CH391L/S13/DnaAssembly

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Introduction

Oligonucleotide Synthesis

from wikipedia

Gene Synthesis

IDT Gene Blocks

Cloning Techniques

Restriction Enzyme

-BioBricks
-BglBricks


in vivo techniques

  • e coli
  • s. cerevisiae

Recombination

-homology/ligase
-cold fusion
-in fusion
-lambda red
-golden gate
-slic
-mage
-Gibson
-CPEC
-MoClo [1]

References

  1. Weber E, Engler C, Gruetzner R, Werner S, and Marillonnet S. A modular cloning system for standardized assembly of multigene constructs. PLoS One. 2011 Feb 18;6(2):e16765. DOI:10.1371/journal.pone.0016765 | PubMed ID:21364738 | HubMed [Weber2011]
    MoClo
  2. Werner S, Engler C, Weber E, Gruetzner R, and Marillonnet S. Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system. Bioeng Bugs. 2012 Jan 1;3(1):38-43. DOI:10.4161/bbug.3.1.18223 | PubMed ID:22126803 | HubMed [Werner2012]
    MoClo
  3. Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juárez P, Fernández-del-Carmen A, Granell A, and Orzaez D. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS One. 2011;6(7):e21622. DOI:10.1371/journal.pone.0021622 | PubMed ID:21750718 | HubMed [SarrionPerdigones2011]
    GoldenBraid
  4. Engler C, Kandzia R, and Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLoS One. 2008;3(11):e3647. DOI:10.1371/journal.pone.0003647 | PubMed ID:18985154 | HubMed [Engler2008]
    GoldenGate
  5. Quan J and Tian J. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One. 2009 Jul 30;4(7):e6441. DOI:10.1371/journal.pone.0006441 | PubMed ID:19649325 | HubMed [Quan2009]
    CPEC
  6. Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, and Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009 May;6(5):343-5. DOI:10.1038/nmeth.1318 | PubMed ID:19363495 | HubMed [Gibson2009]
    T5 exonuclease recombination
  7. Li MZ and Elledge SJ. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods. 2007 Mar;4(3):251-6. DOI:10.1038/nmeth1010 | PubMed ID:17293868 | HubMed [Li2007]
    SLIC
  8. Li MZ and Elledge SJ. SLIC: a method for sequence- and ligation-independent cloning. Methods Mol Biol. 2012;852:51-9. DOI:10.1007/978-1-61779-564-0_5 | PubMed ID:22328425 | HubMed [Li2012]
    SLIC
  9. Sleight SC, Bartley BA, Lieviant JA, and Sauro HM. In-Fusion BioBrick assembly and re-engineering. Nucleic Acids Res. 2010 May;38(8):2624-36. DOI:10.1093/nar/gkq179 | PubMed ID:20385581 | HubMed [Sleight2010]
    In-Fusion biobrick
  10. Zhu B, Cai G, Hall EO, and Freeman GJ. In-fusion assembly: seamless engineering of multidomain fusion proteins, modular vectors, and mutations. Biotechniques. 2007 Sep;43(3):354-9. PubMed ID:17907578 | HubMed [Zhu2007]
    in-fusion
  11. Benoit RM, Wilhelm RN, Scherer-Becker D, and Ostermeier C. An improved method for fast, robust, and seamless integration of DNA fragments into multiple plasmids. Protein Expr Purif. 2006 Jan;45(1):66-71. DOI:10.1016/j.pep.2005.09.022 | PubMed ID:16289702 | HubMed [Benoit2006]
    in-fusion
  12. Geu-Flores F, Nour-Eldin HH, Nielsen MT, and Halkier BA. USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res. 2007;35(7):e55. DOI:10.1093/nar/gkm106 | PubMed ID:17389646 | HubMed [GeuFlores2007]
    USER
  13. Gibson DG. Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res. 2009 Nov;37(20):6984-90. DOI:10.1093/nar/gkp687 | PubMed ID:19745056 | HubMed [Gibson2009-2]
    oligonucleotide assembly
  14. Horton RM, Cai ZL, Ho SN, and Pease LR. Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques. 1990 May;8(5):528-35. PubMed ID:2357375 | HubMed [Horton2009]
    SOEing
  15. Czar MJ, Anderson JC, Bader JS, and Peccoud J. Gene synthesis demystified. Trends Biotechnol. 2009 Feb;27(2):63-72. DOI:10.1016/j.tibtech.2008.10.007 | PubMed ID:19111926 | HubMed [Czar2009]
    review
All Medline abstracts: PubMed | HubMed