Difference between revisions of "CH391L/S13/DnaAssembly"

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(Recombination/Homology)
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-lambda red <br>
 
-lambda red <br>
 +
 
-golden gate <br>
 
-golden gate <br>
 +
-MoClo  <cite>Weber2011</cite>
 +
-GoldenBraid <br>
 +
 
-lic <br>
 
-lic <br>
 
-gateway <br>
 
-gateway <br>
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===Bacterial Mating===
 
===Bacterial Mating===
  
 
-MoClo  <cite>Weber2011</cite>
 
 
-mage <br>
 
-mage <br>
  

Revision as of 21:41, 21 January 2013


Introduction

A large number of parts have been made by the synthetic biology community. Many can be found as part of the Registry of Standard Biological Parts. These modular genetic components are designed to be easy to assemble to facilitate the building of more complex biological devices. To learn more about the Registry and BioBricks™, see last year's wiki page.

Synthetic biology relies on the ability to make testable biological units. This means that the ability to gather, manipulate, or even create genetic material is vital for "doing" synthetic biology. The techniques employed by synthetic biologists include oligonucleotide synthesis, restriction enzyme digestion, ligase, pcr, and recombination (homology).

Trying to get from genes to genomes.

DNA Synthesis

Oligonucleotide Synthesis

from wikipedia

Gene Synthesis

IDT Gene Blocks
DNA2.0
invitrogen (life technologies, geneart)
genscript
celtek
biobasic
sigma?
GENEWIZ
biomatik
OriGene (blue heron)
Epoch Life Science

References
Cost
Time

Molecular Cloning

Restriction Enzyme

BioBricks
BglBricks
list of BioBrick Foundation Standards

Polymerase Chain Reaction

TOPO TA cloning (invitrogen)
SOE (splice by overlap extension) pcr

Ligase

Recombination/Homology

j5 from Nathan Hillson

-In-Fusion (Clontech) poxvirus DNA polymerase with 3′–5′ exonuclease activity
-In-Fusion BioBrick Assembly
-cold fusion (SBI)

-lambda red

-golden gate
-MoClo [1] -GoldenBraid

-lic
-gateway

-SLIC sequence and ligation independent cloning T4 DNA polymerase (exonuclease)
-Gibson T5 exonuclease, Phusion polymerase, Taq ligase
-CPEC circular polymerase extension cloning

-SLiCE (Seamless Ligation Cloning Extract) in vitro homologous recombination

-Fast Seamless Cloning (Dogene) -CloneEZ kit (Genescript) -GENEART

Transformation

  • e coli
  • s. cerevisiae

Bacterial Mating

-mage

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. Hughes RA, Miklos AE, and Ellington AD. Gene synthesis: methods and applications. Methods Enzymol. 2011;498:277-309. DOI:10.1016/B978-0-12-385120-8.00012-7 | PubMed ID:21601682 | HubMed [Hughes2011]
    Gene Synthesis Review
  3. 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
  4. 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
  5. 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
  6. 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
  7. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, and Smith HO. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 2008 Feb 29;319(5867):1215-20. DOI:10.1126/science.1151721 | PubMed ID:18218864 | HubMed [Gibson2008]
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. Stemmer WP, Crameri A, Ha KD, Brennan TM, and Heyneker HL. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene. 1995 Oct 16;164(1):49-53. PubMed ID:7590320 | HubMed [Stemmer1995]
    PCA
  19. Aslanidis C and de Jong PJ. Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 1990 Oct 25;18(20):6069-74. PubMed ID:2235490 | HubMed [Aslanidis1990]
    LIC
  20. Aslanidis C, de Jong PJ, and Schmitz G. Minimal length requirement of the single-stranded tails for ligation-independent cloning (LIC) of PCR products. PCR Methods Appl. 1994 Dec;4(3):172-7. PubMed ID:7580902 | HubMed [Aslanidis1994]
    LIC
  21. Li C and Evans RM. Ligation independent cloning irrespective of restriction site compatibility. Nucleic Acids Res. 1997 Oct 15;25(20):4165-6. PubMed ID:9321675 | HubMed [Li1997]
    LIC
  22. Angrand PO, Daigle N, van der Hoeven F, Schöler HR, and Stewart AF. Simplified generation of targeting constructs using ET recombination. Nucleic Acids Res. 1999 Sep 1;27(17):e16. PubMed ID:10446259 | HubMed [Angrand1999]
    lambda Red recombinase
  23. Hartley JL, Temple GF, and Brasch MA. DNA cloning using in vitro site-specific recombination. Genome Res. 2000 Nov;10(11):1788-95. PubMed ID:11076863 | HubMed [Hartley2000]
    Gateway lambda Int
  24. Khalil AM, Julius JA, and Bachant J. One step construction of PCR mutagenized libraries for genetic analysis by recombination cloning. Nucleic Acids Res. 2007;35(16):e104. DOI:10.1093/nar/gkm583 | PubMed ID:17702758 | HubMed [Khalil2007]
    Gateway lambda Cre
  25. Larionov V, Kouprina N, Graves J, Chen XN, Korenberg JR, and Resnick MA. Specific cloning of human DNA as yeast artificial chromosomes by transformation-associated recombination. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):491-6. PubMed ID:8552668 | HubMed [Larionov1996]
    Transformation-associated recombination (TAR) cloning
  26. j5 DNA Assembly Design Automation Software doi: 10.1021/sb2000116 [Hillson2012]
  27. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, and Venter JC. Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 2010 Jul 2;329(5987):52-6. DOI:10.1126/science.1190719 | PubMed ID:20488990 | HubMed [Gibson2010]
    genome replacement
  28. Li MZ and Elledge SJ. MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules. Nat Genet. 2005 Mar;37(3):311-9. DOI:10.1038/ng1505 | PubMed ID:15731760 | HubMed [Li2005]
    MAGIC, bacterial mating approach
All Medline abstracts: PubMed | HubMed
  1. Zhang2012 pmid=22241772

//SLiCe