The satellite holes in persistent hole burned spectra have been applied to study the hydrogen bond effect of guest-host interactions. Examples include 4, 4-difluoro-5-(4-phenyl-1, 3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, succinimidyl ester doped in polymer film and 9-aminoacridine doped in a glass made by the mixture of glycerol and water. The formation of satellite holes and the relationship between functional group and structural activity have been studied and these results are reviewed. Furthermore, the characters of satellite holes are applied to monitor the localized interactions of chromophore-DNA complexes.