The invention provides an asymmetric cyanine dye compound having the structure ##STR00001## including substituted forms thereof, wherein, at least one of R.sub.1 and R.sub.2 is linking group, X is O, S, or Se, and n ranges from 0 to 2. The invention further provides reporter-quencher dye pairs comprising the asymmetric cyanine dyes, dye-labelled polynucleotides incorporating the asymmetric cyanine dyes, and hybridization detection methods utilizing the dye-labelled polynucleotides.