Difference between revisions of "Team:Aachen/Notebook/Protocols"

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{{Team:Aachen/Protocol|title=B0034_Insertion-Mutagenesis|id=B0034_Insertion-Mutagenesis|text=<span style="display:none;">spacer</span>With this method B0034 can be inserted into any RFC10 part that begins with prefix-CDS.
 
{{Team:Aachen/Protocol|title=B0034_Insertion-Mutagenesis|id=B0034_Insertion-Mutagenesis|text=<span style="display:none;">spacer</span>With this method B0034 can be inserted into any RFC10 part that begins with prefix-CDS.
  
The protocol is taken from Bryksin&nbsp;et&nbsp;al.&nbsp;2014<ref>Bryksin AV, Bachman HN, Cooper SW, Balavijayan T, Blackstone RM, Du H, Jenkins JP, Haynes CL, Siemer JL, Fiore VF, Barker TH. One primer to rule them all: universal primer that adds BBa_B0034 ribosomal binding site to any coding standard 10 BioBrick. ACS Synth Biol. 2014 Dec 19;'3'(12):956-9. doi:10.1021/sb500047r. PubMed PMID: 25524097; PubMed Central PMCID: PMC4277749.</ref>.
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The protocol is taken from Bryksin&nbsp;et&nbsp;al.&nbsp;2014<ref>Bryksin AV, Bachman HN, Cooper SW, Balavijayan T, Blackstone RM, Du H, Jenkins JP, Haynes CL, Siemer JL, Fiore VF, Barker TH. One primer to rule them all: universal primer that adds BBa_B0034 ribosomal binding site to any coding standard 10 BioBrick. ACS Synth Biol. 2014 Dec 19;'''3'''(12):956-9. doi:10.1021/sb500047r. PubMed PMID: 25524097; PubMed Central PMCID: PMC4277749.</ref>.
  
  
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{{Team:Aachen/Protocol|title=Dinitrosalicylic Acid Staining|id=Dinitrosalicylic_Acid_Staining |text=The dinitrosalicylic acid assay is used to analyse the distribution of branches in Glycogen. Dinitrosalicylic acid reacts with the reducing ends of glycogen (or sugars). <ref>S. K. Meur, V. Sitakara Rao, and K. B. De. Spectrophotometric Estimation of Reducing Sugars by Variation of pH. Z. Anal. Chem. '283', 195-197 (1977).
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{{Team:Aachen/Protocol|title=Dinitrosalicylic Acid Staining|id=Dinitrosalicylic_Acid_Staining |text=The dinitrosalicylic acid assay is used to analyse the distribution of branches in Glycogen. Dinitrosalicylic acid reacts with the reducing ends of glycogen (or sugars). <ref>S. K. Meur, V. Sitakara Rao, and K. B. De. Spectrophotometric Estimation of Reducing Sugars by Variation of pH. Z. Anal. Chem. '''283''', 195-197 (1977).
 
</ref>
 
</ref>
  

Revision as of 01:02, 19 September 2015


The most important recipe for effective research and reproducible results are reliable protocols.

On this page we are providing several protocols that we have used over the course of our project.


Culturing


Lysogeny-Broth (LB Medium)[+]

M9 Medium[+]


Overnight Cultures[+]


SOC Medium[+]

Cloning


B0034_Insertion-Mutagenesis[+]

CPEC[+]


Gibson Assembly[+]


Genomic Amplification[+]

Transformation[+]

Plasmid Preparation[+]


RDP Assembly[+]

Analytics

Acid Hydrolysis[+]

Cell Lysis[+]


Electrophoresis[+]

Glycogen Kit[+]

Iodine Staining[+]

Nash Assay[+]


SDS-PAGE[+]


HPLC[+]

Dinitrosalicylic Acid Staining[+]


References

  1. Bryksin AV, Bachman HN, Cooper SW, Balavijayan T, Blackstone RM, Du H, Jenkins JP, Haynes CL, Siemer JL, Fiore VF, Barker TH. One primer to rule them all: universal primer that adds BBa_B0034 ribosomal binding site to any coding standard 10 BioBrick. ACS Synth Biol. 2014 Dec 19;3(12):956-9. doi:10.1021/sb500047r. PubMed PMID: 25524097; PubMed Central PMCID: PMC4277749.
  2. Quan, Jiayuan, and Jingdong Tian. “Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways.” Ed. Paulo Lee Ho. PLoS ONE 4.7 (2009): e6441. PMC. Web. 16 Sept. 2015.
  3. https://j5.jbei.org/j5manual/pages/22.html
  4. https://www.neb.com/protocols/2012/09/25/gibson-assembly-master-mix-assembly
  5. http://www.geneious.com
  6. http://parts.igem.org/Help:Transformation_Protocol Protocol of the iGEM HQ
  7. Blank Lars, Protocol for 13C Tracer Experiments
  8. [http://www.biovision.com/manuals/K646-100.pdf Glycogen Assay Kit Manual]
  9. https://www.thermofisher.com/de/de/home/references/ambion-tech-support/rna-tools-and-calculators/macromolecular-components-of-e.html
  10. http://www.genomics.agilent.com/biocalculators/calcODBacterial.jsp
  11. Nash. 1953. The colorimetric estimation of formaldehyde by means of the Hantzsch reaction. Biochemical Journal, 55(3), 416-421.
  12. Kleeberg & Klinger. 1982. Sensitive formaldehyde determination with Nash's reagent and a tryptophan reaction. Journal of Pharmacological Methods, 8(1), 19-31.
  13. S. K. Meur, V. Sitakara Rao, and K. B. De. Spectrophotometric Estimation of Reducing Sugars by Variation of pH. Z. Anal. Chem. 283, 195-197 (1977).