Common chemicals

Water

1. Tap:
   • pH varies significantly between locations
   • Can interfere with PCR, spectrometry/chromotagraphy, and protein biochemistry
   • Can leave impurities on containers
2. Distilled (dH2O) – vaporized and partially condensed water
   • Sterile initially, but bacteria can grow in it.
   • Can still contain CO2, ammonia, SiO2.
   • Suitable for general lab usage, e.g., cleaning glassware, preparing buffers, dialysis/
3. Pure (RO) – water filtered through a reverse osmosis membrane
   • Removes >95% ionic impurities.
4. Double distilled (ddH2O) – water after two distillations
5. Deionized (diH2O) – water without anions and cations
   • Purified using RO membranes / ion-exchange resin
   • Can contain some organic matter
   • pH varies as there are few ions
6. Ultrapure (Milli-Q, NANOpure):
   • Uses deionized or RO water as input
   • Colloidal substances, gases, and organic matter at very low levels
   • Best for sensitive lab usage, e.g., PCR, HPLC, tissue cultures
7. DEPC-treated:
   • Water treated with .1% v/v diethyl pyrocarbonate for at least 2 hours at 37C, ten autoclaved for at least 15 min to inactivate traces for DEPC
   • RNAse-free

Ethylenediaminetetraacetic acid (EDTA)

• Molar mass: 150.1 g/mol
• Molar mass of EDTA•2H2O: 186.1 g/mol
• Common stock solution: .5 M, pH 8.0
• Aminopolycarboxylic acid
• White
• Water insoluble solid
• Binds one Fe2+ / Fe3+ / Ca2+ / Mg2+ at neutral pH
• Dissolves Fe- and Ca-containing scale
• Delivers Fe ions
• Deactivates metal-dependent enzymes, thus helps protect DNA and proteins from degradation and inhibits dNTP hydrolyzing enzymes (e.g., DNA polymerase I)
• Also prevents enzymes from binding to unwanted metal ions (e.g., Pb+) that have a much higher affinity than Mg2+

Dithiothreitol (DTT)

- Molar mass: 154.253 g/mol - Organosulfur compound - Colorless - Dithiol / diol - Reducing agent: once oxidized, it forms a stable six-membered ring with an internal disulfide bond - Works at pH > 7 - Prevents oxidation of thiol groups - Reduces disulfide bonds (between cysteines) in proteins – useful for stabilizing proteins as it prevents from unwanted sulfide bonds in reducing (often metal-ion-rich) environments. - Can be used to denature proteins - Oxidized by air, but rate is reduced at lower temperatures and lower pH - Non-autoclavable

Sodium dodecyl sulfate (SDS)

• Negatively charged detergent
• Denatures the protein by coating it evenly with a negative charge, stretching the protein out into a linear chain
• Non-autoclavable

Beta-mercaptoethanol (beta-ME)

- Reducing agent: reduces disulphide bonds - Biological antioxidant - Non-autoclavable

Tris(2-carboxyethyl)phosphine (TCEP)

- Reducing agent: breaks disuphide bonds - Odorless - More powerful than beta-ME and DTT, irreversible, more hydrophilic and more resistant to oxidation in air

Urea

- Diamide of carbamic acid - Colorless, odorless solid, highly soluble in water, neutral pH, practically non-toxic - Disrupts noncovalent bonds in proteins - Forms porous lattices that can trap many organic compounds

Spermidine

- Polyamine - Colourless liquid - Found in ribosomes - Maintains membrane potential - Binds and precipitates DNA - Used for in vitro transcription and translation - Increases specificity and reproducibility of Taq-mediated PCR by neutralizing and stabilizing the negative charge on DNA phosphate backbone - Used for electroporation

Formamide

- Formid acid amide - Colorless, oily liquid - RNA stabilizer in electrophoresis by deionizing RNA

Phenol

- Moderately polar solvent

Dimethyl sulfoxide (DMSO)

- Polar aprotic solvent

Chloroform

- Non-polar solvent

Benzene

- Non-polar solvent