Team:TU Darmstadt/Protocols

Protocols

The following page(s) gives an overview of the protocols and possible modifications that where used and proven working during the iGEM PET.erminators project 2012.

Contents 1 In vivo 1.1 [http://en.wikipedia.org/wiki/E._coli Escherichia coli] 1.2 Comamonas testosteroni 2 In vitro 2.1 Nucleic acids 2.2 [http://en.wikipedia.org/wiki/DNA DNA] 2.3 [http://en.wikipedia.org/wiki/RNA RNA] 2.4 Protein 3 In silico 3.1 Data analysis 3.2 Databases 3.3 Modelling 3.4 Sequence analysis 3.5 Structure analysis 4 Material Science 5 Miscellaneous 5.1 Cell culture 5.2 Microscopy 5.3 ILDs / Improvised Lab Devices

In vivo

[http://en.wikipedia.org/wiki/E._coli Escherichia coli]

• Bacterial cell culture
• Bacterial transformation aka TRAFO
• Cell counting/plating
• Chemically competent cells
• Colony PCR
• Electrocompetent cells
• Electroporation
• Engineering BioBrick vectors from BioBrick parts/Colony PCR
• In-fusion BioBrick assembly
• Miniprep / Qiagen kit
• Transformation of chemically competent cells
• Western blot

Comamonas testosteroni

• [http://www.dsmz.de/fileadmin/Bereiche/Microbiology/Dateien/Kultivierungshinweise/engl_Opening.pdf Reviving a freez dried cell culture]
• ...

In vitro

Nucleic acids

• Agarose gel electrophoresis
• PCR techniques
• SOE-PCR

[http://en.wikipedia.org/wiki/DNA DNA]

• Agarose gel electrophoresis
• Annealing and primer extension
• Annealing primers
• Assembly PCR
• Cloning
• DNA Ligation
• DNA Quantification / NanoDrop
• DNA Synthesis from Oligos
• Engineering BioBrick vectors from BioBrick parts/Colony PCR
• Miniprep
• PCR
• Polyacrylamide gel electrophoresis
• Primer Design
• Purification of DNA
• Restriction digest
• Resuspension of primers
• Salting Out
• Sequencing DNA

[http://en.wikipedia.org/wiki/RNA RNA]

Protein

• SDS-Page

In silico

Data analysis

• Information theory
• R Programming
• Mathlab / Simulink

Databases

• PDB
• CAS

Modelling

• Gaussian Network Modelling

Sequence analysis

• BLAST
• SAGE

Structure analysis

• PDB
• Protein structure prediction
• RNA secondary structure prediction

Material Science

• Synthesis of paranitrophenylesters with acyl chlorides in presence of triethylamine

Miscellaneous

Cell culture

• Pouring LB plates

Microscopy

• Determining an objects size
• Preparing slides
• Staining

ILDs / Improvised Lab Devices

• x bp Primer Designer
• Enhancing a thermo cyclers cooling capabilites
• Gel pocket size reduction
• Growing iGEMlers