This invention provides dye phosphoramidites, particularly phosphoramidites of substituted cyclic bridged cyanine and related dyes, of the general formula: In this formula, each dotted line represents carbon atoms necessary to form a fused substituted or unsubstituted aromatic ring; m is an integer from 1 to 18; Y and Z are independently selected from the group consisting of S, O, N, CH.sub.2 and C(CH.sub.3).sub.2; R.sub.1 is an alkyl; (PAM) is a phosphoramidite group; X is a n.sup.{circle around (-)}egative ion; and Q is L-W, wherein L is a conjugated cyclic moiety and W is OR.sub.2, wherein R.sub.2 is a second alkyl. Methods of making and using the dye phosphoramidites are also provided.