GS, Zacharias DA, Tsien RY: A monomeric red fluorescent protein. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:7877-7882.
  • [27]Topcu Z: An optimized recipe for cloning of the polymerase chain reaction-amplified DNA inserts into plasmid vectors. Acta Biochimica Polonica 2000, 47:841-846.
  • [28]Hanahan D: Studies on Transformation of Escherichia-Coli with Plasmids. Journal of Molecular Biology 1983, 166:557-580.
  文献评价指标  
  下载次数:48次 浏览次数:10次