Cyanine dyes

A compound having the formula:

• wherein
• Rf, Rg, Rh, and Ri are members independently selected from halogen, substituted or unsubstituted alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heteroalkyl and a bond to a carrier molecule;
• Rc, and Rd are independently selected from alkyl and heteroalkyl, substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, phosphoric acid and a bond to a carrier molecule;
• a and e are independently selected from the integers 0, 1, 2, 3 and 4, with the proviso that at least one member selected from a and e is 2 or greater, such that when a is 2 or greater, each Ra is independently selected, and when e is 2 or greater, each Re is independently selected;
• wherein when a is 2 or greater, ring A is selected from phenyl substituted at least at the 4- and 6-positions with aRa, and substituted or unsubstituted napthyl;
• and when e is 2 or greater, ring E is selected from phenyl substituted at least at the 4- and 6-positions with eRe, and substituted or unsubstituted naphthyl;
• Q is a member selected from:
• wherein
• n is selected from the integers from 1 to 3;
• Ra and Re, are independently selected from C(O)R9, OR12, NR12R13, CR12C(O)R13, NR12C(O)2R13, SO3H, and C(O)NR12R13, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, a bond to a carrier molecule and a ring structure formed by joining a member selected from two Ra moieties together with the atoms they are attached, two Re moieties together with the atoms they are attached, and a combination thereof, to form said ring structure, which is a member selected from a substituted or unsubstituted aryl and a substituted or unsubstituted heteroaryl
• wherein
• R9 is a member selected from OR10, and NH(CH2)tOR11
• wherein
• R10 is a member selected from H and substituted or unsubstituted alkyl;
• t is selected from the integers from 1 to 12;
• R11 is a member selected from H, and
• wherein
• u is selected from the integers from 1 to 8;
• and
• Y is a nucleobase;
• and
• R12 and R13 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl substituted or unsubstituted heterocycloalkyl and a bond to a carrier molecule,
• wherein, when Ra, Rc, Rd, Re, Rf, Rg, Rh, and Ri are selected from substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl, one or more of Ra, Rc, Rd, Re, Rf, Rg, Rh, Ri is optionally bound to a carrier molecule.