Substituted unsymmetrical cyanine dyes with selected permeability

• US 5,658,751 A
• Filed: 10/27/1994
• Issued: 08/19/1997
• Est. Priority Date: 04/13/1993
• Status: Expired due to Term

• Current Assignee: Molecular Probes Incorporated (Thermo Fisher Scientific Incorporated)
• Original Assignee: Molecular Probes Incorporated (Thermo Fisher Scientific Incorporated)
• Inventors: Mozer, Thomas J., Roth, Bruce L., Jin, Xiaokui, Yue, Stephen T., Haugland, Richard P., Singer, Victoria L., Millard, Paul J., Jones, Laurie J.
• Primary Examiner(s): Kight, John
• Assistant Examiner(s): LEARY, LOUISE N
• Application Number:
  US08/331,031
• Time in Patent Office: 1,027 Days
• Field of Search: 435/34, 435/4, 435/29, 435/6, 436/94, 436/800, 536/26.73, 536/1.11, 536/25.6
• US Class Current: 435/34
• CPC Class Codes: C07D 215/18 Halogen atoms or nitro radicals
• CPC Class Codes: C07D 413/06 linked by a carbon chain containing only aliphatic carbon atoms
• CPC Class Codes: C07D 417/06 linked by a carbon chain containing only aliphatic carbon atoms
• CPC Class Codes: C07D 417/14 containing three or more hetero rings
• CPC Class Codes: C09B 23/02 the polymethine chain containing an odd number of >CH- or >C[alkyl]- groups
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2563/173 staining/intercalating agent, e.g. ethidium bromide
• CPC Class Codes: G01N 15/1459 the analysis being performed on a sample stream
• CPC Class Codes: G01N 2015/1402 Data analysis by thresholding or gating operations performed on the acquired signals or stored data
• CPC Class Codes: Y10S 436/80 Fluorescent dyes, e.g. rhodamine
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The invention describes the preparation and use of fluorescent stains for nucleic acids derived from unsymmetrical cyanine dyes comprising a substituted benzazolium ring system linked by a methine bridge to a pyridinium or quinolinium ring system having at least one substituent on the pyridinium or quinolinium ring that contains a heteroatom. The presence of the heteroatom-containing substituent results in higher sensitivity to oligonucleotides and larger nucleic acid polymers in a wide range of cells and gels, and for use in analysis of cell structure, membrane integrity or function.

Claims

1. A compound of the formula ##STR109## wherein each R¹ is independently H;

or an alkyl group having from 1-6 carbons;

an alkoxy group having from 1-6 carbons;

or a trifluoromethyl;

or a halogen; and

t=1-4;

R² is an alkyl group having 1-6 carbons;

X is O, S, Se or NR¹⁵, where R¹⁵ is H or an alkyl group having 1-6 carbons;

or X is CR¹⁶ R¹⁷ where R¹⁶ and R¹⁷, which may be the same or different, are independently alkyl groups having 1-6 carbons, or R¹⁶ and R¹⁷ taken in combination complete a five or six membered saturated ring;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

Q has the formula Q1 or Q2 ##STR110## wherein Y is --CR³ ═

CR⁴ --;

p and m=0 or 1, such that p+m=1;

R⁵ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or R⁵ is a cyclic substituent that is a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or R⁵ is a TAIL;

R³, R⁴, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

or R⁶ and R⁷, taken in combination are --(CH₂)_v -- where v=3 or 4, or R⁶ and R⁷ form a fused aromatic ring according to formula Q2;

R¹¹, R¹², R¹³, and R¹⁴, 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 a TAIL;

or --OH, --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds;

or single, double, triple or aromatic carbon-carbon bonds;

or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen-nitrogen or nitrogen-oxygen bonds;

or aromatic or heteroaromatic bonds;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR111## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁵, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL; and

when R⁵ is a TAIL, LINK is a single bond; and

where only R⁵ is a TAIL, R³ or R⁴ is not hydrogen; and

, where more than one of R², R³, R⁴, R⁵, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL, each TAIL is optionally the same or different.

2. A compound, as claimed in claim 1, wherein each R¹ is H, and R² is ethyl or methyl.

3. A compound, as claimed in claim 1, wherein X is O or S.

4. A compound, as claimed in claim 1, wherein n=0 or 1.

5. A compound, as claimed in claim 1, wherein at least one of R³, R⁴, R⁵, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a substituted or unsubstituted naphthyl, phenyl, thienyl, or cycloalkyl having 3-8 carbons.

6. A compound, as claimed in claim 1, wherein neither CAP nor CAP'"'"' is --O--R²¹ or --S--R²¹.

7. A compound, as claimed in claim 1, wherein CAP and CAP'"'"', which may be the same or different, are --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^-, wherein R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons.

8. A compound, as claimed in claim 1, wherein R²⁰ is H or a linear or branched alkyl having 1-8 carbons.

9. A compound, as claimed in claim 1, wherein SPACER and SPACER'"'"' are independently linear alkylenes having 1-8 carbons.

10. A compound, as claimed in claim 1, wherein SPACER and SPACER'"'"' are the same, and CAP and CAP'"'"' are the same.

11. A compound, as claimed in claim 1, of the formula ##STR112## or of the formula ##STR113##

12. A compound, as claimed in claim 11, wherein R⁴ is a TAIL.

13. A compound, as claimed in claim 11, wherein R⁵ is a substituted or unsubstituted naphthyl, phenyl, thienyl, or cycloalkyl having 3-8 carbons.

14. A compound, as claimed in claim 11, wherein R⁵ is phenyl or substituted phenyl.

15. A compound, as claimed in claim 13, wherein each of R³, R⁶, and R⁷ is hydrogen.

16. A compound as claimed in claim 13, wherein each of R³, R¹¹, R¹², R¹³ and R¹⁴ is hydrogen.

17. A compound, as claimed in claim 11, wherein R⁵ is a linear or branched alkyl having 1-6 carbons.

18. A compound, as claimed in claim 11, wherein R⁵ is a TAIL and R⁴ is not hydrogen.

19. A compound of the formula ##STR114## or having the formula ##STR115## wherein R² is an alkyl group having 1-6 carbons;

X is O or S;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

R⁵ is a substituted or unsubstituted naphthyl, phenyl, thienyl, or cycloalkyl having 3-8 carbons;

R⁴ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or a halogen;

or a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸,--(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

having 1-6 carbons, or aryl;

R³, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

R¹¹, R¹², R¹³, and R¹⁴, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-8 carbons;

or a TAIL;

or --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, O and S, such that the linkage begins and ends with a carbon atom, and contains any combination of ether, thioether, amine, ester, amide, or aliphatic, oleic or aromatic carbon-carbon bonds, or aromatic carbon-nitrogen or nitrogen-nitrogen bonds;

wherein all heteroatoms in the linear backbone of SPACER are separated by at least two carbon atoms;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR116## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL; and

, where more than one substituent is a TAIL, each TAIL is optionally the same or different.

20. A compound, as claimed in claim 19, wherein R⁴ is a TAIL.

21. A compound having the formula ##STR117## or having the formula ##STR118## wherein R² is an alkyl group having 1-6 carbons;

X is O or S;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

R⁵ is an alkyl having 1-6 carbons;

R⁴ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or a halogen;

or a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR.sup. R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

having 1-6 carbons, or aryl;

R³, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

R¹¹, R¹², R¹³, and R¹⁴, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-8 carbons;

or a TAIL;

or --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, O and S, such that the linkage begins and ends with a carbon atom, and contains any combination of ether, thioether, amine, ester, amide, or aliphatic, olefinic or aromatic carbon-carbon bonds, or aromatic carbon-nitrogen or nitrogen-nitrogen bonds;

wherein all heteroatoms in the linear backbone of SPACER are separated by at least two carbon atoms;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR119## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL; and

, where more than one substituent is a TAIL, each TAIL is optionally the same or different.

22. A compound having the formula ##STR120## wherein R² and R²⁴ are independently a linear or branched alkyl having 1-6 carbons;

X is O, S, Se or NR¹⁵, where R¹⁵ is H or an alkyl group having 1-6 carbons;

or X is C(CH₃)₂ ;

n=0, 1 or2; and

Ψ

^- is a biologically compatible counterion.

23. A fluorescent complex comprising a nucleic acid polymer non-covalently bound to one or more dye molecules of the formula ##STR121## wherein each R¹ is independently H;

or an alkyl group having from 1-6 carbons;

an alkoxy group having from 1-6 carbons;

or a trifluoromethyl;

or a halogen; and

t=1-4;

R² is an alkyl group having 1-6 carbons;

X is O, S, Se or NR¹⁵, where R¹⁵ is H or an alkyl group having 1-6 carbons;

or X is CR¹⁶ R¹⁷ where R¹⁶ and R¹⁷, which may be the same or different, are independently alkyl groups having 1-6 carbons, or R¹⁶ and R¹⁷ taken in combination complete a five or six membered saturated ring;

n=0, 1 or 2;

Ψ

^- is a biologically compatible counterion;

Q has the formula Q 1 or Q2 ##STR122## wherein Y is --CR³ ═

CR⁴ --;

p and m=0 or 1, such that p+m=1;

R⁵ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or R⁵ is a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or R⁵ is a TAIL;

R³, R⁴, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

or R⁶ and R⁷, taken in combination are --(CH₂)_v -- where v=3 or 4, or R⁶ and R⁷ form a fused aromatic ring according to formula Q2;

R¹¹, R¹², R¹³, and R¹⁴, 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 a TAIL;

or --OH, --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds;

or single, double, triple or aromatic carbon-carbon bonds;

or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen-nitrogen or nitrogen-oxygen bonds;

or aromatic or heteroaromatic bonds;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

CAP and CAP'"'"' are independently ##STR123## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁵, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL, and when R⁵ is a TAIL, LINK is a single bond; and

where only R⁵ is a TAIL, R³ or R⁴ is not hydrogen; and

, where more than one of R², R³, R⁴, R⁵, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL, each TAIL is optionally the same or different.

24. A fluorescent complex, as claimed in claim 23, wherein each R¹ is;

R² is ethyl or methyl;

m=1;

R⁴ is not hydrogen;

R⁵ is alkyl having 1-6 carbons;

or a cyclic substituent that is a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or R⁵ is a TAIL; and

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds;

or single, double, triple or aromatic carbon-carbon bonds;

or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen-nitrogen or nitrogen-oxygen bonds;

or aromatic or heteroaromatic bonds.

25. A fluorescent complex, as claimed in claim 24, wherein

X is O or S;

n=0 or 1; and

R⁵ is alkyl having 1-6 carbons, or a cyclic substituent.

26. A fluorescent complex, as claimed in claim 24 wherein at least one of R³, R⁴, R⁵, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a substituted or unsubstituted naphthyl, phenyl, thienyl, or cycloalkyl having 3-8 carbons.

27. A fluorescent complex, as claimed in claim 24, wherein neither CAP nor CAP'"'"' is --O--R²¹ or --S--R²¹.

28. A fluorescent complex, as claimed in claim 23, wherein the nucleic acid polymer is a chromosome.

29. A fluorescent complex, as claimed in claim 23, wherein the nucleic acid polymer is a natural or synthetic oligonucleotide.

30. A fluorescent complex, as claimed in claim 23, wherein said complex is enclosed in a biological structure.

31. A fluorescent complex, as claimed in claim 23, wherein said complex is present in an aqueous or aqueous miscible solution.

32. A fluorescent complex, as claimed in claim 23, wherein said complex is present in an electrophoretic matrix.

33. A fluorescent complex, as claimed in claim 23, wherein said complex is present in a flowing medium.

34. A fluorescent complex, as claimed in claim 23, wherein the nucleic acid polymer comprises modified nucleic acid bases or links.

35. A method of staining nucleic acids, comprising

a) combining a sample that contains or is thought to contain a nucleic acid, with a mixture containing a dye compound of the formula (formula I):

##STR124## or having the formula ##STR125## wherein R² is ethyl or methyl;

X is O or S;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

R⁵ is alkyl having 1-6 carbons;

or a cyclic substituent that is a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or R⁵ is a TAIL;

R⁴ is an alkyl, aIkenyl, polyaIkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or a halogen;

or a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

having 1-6 carbons, or aryl;

R³, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

R¹¹, R¹², R¹³, and R¹⁴, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-8 carbons;

or a TAIL;

or --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, O and S, such that the linkage begins and ends with a carbon atom, and contains any combination of ether, thioether, amine, ester, amide, or aliphatic, olefinic or aromatic carbon-carbon bonds, or aromatic carbon-nitrogen or nitrogen-nitrogen bonds;

wherein all heteroatoms in the linear backbone of SPACER are separated by at least two carbon atoms;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR126## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL; and

, where more than one substituent is a TAIL, each TAIL is optionally the same or different;

and

b) incubating the sample and mixture for a time sufficient for the dye compound to combine with the nucleic acid in the sample to form one or more dye-nucleic acid complexes that give a detectable fluorescent signal.

36. A method of staining nucleic acids, according to claim 35, wherein said sample or said mixture comprises an electrophoretic gel.

37. A method of staining nucleic acids, according to claim 35, wherein the dye-nucleic acid complexes are separated by electrophoresis.

38. A method of staining nucleic acids, according to claim 35, wherein said sample comprises a density or sedimentation gradient.

39. A method of staining nucleic acids, according to claim 35, wherein the sample comprises a biological fluid.

40. A method of staining nucleic acids, according to claim 35, wherein the one or more dye-nucleic acid complexes form in a eukaryote cell, a prokaryote cell, a virus, or a viroid.

41. A method of staining nucleic acids, according to claim 40, wherein the complexes form in a eukaryote cell or prokaryote cell that is in a cell, tissue, or biological fluid.

42. A method of staining nucleic acids, according to claim 35, where the sample contains cell-free nucleic acids.

43. A method of detecting a biological structure, comprising

a) combining a sample that contains or is thought to contain a specific biological structure, with a dye of the formula ##STR127## or having the formula ##STR128## wherein R² is ethyl or methyl;

X is O or S;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

R⁵ is alkyl having 1-6 carbons;

or a cyclic substituent that is a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or R⁵ is a TAIL;

R⁴ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or a halogen;

or a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, (NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

having 1-6 carbons, or aryl;

R³, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

R¹¹, R¹², R¹³, and R¹⁴, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-8 carbons;

or a TAIL;

or --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, O and S, such that the linkage begins and ends with a carbon atom, and contains any combination of ether, thioether, amine, ester, amide, or aliphatic, olefinic or aromatic carbon-carbon bonds, or aromatic carbon-nitrogen or nitrogen-nitrogen bonds;

wherein all heteroatoms in the linear backbone of SPACER are separated by at least two carbon atoms;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^-,

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR129## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL; and

, where more than one substituent is a TAIL, each TAIL is optionally the same or different;

wherein said biological structure contains nucleic acids;

b) incubating the combined sample and dye compound for a time sufficient for the dye compound to combine with the nucleic acids in the biological structure to form a pattern of dye-nucleic acid complexes having a detectable fluorescent signal that corresponds to the biological structure; and

c) detecting the fluorescent signal that corresponds to the biological structure.

44. A method of detecting a biological structure, according to claim 43, wherein said biological structure is a prokayotic cell, eukaryotic cell, virus, or viroid.

45. A method of detecting a biological structure, according to claim 43, wherein the biological structure is a subcellular organelle that is intracellular or extracellular.

46. A method of detecting a biological structure, according to claim 43, wherein the biological structure is a parasitic organism.

47. A method of detecting a biological structure, according to claim 43, wherein the biological structure is a blebbing cell or nucleus.

48. A method of detecting a biological structure, according to claim 43 wherein said fluorescent signal is detected with and instrument.

49. A method of detecting a biological structure, according to claim 43, wherein said sample is a biological fluid, a water sample, or obtained from foodstuffs, or an aqueous wash from a solid surface.

50. A method of characterizing a sample, comprising:

a) combining a sample containing or thought to contain nucleic acid polymers with a dye compound of the formula ##STR130## or having the formula ##STR131## wherein R² is ethyl or methyl;

X is O or S;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

R⁵ is alkyl having 1-6 carbons;

or a cyclic substituent that is a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or R⁵ is a TAIL;

R⁴ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or a halogen;

or a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

having 1-6 carbons, or aryl;

R³, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

R¹¹, R¹², R¹³, and R¹⁴, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-8 carbons;

or a TAIL;

or --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, O and S, such that the linkage begins and ends with a carbon atom, and contains any combination of ether, thioether, amine, ester, amide, or aliphatic, olefinic or aromatic carbon-carbon bonds, or aromatic carbon-nitrogen or nitrogen-nitrogen bonds;

wherein all heteroatoms in the linear backbone of SPACER are separated by at least two carbon atoms;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR132## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL; and

, where more than one substituent is a TAIL, each TAIL is optionally the same or different;

b) incubating the sample for a time sufficient for the dye compound to combine with nucleic acid polymers in the sample to form a staining profile of dye-nucleic acid complexes having detectable fluorescent signals, said staining pattern having a shape, location, spectral property, or intensity that is indicative of a characteristic of the sample; and

c) characterizing the sample based on said staining profile.

51. A method of characterizing a sample, according to claim 50, wherein the sample is characterized as a blebbing cell or blebbing nucleus based on the staining profile.

52. A method of characterizing a sample, according to claim 50, wherein the sample is characterized as containing a type of cell based on the staining profile.

53. A method of characterizing a sample, according to claim 52, wherein the sample is characterized as containing a type of blood cell based on the staining pattern.

54. A method of characterizing a sample as containing single stranded (ss) or double stranded (ds) nucleic acid polymers, according to claim 50, wherein the sample contains natural or synthetic nucleic acid polymers that are combined with the dye compound in a ratio of at least one or more molecules of the dye compound per base of the ss or base pair of the ds nucleic acid polymer to form a staining profile having a spectral property of fluorescence intensity at an emission wavelength that is indicative of ss or ds nucleic acid polymers.

55. A method of characterizing a sample, according to claim 54, wherein the ds nucleic acid polymer is DNA that is differentiated from ass nucleic acid polymer that is DNA.

56. A method of characterizing a sample, according to claim 54, wherein the sample contains a solution of purified nucleic acids.

57. A method of characterizing a sample, according to claim 54, wherein the nucleic acid polymers are in cell extracts.

58. A method of characterizing a sample, according to claim 50, wherein the sample is a solution comprising nucleic acid polymers separated by means of relative mobility;

where the solution is characterized with respect to purity of the solution, size of polymers in the solution, composition of polymers in the solution, or integrity of polymers in the solution based on the staining profile.

59. A method of characterizing a sample, according to claim 50, further comprising adding one or more additional reagents to the sample, where each additional reagent is capable of a response that is detectably different from the fluorescent signal of the dye-nucleic acid complex.

60. A method of characterizing a sample, according to claim 59, wherein the additional detection reagent is an antibody.

61. A method of characterizing a sample, according to claim 59, wherein the additional detection reagent is a stain selective for an organelle.

62. A method of characterizing a sample, according to claim 59, wherein the sample is a chromosome and one additional reagent that is added to the sample quenches or partially quenches the fluorescent signal from one or more of the dye-nucleic acid complexes, such that the chromosome is characterized as having a certain banding based on the staining pattern.

63. A method of determining cell membrane integrity comprising:

a) incubating a sample containing one or more cells with a first dye compound of the formula ##STR133## or having the formula ##STR134## wherein R² is ethyl or methyl;

X is O or S;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

R⁵ is alkyl having 1-6 carbons;

or a cyclic substituent that is a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or R⁵ is a TAIL;

R⁴ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or a halogen;

or a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

having 1-6 carbons, or aryl;

R³, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

R¹¹, R¹², R¹³, and R¹⁴, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-8 carbons;

or a TAIL;

or --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, O and S, such that the linkage begins and ends with a carbon atom, and contains any combination of ether, thioether, amine, ester, amide, or aliphatic, olefinic or aromatic carbon-carbon bonds, or aromatic carbon-nitrogen or nitrogen-nitrogen bonds;

wherein all heteroatoms in the linear backbone of SPACER are separated by at least two carbon atoms;

CAP and CAP'"'"', which may be the same or different, are --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR135## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL; and

, where more than one substituent is a TAIL, each TAIL is optionally the same or different;

for a time sufficient for the dye compound to combine with intracellular nucleic acids to form a first intracellular dye-nucleic acid complex having a detectable fluorescent signal; and

c) determining cell membrane integrity of cells in the sample based on presence of the detectable fluorescent signal, where the presence of the detectable fluorescent signal indicates that the cell membrane integrity is compromised and the absence of the detectable fluorescent signal indicates that the cell membrane integrity is intact.

64. A method of determining cell membrane integrity, according to claim 63, wherein the dye compound has an overall positive charge of 2+ or greater.

65. A method of determining cell membrane integrity, according to claim 63, wherein the dye compound has an overall positive charge of 3+ or greater.

66. A method of determining cell membrane integrity, according to claim 63, wherein the sample contains eukaryotic cells.

67. A method of determining cell membrane integrity, according to claim 63, wherein the sample contains prokaryotic cells.

68. A method of quantitating nucleic acids in a sample, comprising

a) combining an aliquot of a sample, optionally the entire sample, that contains or is thought to contain a nucleic acid, with mixture containing a dye compound of the formula ##STR136## or having the formula ##STR137## wherein R² is ethyl or methyl;

X is O or S;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

R⁵ is alkyl having 1-6 carbons;

or a cyclic substituent that is a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or R⁵ is a TAIL;

R⁴ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or a halogen;

or a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

having 1-6 carbons, or aryl;

R³, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

R¹¹, R¹², R¹³, and R¹⁴, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-8 carbons;

or a TAIL;

or --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, O and S, such that the linkage begins and ends with a carbon atom, and contains any combination of ether, thioether, amine, ester, amide, or aliphatic, olefinic or aromatic carbon-carbon bonds, or aromatic carbon-nitrogen or nitrogen-nitrogen bonds;

wherein all heteroatoms in the linear backbone of SPACER are separated by at least two carbon atoms;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR138## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL; and

, where more than one substituent is a TAIL, each TAIL is optionally the same or different;

b) incubating the aliquot and mixture for a time sufficient for the dye compound to combine with the nucleic acid in the sample to form a dye-nucleic acid complex that gives a detectable fluorescent signal; and

c) quantifying the nucleic acid present in said sample based on comparison of the detectable fluorescent signal with a fluorescent standard characteristic of a given amount of nucleic acid.

69. A method of quantitating nucleic acids in a sample, according to claim 68, wherein said sample or said mixture is an electrophoretic gel.

70. A method of quantitating nucleic acids in a sample, according to claim 68, wherein said nucleic acids are natural or synthetic oligonucleotides that are ssDNA, dsDNA, RNA, or RNA/DNA hybrids.

71. a method of quantitating nucleic acids in a sample, according to claim 68, wherein said nucleic acids are polymerase chain reaction amplification products.

72. A method of quantitating nucleic acids in a sample of cells that has been grown in a tissue or in a culture medium, according to claim 68, wherein said aliquot is an aliquot prepared by the lysis of all or a portion of said cells.

73. A method of quantitating nucleic acids in a sample, according to claim 72, further comprising

d) taking one or more additional aliquots from the sample over time, where each aliquot is prepared by lysis of a portion of said cells;

e) repeating steps a) through c) for each aliquot; and

f) comparing the amount of nucleic acid in the sample over time to determine cell proliferation in the sample.

74. A method of quantitating ds nucleic acids in a sample, according to claim 68, wherein the aliquot of a sample that contains a specified amount of total nucleic acid is combined with more than one molar equivalent of the dye, where the dye is selective for ds nucleic acids, to form a dye-nucleic acid complex that gives a detectable fluorescent signal having fluorescence intensity at an emission wavelength that is indicative of ds nucleic acid polymers;

quantifying the ds nucleic acid present in said sample based on comparison of the detectable fluorescent signal with a fluorescent standard characteristic of a given amount of ds nucleic acid.

75. A method of analyzing nucleic acid-analyte interactions, comprising:

a) forming a fluorescent complex comprising a nucleic acid polymer and one or more dye molecules of the formula;

##STR139## or having the formula ##STR140## wherein R² is ethyl or methyl;

X is O or S;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

R⁵ is alkyl having 1-6 carbons;

or a cyclic substituent that is a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or R⁵ is a TAIL;

R⁴ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or a halogen;

or a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ and R⁹, which can be the same or different, are independently H;

or alkyl groups having 1-6 carbons;

or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring, and where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

having 1-6 carbons, or aryl;

R³, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

R¹¹, R¹², R¹³, and R¹⁴, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-8 carbons;

or a TAIL;

or --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons;

or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, O and S, such that the linkage begins and ends with a carbon atom, and contains any combination of ether, thioether, amine, ester, amide, or aliphatic, olefinic or aromatic carbon-carbon bonds, or aromatic carbon-nitrogen or nitrogen-nitrogen bonds;

wherein all heteroatoms in the linear backbone of SPACER are separated by at least two carbon atoms;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR141## where R²¹, R²² and Ψ

^- are as defined previously;

such that at least one of R³, R⁴, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL; and

, where more than one substituent is a TAIL, each TAIL is optionally the same or different;

wherein the fluorescent complex has a set of characteristic spectral properties;

b) combining the fluorescent complex with a sample that contains or is thought to contain an analyte that interacts with the nucleic acid polymer;

c) detecting a change in the spectral properties of the fluorescent complex; and

d) determining the presence or activity of the analyte in said sample based on comparison of the change in spectral properties of the complex with a fluorescent standard characteristic of analyte activity.

76. A method of analyzing nucleic acid-analyte interactions, according to claim 75, wherein the sample is a cell that is combined with the fluorescent complex by artificial means.

77. A method of analyzing nucleic acid-analyte interactions, according to claim 75, wherein the sample contains cell-free nucleic acid polymers.

78. A method analyzing nucleic acid-analyte interactions, according to claim 75, wherein the analyte is a protein.

79. A method of analyzing nucleic acid-analyte interactions, according to claim 75, wherein the analyte is a drug.

80. A compound having the formula ##STR142## wherein R²⁴ is a linear or branched alkyl having 1-6 carbons;

and Ψ

^- is a biologically compatible counterion.

81. A compound of the formula ##STR143## wherein each R¹ is independently H;

or an alkyl group having from 1-6 carbons;

an alkoxy group having from 1-6 carbons;

or a trifluoromethyl;

or a halogen; and

t=1-4;

R² is an alkyl group having 1-6 carbons;

X is O, S, Se or NR¹⁵, where R¹⁵ is an alkyl group having 1-6 carbons;

or X is CR¹⁶ R¹⁷ where R¹⁶ and R¹⁷, which may be the same or different, are independently alkyl groups having 1-6 carbons, or R¹⁶ and R¹⁷ taken in combination complete a five or six membered saturated ring;

n=0, 1 or2;

Ψ

^- is a biologically compatible counterion;

Q has the formula Q 1 or Q2 ##STR144## wherein Y is --CR³ ═

CR⁴ --;

p and m=0 or 1, such that p+m=1;

R⁵ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or R⁵ is a TAIL;

R⁴ is an alkyl, alkenyl, polyalkenyl, alkynyl or polyalkynyl group having 1-6 carbons;

or a halogen;

or a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

where R⁸ is an alkyl group having 1-6 carbons, or 1-2 alicyclic or aromatic rings; and

R⁹ is H, an alkyl group having 1-6 carbons, or 1-2 alicyclic or aromatic rings;

or R⁸ and R⁹ taken in combination are --(CH₂)₄ -- or --(CH₂)₅ -- to give a 5 or 6 membered ring; and

where R¹⁹ is alkyl having 1-6 carbons, or perfluoroalkyl having 1-6 carbons, or aryl;

R³, R⁶ and R⁷, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-10 carbons;

or --OR⁸, --SR⁸, --(NR⁸ R⁹);

or --OSO₂ R¹⁹ ;

or a TAIL;

or R⁶ and R⁷, taken in combination are --(CH₂)_v -- where v=3 or 4, or R⁶ and R⁷ form a fused aromatic ring according to formula Q2;

R¹¹, R¹², R¹³, and R¹⁴, 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 a substituted or unsubstituted aryl or heteroaryl;

or a substituted or unsubstituted cycloalkyl having 3-8 carbons;

or a TAIL;

or --OR⁸, --SR⁸, or --(NR⁸ R⁹);

TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

wherein

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"', which may be the same or different are linear or branched, cyclic or heterocyclic, saturated or unsaturated covalent linkages, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds;

or single, double, triple or aromatic carbon-carbon bonds;

or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen-nitrogen or nitrogen-oxygen bonds;

or aromatic or heteroaromatic bonds;

CAP and CAP'"'"', which may be the same or different, are --O--R²¹, --S--R²¹, --NR²¹ R²², or --N⁺ R²¹ R²² R²³ Ψ

^- ;

wherein

R²¹, R²², and R²³ are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons;

or, one or more of R²¹, R²² and R²³, taken in combination with SPACER or SPACER'"'"' or R²⁰ forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S;

where Ψ

^- is a biologically compatible counterion;

or

CAP and CAP'"'"' are independently ##STR145## where R²¹, R²² and Ψ

^- are as defined previously;

such that when R⁵ is a TAIL, LINK is a single bond; and

, where more than one of R², R³, R⁴, R⁵, R⁶, R⁷, R¹¹, R¹², R¹³, and R¹⁴ is a TAIL, each TAIL is optionally the same or different.

82. A compound, as claimed in claim 81, of the formula ##STR146## wherein R² is an alkyl group having 1-2 carbons;

X is O or S;

n=0 or 1;

R³ is H;

R⁵ is an alkyl having 1-6 carbons; and

where TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP;

LINK is a single covalent bond, --O--, --S--, or --NR²⁰ --;

where R²⁰ is H, a linear or branched alkyl having 1-8 carbons, or R²⁰ is --SPACER'"'"'--CAP'"'"';

SPACER and SPACER'"'"' independently have the formula --(CH₂)_k --, where k=1-8;

CAP and CAP'"'"', which may be the same or different, are --NR²¹ R²² or --N⁺ R²¹ R²² R²³ Ψ

^- ;

where R²¹, R²², and R²³ are independently methyl or ethyl.

83. A compound, as claimed in claim 82, wherein R⁴ is a TAIL.

84. A compound, as claimed in claim 82, wherein R⁴ is a halogen, --OR⁸, --SR⁸, --(NR⁸ R⁹) or --OSO₂ R¹⁹.

85. A compound, as claimed in claim 82, wherein R⁴ is an alkyl having 1-6 carbons.

86. A compound, as claimed in claim 81, wherein none of R³, R⁴, R⁶, R⁷, R¹¹, R¹², R¹³ and R¹⁴ is a substituted or unsubstituted aryl or heteroaryl or a substituted or unsubstituted cycloalkyl having 3-10 carbons.

87. A compound, as claimed in claim 86, wherein p is 0 and m is 1.

88. A compound, as claimed in claim 86, wherein each R¹ is H, R² is methyl or ethyl, and X is O or S.

89. A compound, as claimed in claim 86, wherein p=0, m=1;

and n=0 or 1.

90. A compound, as claimed in claim 86, wherein R⁴ is a halogen, --OR⁸, --SR⁸, --(NR⁸ R⁹), or --OSO₂ R¹⁹.

91. A compound, as claimed in claim 86, wherein R⁴ is an alkyl having 1-6 carbons.

92. A compound, as claimed in claim 86, wherein R⁴ is a TAIL.

93. A compound, as claimed in claim 86, wherein R²⁰ is H or a linear or branched alkyl having 1-8 carbons.

94. A compound, as claimed in claim 86, wherein SPACER and SPACER'"'"' independently have the formula --(CH₂)_k --, where k=1-8.

95. A compound, as claimed in claim 86, wherein R²¹, R²², and R²³ are independently methyl or ethyl.

96. A compound, as claimed in claim 86, wherein R⁵ is a TAIL.

97. A compound, as claimed in claim 86, wherein R⁵ is an alkyl having 1-6 carbons.