Chemical Structure

Control of Substances Hazardous to Health (COSHH) Assessment

• Not a hazardous substance

Use in our project:

Sodium Fluorescein was a very useful chemical in our prject and was used in several aspects; the interlab study and in relation to the beads.

It's main use was to create a calibration curve for fluorescence levels in the interlab study and also for the diffusion out of the beads.

The diffusion of sodium fluorescein out of the beads and then past along to the modelers in order to model the diffusion of our anti-biofilm agents out of the beads.

• Fluorescein gets its name from the intense green fluorescence it gives in alkaline solutions, visible even at dilutions of 1 in 50,000,000!
• It is used in optometry to reveal damaged areas of the cornea, as well as in the diagnosis of several important eye conditions including “dry eye”. The eye shown below is normal and healthy.
• Synthetic biologists and microbiologists use it to stain cells and cell structures under the microscope - such as the cell cytoskeleton marked out in bright green in the picture below!
• Fluorescein can be used to fight crime - investigators spray a watery fluorescein mist over a crime scene to reveal bloodstains that might have been cleaned away by the perpetrator.
• During World War II, German aircrews carried small containers of fluorescein with them into battle. If they were shot down and forced to parachute out of the plane, the fluorescein produced a vivid and highly conspicuous marking in the water that helped air-to-sea rescue teams find them.
• A more familiar and everyday use of fluorescein might be as the pigment in spirit levels, helping to make the air bubble more visible in contrast to the alcohols filling the tube.

Chemical Structure

Control of Substances Hazardous to Health (COSHH) Assessment

• H302 - Harmful if swallowed.
• H318 - Causes serious eye damage.
• H350 - May cause cancer.
• H410 - Very toxic to aquatic life with long lasting effects.
• P201- Obtain special instructions before use.
• P273 - Avoid release to the environment.
• P280 - Wear protective gloves/ eye protection/ face protection.
• P305 + P351 + P338 - IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing.
• P308 + P313 - IF exposed or concerned: Get medical advice/ attention.
• P501 -Dispose of contents/ container to an approved waste disposal plant.

Use in our project:

Crystal Violet was used in two different sections of our project.

It's first use was to stain the biofilms ready for the biofilm assays. It was also was used along side Sodium Fluorecence to aquire data for the diffusion rates out of the beads.

• It is most famous for its use in the Gram method of classifying bacteria - “Gram positive” = walls are stained purple, “Gram negative” = walls are not stained.
• Used to develop fingerprints in forensics.
• Crystal violet is a main component of black and navy inks for printers and ballpoint pens.
• It can also be used as an antiseptic/antifungal in resource-limited settings, but has otherwise been superseded by other more modern antiseptics.

Chemical Structure

Control of Substances Hazardous to Health (COSHH) Assessment

• H225 – Highly flammable liquid and vapour.
• H319 – Causes serious eye irritation.
• H336 – May cause drowsiness or dizziness.
• P210 – Keep away from heat, hot surfaces, sparks, open flames and other ignition sources. No smoking.
• P261 – Avoid breathing vapours.
• P305+P351+P338 – IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do so. Continue rinsing.

Use in our project

Ethyl Acetate played a small but important role in our project, it was used to dissovle a petri-dish in an attempt to create a coating for our beads... It was some what unsucessful.

• It is the most common ester in wine, and is responsible for their fruity taste and smell.
• It is used as an asphyxiant by insect collectors, which allows them to kill insects without physically damaging the specimen.
• It is used industrially as a solvent - we used it to dissolve petri dishes to coat our bacterial beads!

Chemical Structure

Control of Substances Hazardous to Health (COSHH) Assessment

• Not a hazardous substance

Chemical Structure

Control of Substances Hazardous to Health (COSHH) Assessment

• H331 - Toxic if inhaled
• H341 - Suspected of causing genetic defects


• P261 - AVoid breathing dust/ fume/ gas/ mist/ vapour/ spray.
• P281 - Use personal protective equipment as required
• P311 - Call a POISON CENTRE or doctor/ physician

Use in Our Project

Ethidium Bromide was one our biggest hazardous in the lab, however it was one of our most useful chemicals. We used it to stain gels and visualise bands of DNA. Without it Mabel, our Queen of molecular cloning would have had a much tougher time cutting out her bands of DNA.

• Ethidium bromide intercalates and binds between the layers of DNA helices.
• It fluoresces orange under UV light, but this light is 20x as intense while it is bound to DNA - making it incredibly useful as a fluorescent tag for nucleic acids.
• Its tight binding to DNA is also what makes it toxic, mutagenic and carcinogenic.
• It can be used to treat trypanosome infections in cattle, but has fallen out of favor more recently due to a high incidence of resistance.

Chemical Structure

Control of Substances Hazardous to Health (COSHH) Assessment

• H315 - Causes skin irritation.
• H317 - May cause an allergic skin reaction.
• H319 - Causes serious eye irritation.
• H334 - May cause allergy or asthma symptoms or breathing difficulties if inhaled.
• H335 - May cause respiratory irritation.


• P261 - Avoid breathing dust.
• P280 - Wear protective gloves.
• P305 + P351 + P338 - IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing.
• P342 + P311 - If experiencing respiratory symptoms: Call a POISON CENTER or doctor/ physician.

Use in Our Project

The use of the antibiotic Ampicillin was vital in our project. It acted a selectable marker for transformed cells as those that haven't taken up the plasmid with the ampicillin resistance gene will not grow on ampicillin plates. Therefore we could ensure that the bacteria that was growing on our plate containted the plasmid that we wanted.

• It is an antibiotic used to treat several bacterial infections, including urinary tract infections, salmonella, and meningitis.
• It is a variant of penicillin, and when it was first produced in 1961 it was the first penicillin therapy to show activity against gram negative bacteria.
• Very cheap (a 10 treatment for a patient only costs $13) making it ideal for use in synthetic biology research.

Chemical Structure

Control of Substances Hazardous to Health (COSHH) Assessment

• H350 - May cause cancer.


• P201 - Obtain special instructions before use.
• P308 + P313 - IF exposed or concerned: Get medical advice/ attention.

Use in Our Project

Chloramphenicol had the same role in our project as Ampicillin, however some plasmids contained the Chl resistance gene rather than the Amp one.

• An antibiotic that stops bacterial growth by preventing protein synthesis.
• Outside of the lab it can be useful for the treatment of severe bacterial infections such as plague, cholera, and typhoid fever.
• It is used sparingly due to its serious side effects - including suppression of blood cell production in the bone marrow, which can lead to death. Patients must be carefully monitored during treatment.

Chemical Structure

Control of Substances Hazardous to Health (COSHH) Assessment

• Not a hazardous substance

Use in Our Project

DMSO was used in our war against the stubborn construcst that would just refuse to PCR. It was used as it prevents DNA secondary structure formation.

• Dimethyl sulfoxide (DMSO) is a solvent that has the useful property of being able to dissolve both polar and nonpolar compounds while still mixing well with other organic solvents and water
• DMSO can be used for drug delivery due to the fact that it passes through the skin very easily while carrying dissolved chemicals with it.
• It is also used an an industrial solvent and a solvent for several chemical processes in chemistry labs.
• It can be used as a cryoprotectant in cell media by reducing the freezing temperature of the medium.
• Bizarrely, in many individuals it causes a garlic-like taste in the mouth after skin contact.

Chemical Structure

Control of Substances Hazardous to Health (COSHH) Assessment

• Not a hazardous substance.

Use in Our Project

Thiamine hydrochloride had a small but useful role in our project as a part of M9 media which was used for a lot of interlab work and in relation to the beads. The tube of Thiamine must be kept wrapped in foil as it is unstable to light.