Carotenoids in light-harvesting proteins and reaction centers increase the overall efficiency of photosynthesis by transferring absorbed light energy to chlorophylls, Peridinin and beta-carotene were isolated from Gonyaulax polyedra in a one-step purification protocol using the preparative circular chromatography (Chromatotron), performed on silica gel under N-2 atmosphere and n-hexane/acetone 8:2 as mobile phase and characterized by extensive H-1 NMR, infrared, and electrospray ionization mass spectrometry analyses. The quenching of singlet molecular oxygen [O-2 ((1)Delta(g))] was evaluated by NIR-emission assays using singlet oxygen generated by sensitization of either perinaphthenone or methylene blue, The NIR-emission assay showed that peridinin quench as singlet oxygen (k(q) = 9.5 x 10(8) M-1 s(-1)) 5-fold less efficiently than beta-carotene (52 x 10(8) M-1 s(-1)). A method, based on the use of high-performance liquid chromatography with UV-VIS detection, was then developed for the sensitive quantification of peridinin (55% of total carotenoids) and beta-carotene (4.1% of total carotenoids), Thus, since peridinin is 10-fold more abundant than beta-carotene, it is expected to be the major protector against the deleterious effects of O-2 ((1)Delta(g)) in Gonyaulax polyedra.