Protocols

A list of all protocols developed during the project. We used this page as a reference throughout the competition.

Amplification of DNA

• Polymerase Chain Reaction : A method for amplifying a section of DNA.
• Colony PCR : PCR with cells as a template. Useful for checking the length of an insert in an introduced plasmid.

Analysis of DNA

• Gel Electrophoresis : A method used to separate DNA fragments of different sizes.
• Gel Extraction of DNA : A technique used to isolate a desired fragment of intact DNA from an agarose gel following agarose gel electrophoresis.
• Rescue Precipitation of DNA : Creating a clean DNA solution after dissolving agarose gel.
• Restriction Enzyme Digestion : A method for creating a restriction map of a plasmid.

Preparation of DNA Constructs

• Primer Design : Some general guidelines on how to design successful primers.
• Gibson Assembly : An extremely powerful technique for joining multiple, arbitrary DNA sequences in one step, compatible with standard assembly.

Transformation of Bacterial Cells

• Making Electro-Competent Bacterial Cells : The methods required to make various cells competent.
• Transformation of E.coli : A simple method of transforming competent E.coli with your DNA of choice.
• Tranformation of B.subtilis : A technique used to introduce foreign DNA into Bacillus cells.
• Transformation of E.coli by Electroporation: A technique for rapidly inserting DNA into cells, typically plasmid DNA, providing the cells are made competent in the correct manner.

Bacterial Cultures

• E.coli Cell Culture : A method for growing a cell culture in liquid medium.
• Glycerol Stocks: A method of storing E.coli cells preserving their viability.

Extraction of DNA

• MiniPrep : Extracting DNA from bacterial cells.
• Extraction of Genomic DNA from Squid : Two methods to extract genomic DNA from squid tissue.
• Extraction of DNA from Filter Paper  : Extraction of DNA from filter paper which is a safe way of shipping DNA.

Microscopy

• Confocal Microscopy : A method to visualise reflectins from squid samples.
• Slide Preparation for Confocal Microscopy : A method of growing a monolayer of bacterial cells on a slide to aid their microscopic viewing.
• Trypsinisation : A method of dispersing cells from tissue, for microscopy.

Protein Purification

• Buffer Preparation : Methods to prepare the various buffers used to purify his-tagged reflectin from inclusion bodies in E. coli.
• Inclusion Body Prep : Isolation of insoluble inclusion bodies of recombinant proteins.
• His-Trap Protein Purification : A method to purify reflectin from E. coli lysate using an affinity column.
• Acetone Precipitation of Proteins : A method to concentrate solutions of protein.
• Ethanol Precipitation of Proteins : A method to concentrate solutions of protein.
• Chloroform/Methanol Precipitation of Proteins : A method to concentrate solutions of protein whilst removing salts and detergents.
• Dialysis of Proteins : A method for removing salts, urea and contaminants by the use of a semi-permeable membrane and a concentration gradient.
• Norgen Proteospin Inclusion Body Prep : A proprietary kit.

Thin Film Preparation

• Substrate Preparation:How to prepare a substrate for flow coating and spin coating.
• Spin Coating to Make a Thin Film: Our Spin Coating Protocol.
• Flow Coating: How to flow coat a thin film.
• Altering Substrate Surface Chemistry: Various methods to alter the surface chemistry of silicon and PDMS to achieve better wetting and thin film production

Gel Electrophoresis by SDS PAGE

• Protein Identification by SDS PAGE: A method used to separate polypeptides of different lengths.