Dyes and Stains
Dyes and Stains

Before using a dye look at its chemical structure. Is it hydrophobic, an anion, a cation? Is it likely to form specific hydrogen bonds when it binds (most dyes don't.) Is it soluble in water (organic solvents)? If it has both ionic and hydrophobic regions it's likely to be a surfactant (and aggregate into micelles.) What's the absorption spectrum of the dye? If it fluoresces, what are excitation and emission maxima?

Basic information on dyes and stains is surprising hard to come by. Most users simply follow recipes and have little idea of the nature and mechanism of "specificity".

Useful tip - Work out staining (destaining) protocols by dotting substrate onto a small piece of filter paper and dipping. Dye concentrations, pHs, salt and solvent concentrations can be explored on a "micro" scale.
Stains File (histology)

At SigmaAldrich @ wikipedia

Formaldehyde, formalin, paraformaldehyde and glutaraldehyde: What they are and what they do.

IR dyes

Crowle's Stain - (immunodiffusion)

Indigo @ wikipedia

Staining polyanions
Alcian Blue properties - protocol

If you use Alcian blue the following is a great read:
J.E. Scott, Alcian Blue. Now you see it, now you don't - Eur. J. Oral Sci. 104, 2-9 (1996)
Congo red at wikipedia - properties

Touidine blue O - at stains file

UV Products Epi Chem 3