CH391L/S13/DnaAssembly

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Revision as of 01:45, 22 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
PCA

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)

-golden gate
-MoClo [1]
-GoldenBraid

-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

Uncategorized
-Fast Seamless Cloning (Dogene)
-CloneEZ kit (Genescript)
-GENEART
-lic
-gateway
-lambda red

Transformation

• e coli
  
• s. cerevisiae
  

Bacterial Mating

MAGIC

-mage

References

1. Error fetching PMID 21364738: [Weber2011]

   MoClo

2. Error fetching PMID 21601682: [Hughes2011]

   Gene Synthesis Review

3. Error fetching PMID 22126803: [Werner2012]

   MoClo

4. Error fetching PMID 21750718: [SarrionPerdigones2011]

   GoldenBraid

5. Error fetching PMID 18985154: [Engler2008]

   GoldenGate

6. Error fetching PMID 19649325: [Quan2009]

   CPEC

7. Error fetching PMID 18218864: [Gibson2008]
8. Error fetching PMID 19363495: [Gibson2009]

   T5 exonuclease recombination

9. Error fetching PMID 17293868: [Li2007]

   SLIC

10. Error fetching PMID 22328425: [Li2012]

    SLIC

11. Error fetching PMID 20385581: [Sleight2010]

    In-Fusion biobrick

12. Error fetching PMID 17907578: [Zhu2007]

    in-fusion

13. Error fetching PMID 16289702: [Benoit2006]

    in-fusion

14. Error fetching PMID 17389646: [GeuFlores2007]

    USER

15. Error fetching PMID 19745056: [Gibson2009-2]

    oligonucleotide assembly

16. Error fetching PMID 2357375: [Horton2009]

    SOEing

17. Error fetching PMID 19111926: [Czar2009]

    review

18. Error fetching PMID 7590320: [Stemmer1995]

    PCA

19. Error fetching PMID 2235490: [Aslanidis1990]

    LIC

20. Error fetching PMID 7580902: [Aslanidis1994]

    LIC

21. Error fetching PMID 9321675: [Li1997]

    LIC

22. Error fetching PMID 10446259: [Angrand1999]

    lambda Red recombinase

23. Error fetching PMID 11076863: [Hartley2000]

    Gateway lambda Int

24. Error fetching PMID 17702758: [Khalil2007]

    Gateway lambda Cre

25. Error fetching PMID 8552668: [Larionov1996]

    Transformation-associated recombination (TAR) cloning

26. j5 DNA Assembly Design Automation Software doi: 10.1021/sb2000116 [Hillson2012]
27. Error fetching PMID 20488990: [Gibson2010]

    genome replacement

28. Error fetching PMID 15731760: [Li2005]

    MAGIC, bacterial mating approach

1. Zhang2012 pmid=22241772

//SLiCe