Isolated allophycocyanin dissociates when in diluted solutions or when it is exposed to chaotropic salts, therefore APC is usually cross-linked such that it is stable for use in biological assay formats. Columbia Biosciences uses a proprietary, non-destructive cross-linking process that increases the thermal stability while maintaining fluorescent and spectral integrity of the native dye.
Allophycocyanin can be isolated from various species of red or blue-green algae, each producing slightly different forms of the molecule. It is composed of two different subunits (α and β) in which each subunit has one phycocyanobilin (PCB) chromophore. The subunit structure for APC has been determined as (αβ)3. The molecular weight of APC is 105,000 Daltons.