Fluorescent stokes shift probes for polynucleotide hybridization

• US 4,996,143 A
• Filed: 04/13/1990
• Issued: 02/26/1991
• Est. Priority Date: 12/23/1985
• Status: Expired due to Term

• Current Assignee: Syngene Incorporated
• Original Assignee: Syngene Incorporated
• Inventors: Heller, Michael J., Jablonski, Edward J.
• Primary Examiner(s): Yarbrough, Amelia Burgess
• Application Number:
  US07/511,834
• Time in Patent Office: 319 Days
• Field of Search: 435/6, 435/803, 436/501, 436/800, 537/27, 935/78
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/705 for herpetoviridae, e.g. herpes simplex, varicella zoster
• CPC Class Codes: G01N 33/533 with fluorescent label
• CPC Class Codes: Y10S 436/80 Fluorescent dyes, e.g. rhodamine

Abstract

Fluorescent stokes shift probes for polynucleotide hybridization assays are designed to provide predetermined nucleotide base unit spacings between the donor and acceptor fluorophores. When the probes are hybridized to the target polynucleotide the fluorophores paired for non-radiative energy transfer are separated by 2 to 7 nucleotide base units. The fluorophores are attached to the DNA or RNA probes by linker arms having lengths of 4 to 30 Angstroms. Fluorescein is a preferred donor for use with a Texas Red acceptor.

Claims

1. The spectroscopy method for detecting a target single-strand polynucleotide sequence in a polynucleotide sample in which either (i) a fluorescent polynucleotide single probe sequence complementary to said target sequence is hybridized thereto, or (ii) a plurality of probes of such sequences complementary to sequentially adjacent portions of said target sequences are hybridized thereto, wherein the improvement comprises having present in said single probe or in said plurality of probes at least one pair of fluorescent moieties connected by linker arms to nucleic acid base units, said fluorescent moieties comprising respectively donor and acceptor moieties selected so that the emission spectrum of the donor moiety overlaps the excitation spectrum of the acceptor moiety to permit non-radioactive energy transfer with efficient fluorescent emission by the acceptor fluorophores, the wavelength maximum of the emission spectrum of the acceptor moiety being at least 100 nm greater than the wavelength maximum of the excitation spectrum of the donor moiety, said linker arms having lengths of 4 to 30 Angstroms, the donor and acceptor moieties being connected to non-contiguous base units in said single probe or to base units in said plural probes other than 3'"'"' and 5'"'"' and units thereof, when said single probe or said plural probes are hybridized to the target sample the base units to which said donor and acceptor moieties are connected being paired through hybridization to base units of said target sequence which are separated by 2 to 7 intervening nucleotide base units of the target sequence.

2. The method improvement of claim 1 in which said donor and acceptor moieties are on a single probe.

3. The method improvement of claim 1 in which said donor and acceptor moieties are on a pair of probes.

4. The method of claim 1, 2, or 3 in which said donor moiety is fluorescein and said acceptor moiety is Texas Red.

5. The method of claim 1 in which said linker arms have lengths of from 10 to 25 Angstroms.

6. The method of claim 1 in which when said single probes or said dual probe are hybridized to the target sequence the base units connected to said donor and acceptor moieties are paired with nucleotide base units of the target sequence which are separated by 3 to 6 intervening base units.

11. The method of claim 1 or 7 in which said donor and acceptor moieties are on a single probe and are connected to base units thereof other than the 3'"'"' and 5'"'"' end units and which are separated by 4 to 6 intervening base units.

12. The method of claim 1 or 7 in which said moieties are on a pair of probes respectively having 3'"'"' and 5'"'"' ends hybridizing to adjacent base units of the target polynucleotide and when so hybridized the donor and acceptor moieties being separated by 4 to 6 intervening base units.

13. The methods of claim 11 or 12 in which said donor moiety is fluorescein and said acceptor moiety is Texas Red.

7. The spectroscopy method for detecting a target single-strand polynucleotide sequence in a polynucleotide sample immobilized on a support in which either (i) a fluorescent polynucleotide single probe sequence complementary to said target sequence is hybridized thereto, or (ii) a plurality of probes of such sequences complementary to sequentially adjacent portions of said target sequences are hybridized thereto, said probes being synthetic polynucleotides of from 10 to 100 base units in length, wherein the improvement comprises having present in said single probe or in said plurality of probes at least one pair of fluorescent moieties connected by linker arms to nucleic acid base units, said fluorescent moieties comprising respectively donor and acceptor moieties selected so that the emission spectrum of the donor moiety overlaps the excitation spectrum of the acceptor moiety to permit non-radiative energy transfer with efficient fluorescent emission by the acceptor fluorophore, the wavelength maximum of the emission spectrum of the acceptor moiety being at least 100 nm greater than the wavelength maximum of the excitation spectrum of the donor moiety, said linker arms having lengths of 10 to 25 Angstroms, the donor and acceptor moieties being connected to non-contiguous base units in said single probe and to base units in said plural probes other than the 3'"'"' and 5'"'"' end units, when said single probe or plural probes are hybridized to the target polynucleotide the base units to which said donor and acceptor moieties are connected being paired with hybridized base units of said target sequence which are separated by 2 to 7 intervening nucleotide base units of the target sequence.

8. The method of claim 7 in which said donor and acceptor moieties are on a single probe.

9. The method of claim 7 in which said donor and acceptor moieties are on a pair of probes.

10. The method of claim 7, 8, of 9 in which said donor moiety is fluorescein and said acceptor moiety is Texas Red.

14. A polynucleotide probe for fluorescent spectroscopy assaying of a target single-stranded polynucleotide, comprising a synthetic single-stranded polynucleotide containing from 10 to 100 nucleic acid base units, two of said base units having respectively attached thereto by separate linker arms a donor fluorescent moiety and an acceptor fluorescent moiety, said fluorescent moieties being selected so that the emission spectrum of the donor moiety overlaps the excitation spectrum of the acceptor moiety to permit non-radiative energy transfer with efficient fluroescent emission by the acceptor fluorophore, the wavelength maximum of the emission spectrum of the acceptor moiety being at least 100 nm greater than the wavelength maximum of the excitation spectrum of the donor moiety, said linker arms having lengths of 4 to 30 Angstroms, said donor and acceptor moieties being connected to base units other than the 3'"'"' and 5'"'"' end units and which units are separated by 2 to 7 intervening base units.

15. The probe of claim 14 in which said linker arms have lengths of from 10 to 25 Angstroms.

16. The probe of claim 14 in which said donor moiety is fluorescein and said acceptor moiety in Texas Red.

17. A polynucleotide probe for fluorescent spectroscopy assaying of a target single-stranded polynucleotide, comprising a synthetic single-stranded polynucleotide containing from 10 to 100 nucleic acid base units, two of said base units having respectively attached thereto by linker side chains a donor fluorescent moiety and an acceptor fluorescent moiety, said fluorescent moieties being selected so that the emission spectrum of the donor moiety overlaps the excitation spectrum of the acceptor moiety to permit non-radiative energy transfer with efficient fluorescent emission by the acceptor fluorophore, the wavelength maximum of the emission spectrum of the acceptor moiety being at least 100 nm greater than the wavelength maximum of the excitation spectrum of the donor moiety, said linker side chains having lengths of 10 to 25 Angstroms, said donor and acceptor moieties being connected to base units other than the 3'"'"' and 5'"'"' end units and which units are separated by 3 to 6 intervening base units.

18. The probe of claim 17 in which said donor moiety is fluorescein and said acceptor moiety is Texas Red.

19. A pair of polynucleotide probes for fluorescent spectroscopy assaying of a target single-stranded polynucleotide, comprising first and second synthetic single-stranded polynucleotide probes each containing from 10 to 100 nucleic acid base units, said probes hybridizing to adjacent sequences of said target polynucleotide with the 3'"'"' end of the first probe adjacent to the 5'"'"' end of the second probe, said probes having fluorescent moieties attached to base units thereof other than said adjacent 3'"'"' and 5'"'"' end units by linker arms having lengths of 4 to 30 Angstroms, one of said arms being connected to a donor moiety and other to an acceptor moiety, said moieties being selected so that the emission spectrum of the donor moiety overlaps the excitation spectrum of the acceptor moiety to permit non-radiative energy transfer with efficient fluorescent emission by the acceptor fluorophore, the wavelength maximum of the emission spectrum of the acceptor moiety being at least 100 nm greater than the wavelength maximum of the excitation spectra of the donor moiety, said linker arms having lengths of from 4 to 30 Angstroms, and being connected to base units other than the 3'"'"' and 5'"'"' end units, when said probes are hybridized to the target polynucleotide sequences the base units to which said donor and acceptor moieties are connected being paired with hybridized base units of said target sequences which are separated by 2 to 7 intervening base units.

20. The pair of probes of claim 19 in which said linker arms have lengths of from 10 to 25 Angstroms.

21. The pair of probes of claim 19 in which said donor moiety is fluorescein and acceptor moiety is Texas Red.

22. A pair of polynucleotide probes for fluorescent spectroscopy assaying of a target single-stranded polynucleotide, comprising first and second synthetic single-stranded polynucleotide probes hybridizing to adjacent sequences of said target polynucleotide with the 3'"'"' end of the first probes adjacent to the 5'"'"' end of the second probe, said probes having fluorescent moieties attached to base units other than said adjacent 3'"'"' and 5'"'"' end units by linker arms having lengths of 10 to 25 Angstroms, one of said side chains being connected to a donor moiety and the other to an acceptor moiety, said moieties being selected so that the emission spectrum of the donor moiety overlaps the excitation spectrum of the acceptor moiety to permit non-radiative energy transfer with efficient fluorescent emission by the acceptor fluorophore, the wavelength maximum of the emission spectrum of the acceptor moiety being at least 100 nm greater than the wavelength maximum of the excitation spectrum of the donor moiety, said linker arms having lengths of from 10 to 25 Angstroms, and being connected to base units other than the 3'"'"' and 5'"'"' end units when said probes are hybridized to the target polynucleotide sequences the base units to which said donor and acceptor moieties are connected being paired with base units of the target sequences which are separated by 4 to 6 intervening base units.

23. The pair of probes of claim 22 in which said donor moiety is fluorescein and said acceptor moiety is Texas Red.

24. A method of detecting a target nucleic acid comprising hybridizing a poly- or oligonucleotide probe or proves to said nucleic acid, wherein said probe or probes have or hybridize to form a pair of fluorescent moieties connected to separate nucleotides and wherein the nucleotides connected to the fluorescent moieties are separated by as least two but not more than seven nucleotides, and detecting the hybridization by fluorescent means based on the interaction between the moieties.

25. The method of claim 24, wherein the fluorescent moieties are separated by at least three but not more than six nucleotides.

26. The method of claim 24, wherein the fluroescent moieties are separated by at least four but not more than six nucleotides.

27. A poly- or oligonucleotide probe comprising a pair of fluorescent moieties connected to separate nucleotides and wherein the nucleotides connected to the fluorescent moieties are separated by at least two but not more than seven nucleotides.

28. The nucleotide probe of claim 27, wherein the fluorescent moieties are separated by at least three but not more than six nucleotides.

29. The nucleotide probe of claim 27, wherein the fluorescent moieties are separated by at least four but not more than six nucleotides.