Cyclic-substituted unsymmetrical cyanine dyes

Claim 1

A compound of the formula ##STR34## wherein: each R 1 is independently H; or an alkyl group having from 1-6 carbons; or a trifiuoromethyl; or a halogen; or --OR 8 ,-- SR 8 or --(NR 8 R 9 ) where R 8 and R 9 , which can be the same or different, are independently H; or alkyl groups having 1-6 carbons; or 1-2 allcyclic, heteroalicyclic, aromatic or heterouromatic nngs, containing 1-4 heteroatoms, wherein the hetero atoms are O, N or S; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --L--(CH 2 ) 2 -- where L=a single bond, --O--, --CH 2 --, or --NR 10 --,where R 10 is H or an alkyl group having 1-6 carbons; and t=1-4; R 2 is an alkyl group having 1-6 carbons; X is O, S, Se or --NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons, or R 16 and R 17 taken in combination complete a five or six membered saturated ring; n=0, 1 or 2; Z - is a biologically compatible counterion; Q has the formula Q1 or Q2 ##STR35## wherein Y is --CR 3 =CR 4 --; p and m=0 or 1, such that p+m=t; R 5 is an alkyl, alkenyl, polyalkenyl, alkynyl or polyailkynyl group having 1-6 carbons; or R 5 is aa OMEGA; R 3 , R 4 , R 6 and R 7 , which may be the same or dillSrent, are independently H; or an alkyl, alkenyl, polyalkenyl, alkynyl or polyatlcynyl group having 1-6 carbons; or a halogen; or --OH, --OR 8 , --SR 8 , --(NR 8 R 9 ); or --OSO 2 R 19 where R 19 is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl; or an OMEGA; or R 6 and R 7 , taken in combination are --(CH 2 ) v -- where v=3 or 4, or R 6 and R 7 form a fused aromatic ring according to formula Q2; R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H, or an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons; or a halogen; or an OMEGA; or --OH, --OR 8 , --SR 8 , or --(NR 8 R 9 ); OMEGA is a cyclohexyl, cyclohexenyl, morpholino, piperidinyl, naphthyl, phenyl, thienyl, benzothiazolyl, furanyl, oxazolyl, benzoxazolyl or pyridinyl that is unsubstituted or optionally substituted one or more times, independently, by halogen, alkyl, perfluoroalkyl, areinc, alkylamino, dialkylamino, alkoxy or carboxyalkyl, having 1-6 carbons, and that is attached as R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , or R 14 by a single bond; such that at least one of R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 , is an OMEGA, and, where more than one of R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is an OMEGA, each OMEGA is optionally the same or different; and such that when O has the formula Q1, n=O.

Claim 51

A method of staining nucleic acids in a sample, comprising a) combining a sample that contains nucleic acids with a dye compound of the formula: ##STR42## wherein: each R 1 is independently H; or an alkyl group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or --OR 8 , --SR 8 or --(NR 8 R 9 ) where R 8 and R 9 , which can be the same or different, are independently H; alkyl groups having 1-6 carbons; or 1-2 alicyclic, heteroalicyclic, aromatic or heteroaromatic rings, containing 1-4 heteroatoms, wherein the hetero atoms are O, N or S; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --L--(CH 2 ) 2 -- where L=--O--, --NR 10 ', --CH 2 -- or a single bond where R 10 is H or an alkyl group having 1-6 carbons; and t=1-4; R 2 is an alkyl group having 1-6 carbons; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons, or R 16 and R 17 taken in combination complete a five or six membered saturated ring; n=0, 1 or2; Z - is a biologically compatible counter ion; Q has the ;formula Q1 or Q2 ##STR43## wherein Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+m=1; R 5 is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons; or R 5 is an OMEGA; R 3 , R 4 , R 6 and R 7 , which may be the same or different, are independently H; or an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons; or a halogen; or --OH, --OR 8 , --SR 8 , --(NR 8 R 9 ); or --OSO 2 R 19 where R 19 is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons or aryl; or an OMEGA; or R 6 and R 7 , taken in combination are --(CH 2 ) v -- where v=3 or 4, or R 6 and R 7 form a fused aromatic ring according to formula Q2; R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons; or a halogen; or an OMEGA: or --OH, --OR 8 , --SR 8 , or --(NR 8 R 9 ); OMEGA is a saturated or unsaturated substituted or unsubstituted, cyclic substituent that has a total of 3-16 ring carbon atoms in 1-2 alicyclic, heteroalicyclic, aromatic, or heteroaromatic rings, containing 1-4 heteroatoms wherein the hetero atoms are O, N or S, that is unsubstituted or optionally substituted by halogen, alkyl, perfluoroalkyl, amino, alkylamino, dialkylamino, alkoxy or carboxyalkyl, having 1-16 carbons, and that is attached as R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , or R 14 by a single bond; such that at least one of R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is an OMEGA, and, where more than one of R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is an OMEGA, each OMEGA is optionally the same or different. b) incubating the sample for a time sufficient for the dye compound to combine with the nucleic acid in the sample to form a nucleic acid-dye complex that gives a detectable fluorescent signal; c) observing the detectable fluorescent signal of the nucleic acid-dye complex.

Claim 52

A method of staining nucleic acids in a sample, comprising a) combining a sample that contains nucleic acids with a dye compound of the formula: ##STR42## wherein: each R 1 is independently H; or an alkyl group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or --OR 8 , --SR 8 or --(NR 8 R 9 ) where R 8 and R 9 , which can be the same or different, are independently H; alkyl groups having 1-6 carbons; or 1-2 alicyclic, heteroalicyclic, aromatic or heteroaromatic rings, containing 1-4 heteroatoms, wherein the hetero atoms are O, N or S; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --L--(CH 2 ) 2 -- where L=--O--, --NR 10 ', --CH 2 -- or a single bond where R 10 is H or an alkyl group having 1-6 carbons; and t=1-4; R 2 is an alkyl group having 1-6 carbons; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons, or R 16 and R 17 taken in combination complete a five or six membered saturated ring; n=0, 1 or2; Z - is a biologically compatible counter ion; Q has the ;formula Q1 or Q2 ##STR43## wherein Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+m=1; R 5 is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons; or R 5 is an OMEGA; R 3 , R 4 , R 6 and R 7 , which may be the same or different, are independently H; or an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons; or a halogen; or --OH, --OR 8 , --SR 8 , --(NR 8 R 9 ); or --OSO 2 R 19 where R 19 is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons or aryl; or an OMEGA; or R 6 and R 7 , taken in combination are --(CH 2 ) v -- where v=3 or 4, or R 6 and R 7 form a fused aromatic ring according to formula Q2; R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons; or a halogen; or an OMEGA: or --OH, --OR 8 , --SR 8 , or --(NR 8 R 9 ); OMEGA is a saturated or unsaturated substituted or unsubstituted, cyclic substituent that has a total of 3-16 ring carbon atoms in 1-2 alicyclic, heteroalicyclic, aromatic, or heteroaromatic rings, containing 1-4 heteroatoms wherein the hetero atoms are O, N or S, that is unsubstituted or optionally substituted by halogen, alkyl, perfluoroalkyl, amino, alkylamino, dialkylamino, alkoxy or carboxyalkyl, having 1-16 carbons, and that is attached as R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , or R 14 by a single bond; such that at least one of R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is an OMEGA, and, where more than one of R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is an OMEGA, each OMEGA is optionally the same or different. b) incubating the sample for a time sufficient for the dye compound to combine with the nucleic acid in the sample to form a nucleic acid-dye complex that gives a detectable fluorescent signal; c) observing the detectable fluorescent signal of the nucleic acid-dye complex.