CH391L/S13/DnaAssembly

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Contents

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

Polymerase Chain Reaction

Ligase

Recombination/Homology

Transformation

TOPO TA cloning (invitrogen)

-BioBricks
-BglBricks


in vivo techniques

  • e coli
  • s. cerevisiae

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

References

  1. Weber E, Engler C, Gruetzner R, Werner S, and Marillonnet S. . pmid:21364738. PubMed HubMed [Weber2011]
    MoClo

  2. Hughes RA, Miklos AE, and Ellington AD. . pmid:21601682. PubMed HubMed [Hughes2011]
    Gene Synthesis Review

  3. Werner S, Engler C, Weber E, Gruetzner R, and Marillonnet S. . pmid:22126803. PubMed HubMed [Werner2012]
    MoClo

  4. Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juárez P, Fernández-del-Carmen A, Granell A, and Orzaez D. . pmid:21750718. PubMed HubMed [SarrionPerdigones2011]
    GoldenBraid

  5. Engler C, Kandzia R, and Marillonnet S. . pmid:18985154. PubMed HubMed [Engler2008]
    GoldenGate

  6. Quan J and Tian J. . pmid:19649325. PubMed 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. . pmid:18218864. PubMed HubMed [Gibson2008]
  8. Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, and Smith HO. . pmid:19363495. PubMed HubMed [Gibson2009]
    T5 exonuclease recombination

  9. Li MZ and Elledge SJ. . pmid:17293868. PubMed HubMed [Li2007]
    SLIC

  10. Li MZ and Elledge SJ. . pmid:22328425. PubMed HubMed [Li2012]
    SLIC

  11. Sleight SC, Bartley BA, Lieviant JA, and Sauro HM. . pmid:20385581. PubMed HubMed [Sleight2010]
    In-Fusion biobrick

  12. Zhu B, Cai G, Hall EO, and Freeman GJ. . pmid:17907578. PubMed HubMed [Zhu2007]
    in-fusion

  13. Benoit RM, Wilhelm RN, Scherer-Becker D, and Ostermeier C. . pmid:16289702. PubMed HubMed [Benoit2006]
    in-fusion

  14. Geu-Flores F, Nour-Eldin HH, Nielsen MT, and Halkier BA. . pmid:17389646. PubMed HubMed [GeuFlores2007]
    USER

  15. Gibson DG. . pmid:19745056. PubMed HubMed [Gibson2009-2]
    oligonucleotide assembly

  16. Horton RM, Cai ZL, Ho SN, and Pease LR. . pmid:2357375. PubMed HubMed [Horton2009]
    SOEing

  17. Czar MJ, Anderson JC, Bader JS, and Peccoud J. . pmid:19111926. PubMed HubMed [Czar2009]
    review

  18. Stemmer WP, Crameri A, Ha KD, Brennan TM, and Heyneker HL. . pmid:7590320. PubMed HubMed [Stemmer1995]
    PCA

  19. Aslanidis C and de Jong PJ. . pmid:2235490. PubMed HubMed [Aslanidis1990]
    LIC

  20. Aslanidis C, de Jong PJ, and Schmitz G. . pmid:7580902. PubMed HubMed [Aslanidis1994]
    LIC

  21. Li C and Evans RM. . pmid:9321675. PubMed HubMed [Li1997]
    LIC

  22. Angrand PO, Daigle N, van der Hoeven F, Schöler HR, and Stewart AF. . pmid:10446259. PubMed HubMed [Angrand1999]
    lambda Red recombinase

  23. Hartley JL, Temple GF, and Brasch MA. . pmid:11076863. PubMed HubMed [Hartley2000]
    Gateway lambda Int

  24. Khalil AM, Julius JA, and Bachant J. . pmid:17702758. PubMed HubMed [Khalil2007]
    Gateway lambda Cre

  25. Larionov V, Kouprina N, Graves J, Chen XN, Korenberg JR, and Resnick MA. . pmid:8552668. PubMed 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. . pmid:20488990. PubMed HubMed [Gibson2010]
    genome replacement

All Medline abstracts: PubMed HubMed
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