U.S. patent number 5,800,996 [Application Number 08/726,462] was granted by the patent office on 1998-09-01 for energy transfer dyes with enchanced fluorescence.
This patent grant is currently assigned to The Perkin Elmer Corporation. Invention is credited to Linda G. Lee, Barnett Rosenblum, Sandra L. Spurgeon.
United States Patent |
5,800,996 |
Lee , et al. |
September 1, 1998 |
**Please see images for:
( Certificate of Correction ) ** |
Energy transfer dyes with enchanced fluorescence
Abstract
Novel linkers for linking a donor dye to an acceptor dye in an
energy transfer fluorescent dye are provided. These linkers
faciliate the efficient transfer of energy between a donor and
acceptor dye in an energy transfer dye. One of these linkers for
linking a donor dye to an acceptor dye in an energy transfer
fluorescent dye has the general structure R.sub.21 Z.sub.1
C(O)R.sub.22 R.sub.28 where R.sub.21 is a C.sub.1-5 alkyl attached
to the donor dye, C(O) is a carbonyl group, Z.sub.1 is either NH,
sulfur or oxygen, R.sub.22 is a substituent which includes an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon, and R.sub.28 includes a functional group which
attaches the linker to the acceptor dye.
Inventors: |
Lee; Linda G. (Palo Alto,
CA), Spurgeon; Sandra L. (San Mateo, CA), Rosenblum;
Barnett (San Jose, CA) |
Assignee: |
The Perkin Elmer Corporation
(Foster City, CA)
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Family
ID: |
27093992 |
Appl.
No.: |
08/726,462 |
Filed: |
October 4, 1996 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
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642330 |
May 3, 1996 |
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672196 |
Jun 27, 1996 |
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Current U.S.
Class: |
435/6.12;
435/91.2; 536/25.3; 536/26.6 |
Current CPC
Class: |
C07H
21/00 (20130101); C09B 11/04 (20130101); C09B
11/08 (20130101); C09B 11/24 (20130101); C09B
23/083 (20130101); C12Q 1/6869 (20130101); C09B
69/00 (20130101); C12Q 1/6869 (20130101); C12Q
2563/107 (20130101); C12Q 2535/101 (20130101) |
Current International
Class: |
C07H
21/00 (20060101); C09B 11/00 (20060101); C09B
11/24 (20060101); C09B 23/08 (20060101); C09B
11/04 (20060101); C09B 23/00 (20060101); C09B
69/00 (20060101); C12Q 001/68 () |
Field of
Search: |
;435/6,91.2
;536/25.3,26.6 |
References Cited
[Referenced By]
U.S. Patent Documents
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4996143 |
February 1991 |
Heller et al. |
5188934 |
February 1993 |
Menchen et al. |
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Foreign Patent Documents
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0 201 751 A2 |
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Nov 1985 |
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EP |
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0 229 943 A2 |
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Jul 1987 |
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EP |
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0 601 889 A2 |
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Jun 1994 |
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EP |
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WO 93/13224 |
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Jul 1993 |
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WO |
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WO 95/21266 |
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Aug 1995 |
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WO |
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Other References
Stenzel et al., Clin. Chem. 39(11):228-2232, 1992. .
Lee et al., Nucleic Acid Res. 20(10):2471-2483, 1992. .
Drake, et al., Science, vol. 251, pp. 1574-1579 (1991). .
Cooper, et al. Biochemistry, vol. 29, pp. 9261-9268 (1990). .
Ju, et al, PNAS USA 92 4347-4351 (1995). .
Tyagi, et al., Nature Biotechnology, vol. 14, pp. 303-308 (1966).
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Cardullo, et al. "Detection of nucleic acid hybridization by
nonradiative fluorescence resonance energy transfer", Proc. Nat.
Acad. Sci., vol. 85, pp. 8790-8794 (Dec. 1988). .
Clegg, "Fluorescence Resonance Energy Transfer and Nucleic Acids",
Methods in Enzymology, vol. 211, pp. 353-388 (1992). .
Jue, et al., "Design and Synthesis of Fluorescence Energy Transfer
Dye-Labeled Primers and Their Application for DNA Sequencing and
Analysis", Analytical Biochemistry, vol. 231, pp. 131-140 (1995).
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Jue, et al., "Fluorescence energy transfer dye-labeled primers for
DNA sequencing and analysis", Proc. Natl. Acad. Sci., vol. 92, pp.
4347-4351 (1995). .
Lee, et al., "Allelic discrimination by nick-translation PCR with
fluorogenic probes", Nucleic Acids Research, vol. 21, No. 16, pp.
3761-3766 (1993). .
Lee, et al., "DNA sequencing and dye-labeled terminates and T7 DNA
polymerase: effect of dyes and dNTPs on incorporation of
dye-terminators and probability analysis of termination fragments",
vol. 20, No. 10, pp. 2471-2483 (1992). .
Livak, et al., "Oligonucleotides with Fluorescent Dyes at Opposite
Ends Provide a Quenched Probe System Useful for Detecting PCR
Produce and Nucleic Acid Hybridization", PCR Methods and
Applications, pp. 357-362 (1995). .
Shipchandler, et al., "4'-[Aminomethyl] fluorescein and Its N-Alkyl
Derivatives: Useful Reagents in Immunodiagnostic Techniques",
Analytical Biochemistry, vol. 162, pp. 89-101 (1987). .
Stryer, et al., "Energy Transfer: A Spectroscopic Ruler", Proc.
Natl'l Acad. Sci., pp. 719-726 (1967). .
Wu, et al., "Resonance Energy Transfer:Methods and Applications",
Analytical Biochemistry, vol. 218, pp. 1-13 (1994)..
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Primary Examiner: Houtteman; Scott W.
Attorney, Agent or Firm: Wilson Sonsini Goodrich &
Rosati
Parent Case Text
RELATIONSHIP TO COPENDING APPLICATIONS
This application is a continuation-in-part of "ENERGY TRANSFER DYES
WITH ENHANCED FLUORESCENCE," application Ser. No.: 08/642,330;
Filed: May 3, 1996 and U.S. application Ser. No.: 08/672,196;
filed: Jun. 27, 1996; entitled: "4,7-DICHLORORHODAMINE DYES" which
are incorporated herein by reference.
Claims
What is claimed is:
1. An energy transfer dye having the structure ##STR121## where
DONOR is a dye capable of absorbing light at a first wavelength and
emitting excitation energy in response;
ACCEPTOR is dye which is capable of absorbing the excitation energy
emitted by the donor dye and fluorescing at a second wavelength in
response;
C(O) is a carbonyl group;
Z.sub.1 is selected from the group consisting of NH, sulfur and
oxygen;
R.sub.21 is a C.sub.1-5 alkyl attached to the donor dye;
R.sub.22 is a substituent selected from the group consisting of an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon; and
R.sub.28 includes a functional group which attaches the linker to
the acceptor dye.
2. The energy transfer dye according to claim 1 wherein R.sub.22 is
a five or six membered ring selected from the group consisting of
cyclopentene, cyclohexene, cyclopentadiene, cyclohexadiene, furan,
thiofuran, pyrrole, isopyrole, isoazole, pyrazole, isoimidazole,
pyran, pyrone, benzene, pyridine, pyridazine, pyrimidine, pyrazine
oxazine, indene, benzofuran, thionaphthene, indole and
naphthalene.
3. The energy transfer dye according to claim 1 wherein the linker
has the structure ##STR122## wherein Z.sub.2 is selected from the
group consisting of NH, sulfur and oxygen; and
R.sub.29 is a C.sub.1-5 alkyl.
4. The energy transfer dye according to claim 1 wherein the linker
has the structure ##STR123##
5. The energy transfer dye according to claim 1 wherein the donor
dye is a member of the xanthene class of dyes.
6. The energy transfer dye according to claim 5 wherein the
acceptor dye is a member of a class of dyes selected from the group
consisting of xanthene, cyanine, phthalocyanine and squaraine
dyes.
7. The energy transfer dye according to claim 1 wherein the donor
dye is a member of a class of dyes selected from the group
consisting of fluorescein, rhodamine and asymmetric benzoxanthene
dyes.
8. The energy transfer dye according to claim 7 wherein the
acceptor dye is a member of a class of dyes selected from the group
consisting of xanthene, cyanine, phthalocyanine and squaraine
dyes.
9. The energy transfer dye according to claim 1 wherein the donor
dye is selected from the group consisting of carboxyfluoresceins,
4,7-dichlorofluorescein dyes, asymmetric benzoxanthene dyes,
rhodamine, 4,7-dichlororhodamine dyes, carboxyrhodamines,
N,N,N',N'-tetramethyl carboxyrhodamines, carboxy R110, and carboxy
R6G.
10. The energy transfer dye according to claim 1 wherein the
acceptor dye is selected from the group consisting of
4,7-dichlorofluorescein dyes, asymmetric benzoxanthene dyes,
rhodamine, 4,7-dichlororhodamine dyes, carboxyrhodamines,
N,N,N',N'-tetramethyl carboxyrhodamines, carboxy R110, carboxy R6G,
carboxy-X-rhodamines and Cy5.
11. The energy transfer dye according to claim 1 wherein the
acceptor dye is selected from the group consisting DR110-2, DR6G-2,
DTMR and DROX.
12. An energy transfer dye having the structure ##STR124## where
C(O) is a carbonyl group;
Y.sub.1 and Y.sub.2 are each independently selected from the group
consisting of hydroxyl, oxygen, iminium and amine;
Z.sub.1 is selected from the group consisting of NH, sulfur and
oxygen;
R.sub.11 -R.sub.17 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, amino, ammonium, amido,
nitrile, alkoxy, phenyl, substituted phenyl, where adjacent
substituents are taken together to form a ring, and combinations
thereof;
R.sub.21 is a C.sub.1-5 alkyl;
R.sub.22 is a substituent selected from the group consisting of an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon;
R.sub.28 includes a functional group which attaches the linker to
the acceptor dye; and
ACCEPTOR is dye which is capable of absorbing excitation energy
emitted by a member of the xanthene class of dyes.
13. The energy transfer dye according to claim 12 wherein R.sub.22
is a five or six membered ring selected from the group consisting
of cyclopentene, cyclohexene, cyclopentadiene, cyclohexadiene,
furan, thiofuran, pyrrole, isopyrole, isoazole, pyrazole,
isoimidazole, pyran, pyrone, benzene, pyridine, pyridazine,
pyrimidine, pyrazine oxazine, indene, benzofuran, thionaphthene,
indole and naphthalene.
14. The energy transfer dye according to claim 12 wherein the dye
has the structure ##STR125## wherein Z.sub.2 is selected from the
group consisting of NH, sulfur and oxygen; and
R.sub.29 is a C.sub.1-5 alkyl.
15. The energy transfer dye according to claim 12 wherein the
linker has the structure ##STR126##
16. The energy transfer dye according to claim 12 wherein the
acceptor dye is a member of a class of dyes selected from the group
consisting of xanthene, cyanine, phthalocyanine and squaraine
dyes.
17. The energy transfer dye according to claim 12 wherein the donor
dye is a member of a class of dyes selected from the group
consisting of fluorescein, rhodamine and asymmetric benzoxanthene
dyes.
18. The energy transfer dye according to claim 17 wherein the
acceptor dye is a member of a class of dyes selected from the group
consisting of xanthene, cyanine, phthalocyanine and squaraine
dyes.
19. The energy transfer dye according to claim 12 wherein the donor
dye is selected from the group consisting of carboxyfluoresceins,
4,7-dichlorofluorescein dyes, asymmetric benzoxanthene dyes,
rhodamine, carboxyrhodamines, N,N,N',N'-tetramethyl
carboxyrhodamines, carboxy R110, and carboxy R6G.
20. The energy transfer dye according to claim 19 wherein the
acceptor dye is a member of a class of dyes selected from the group
consisting of xanthene, cyanine, phthalocyanine and squaraine
dyes.
21. The energy transfer dye according to claim 12 wherein the
acceptor dye is selected from the group consisting of
4,7-dichlorofluorescein dyes, asymmetric benzoxanthene dyes,
rhodamine, 4,7-dichlororhodamine dyes, carboxyrhodamines,
N,N,N',N'-tetramethyl carboxyrhodamines, carboxy R110, carboxy R6G,
carboxy-X-rhodamines and Cy5.
22. The energy transfer dye according to claim 12 wherein the
acceptor has the general structure ##STR127## wherein: Y.sub.1 and
Y.sub.2 are each independently selected from the group consisting
of hydroxyl, oxygen, iminium and amine;
R.sub.11 -R.sub.16 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine, bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, amino, ammonium, amido,
nitrile, alkoxy, phenyl, substituted phenyl, where adjacent
substituents are taken together to form a ring, and combinations
thereof;
X.sub.1 -X.sub.5 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine, bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, amino, ammonium, amido,
nitrile, alkoxy, where adjacent substituents are taken together to
form a ring, and combinations thereof; and
one of X.sub.3 and X.sub.4 is attached to the R.sub.28 group.
23. The energy transfer dye according to claim 12 wherein the
acceptor dye has the general structure ##STR128## wherein: R.sub.1
-R.sub.4 are each independently selected from the group consisting
of hydrogen, and alkyl or where one or more of the groups of
R.sub.1 and R.sub.5, R.sub.2 and R.sub.6, R.sub.3 and R.sub.8,
R.sub.4 and R.sub.9 are taken together to form a ring;
R.sub.5 -R.sub.10 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine, bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, sulfone, amino,
ammonium, amido, nitrile, alkoxy, phenyl, and substituted phenyl,
or where two or more of R.sub.5 -R.sub.10 are taken together to
form one or more rings;
X.sub.1, X.sub.3 and X.sub.4 are each independently selected from
the group consisting of hydrogen, fluorine, chlorine, bromine,
iodine, carboxyl, alkyl, alkene, alkyne, sulfonate, sulfone, amino,
ammonium, amido, nitrile, or alkoxy;
X.sub.2 and X.sub.5 are chlorine; and
one of X.sub.3 and X.sub.4 are attached to R.sub.28.
24. The energy transfer dye according to claim 23 wherein the rings
formed by substituents R.sub.5 -R.sub.10 are 5, 6 or 7 membered
rings.
25. The energy transfer dye according to claim 23 wherein one or
more of the groups of R.sub.1 and R.sub.5, R.sub.2 and R.sub.6,
R.sub.3 and R.sub.8, R.sub.4 and R.sub.9 are taken together to form
a 5, 6 or 7 membered ring.
26. The energy transfer dye according to claim 23 wherein R.sub.1
-R.sub.10, X.sub.1, X.sub.3 and X.sub.4 are selected to correspond
to a dye selected from the group consisting of DR110-2, DR6G-2,
DTMR-2, and DROX-2.
27. An energy transfer fluorescent dye having the general structure
##STR129## wherein: Y.sub.1, Y.sub.1 ', Y.sub.2 and Y.sub.2 ' are
each independently selected from the group consisting of hydroxyl,
oxygen, iminium and amine,
R.sub.11 -R.sub.16 and R.sub.11 '-R.sub.16 ' are each independently
selected from the group consisting of hydrogen, fluorine, chlorine,
bromine, iodine carboxyl, alkyl, alkene, alkyne, sulfonate, amino,
ammonium, amido, nitrile, alkoxy, phenyl, substituted phenyl, where
adjacent substituents are taken together to form a ring, and
combinations thereof, and
X.sub.1 -X.sub.5 and X.sub.1 '-X.sub.5 ' are each independently
selected from the group consisting of hydrogen, fluorine, chlorine,
bromine, iodine, carboxyl, alkyl, alkene, alkyne, sulfonate, amino,
ammonium, amido, nitrile, alkoxy, where adjacent substituents are
taken together to form a ring, and combinations thereof;
Y.sub.1, Y.sub.2, R.sub.11 -R.sub.16, and X.sub.1 -X.sub.5 are
selected to correspond to a donor dye capable of absorbing light at
a first wavelength and emitting excitation energy in response;
Y.sub.1 ', Y.sub.2 ', R.sub.11 '-R.sub.16 ', and X.sub.1 '-X.sub.5
' are selected to correspond to an acceptor dye which is capable of
absorbing the excitation energy emitted by the donor dye and
fluorescing at a second wavelength in response; and
one of X.sub.3 and X.sub.4 and one of X.sub.3 ' and X.sub.4 ' are
taken together to form a linker linking the donor to the acceptor
dye such that energy is transferred from the donor to the acceptor
dye.
28. The energy transfer dye according to claim 27 wherein the
linker has a backbone attaching the donor to the acceptor which is
less than 9 atoms in length.
29. The energy transfer dye according to claim 27 wherein the
linker has the general formula R.sub.25 Z.sub.3 C(O) where R.sub.25
is a C.sub.1-4 alkyl attached to the donor dye at the X.sub.3 or
X.sub.4 substituent, Z.sub.3 is either NH, O or S, C(O) is a
carbonyl group and the terminal carbonyl group is attached to the
acceptor dye at the X.sub.3 ' or X.sub.4 ' substituent.
30. The energy transfer dye according to claim 27 wherein the
linker has the general formula R.sub.25 Z.sub.3 C(O)R.sub.26
Z.sub.4 C(O) where R.sub.25 is a C.sub.1-4 alkyl attached to the
donor dye at the X.sub.3 or X.sub.4 substituent, R.sub.26 is a
C.sub.1-4 alkyl, Z.sub.3 and Z.sub.4 are each independently either
NH, O or S, C(O) is a carbonyl group and the terminal carbonyl
group is attached to the acceptor dye at the X.sub.3 ' or X.sub.4 '
substituent.
31. An energy transfer fluorescent dye selected from the group
consisting of: 5 or 6 carboxy TMR-B-CF, 5 or 6 carboxy TMR-F-CF, 5
or 6 carboxy TMR-P-CF, 5 or 6 carboxy TMR-P-CF, 5 or 6 carboxy
TMR-A-CF, 5 or 6 carboxy TMR-D-CF, 5 or 6 carboxy TMR-N-CF, 5 or 6
carboxy ROX-CF, CY5-CF, 5 or 6 carboxy TMR-gly-5AMF and 5 or 6
carboxy TMR-5AMF, 5 or 6 carboxy CF-B-TMR-2, 5 or 6 carboxy
CFB-DR110-2, 5 or 6 carboxy CFB-DR6g-2, and 5 or 6 carboxy
CFB-DROX-2.
32. A fluorescently labeled reagent comprising:
a reagent selected from the group consisting of a nucleoside,
nucleoside monophosphate, nucleoside diphosphate, nucleoside
triphosphate, oligonucleotide and oligonucleotide analog, modified
to be linked to an energy transfer fluorescent dye; and
an energy transfer fluorescent dye attached to the reagent, the
energy transfer fluorescent dye including a dye having the
structure ##STR130## where DONOR is a dye capable of absorbing
light at a first wavelength and emitting excitation energy in
response;
ACCEPTOR is dye which is capable of absorbing the excitation energy
emitted by the donor dye and fluorescing at a second wavelength in
response;
C(O) is a carbonyl group;
Z.sub.1 is selected from the group consisting of NH, sulfur and
oxygen;
R.sub.21 is a C.sub.1-5 alkyl attached to the donor dye;
R.sub.22 is a substituent selected from the group consisting of an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon; and
R.sub.28 includes a functional group which attaches the linker to
the acceptor dye.
33. The fluorescently labeled reagent according to claim 32 wherein
R.sub.22 is a five or six membered ring selected from the group
consisting of cyclopentene, cyclohexene, cyclopentadiene,
cyclohexadiene, furan, thiofuran, pyrrole, isopyrole, isoazole,
pyrazole, isoimidazole, pyran, pyrone, benzene, pyridine,
pyridazine, pyrimidine, pyrazine oxazine, indene, benzofuran,
thionaphthene, indole and naphthalene.
34. The fluorescently labeled reagent according to claim 32 wherein
the linker has the structure ##STR131## wherein Z.sub.2 is selected
from the group consisting of NH, sulfur and oxygen; and
R.sub.29 is a C.sub.1-5 alkyl.
35. The fluorescently labeled reagent according to claim 32 wherein
the linker has the structure ##STR132##
36. The fluorescently labeled reagent according to claim 32 wherein
the donor dye is a member of the xanthene class of dyes.
37. The fluorescently labeled reagent according to claim 36 wherein
the acceptor dye is a member of a class of dyes selected from the
group consisting of xanthene, cyanine, phthalocyanine and squaraine
dyes.
38. The fluorescently labeled reagent according to claim 32 wherein
the donor dye is a member of a class of dyes selected from the
group consisting of fluorescein, rhodamine and asymmetric
benzoxanthene dyes.
39. The fluorescently labeled reagent according to claim 32 wherein
the donor dye is selected from the group consisting of
carboxyfluoresceins, 4,7-dichlorofluorescein dyes, asymmetric
benzoxanthene dyes, rhodamine, 4,7-dichlororhodamine dyes,
carboxyrhodamines, N,N,N',N'-tetramethyl carboxyrhodamines, carboxy
R110, and carboxy R6G.
40. The fluorescently labeled reagent according to claim 32 wherein
the acceptor dye is selected from the group consisting of
4,7-dichlorofluorescein dyes, asymmetric benzoxanthene dyes,
rhodamine, 4,7-dichlororhodamine dyes, carboxyrhodamines,
N,N,N',N'-tetramethyl carboxyrhodamines, carboxy R110, carboxy R6G,
carboxy-X-rhodamines and Cy5.
41. The fluorescently labeled reagent according to claim 32 wherein
the acceptor dye is selected from the group consisting DR110-2,
DR6G-2, DTMR and DROX.
42. The fluorescently labeled reagent according to claim 32 wherein
the reagent is selected from the group consisting of
deoxynucleoside, deoxynucleoside monophosphate, deoxynucleoside
diphosphate and deoxynucleoside triphosphate.
43. The fluorescently labeled reagent according to claim 42 wherein
the deoxynucleotides are selected from the group consisting of
deoxycytosine, deoxyadenosine, deoxyguanosine, and
deoxythymidine.
44. The fluorescently labeled reagent according to claim 32 wherein
the reagent is selected from the group consisting of
dideoxynucleoside, dideoxynucleoside monophosphate,
dideoxynucleoside diphosphate and dideoxynucleoside
triphosphate.
45. The fluorescently labeled reagent according to claim 32 wherein
the dideoxynucleotides are selected from the group consisting of
deoxycytosine, deoxyadenosine, deoxyguanosine, and
deoxythymidine.
46. The fluorescently labeled reagent according to claim 42 wherein
the reagent is an oligonucleotide.
47. The fluorescently labeled reagent according to claim 46 wherein
the oligonucleotide has a 3' end which is extendable by using a
polymerase.
48. A fluorescently labeled reagent comprising:
a reagent selected from the group consisting of a nucleoside,
nucleoside monophosphate, nucleoside diphosphate, nucleoside
triphosphate, oligonucleotide and oligonucleotide analog, modified
to be linked to an energy transfer fluorescent dye; and
an energy transfer fluorescent dye attached to the reagent, the
energy transfer fluorescent dye including a dye having the
structure ##STR133## where C(O) is a carbonyl group;
Y.sub.1 and Y.sub.2 are each independently selected from the group
consisting of hydroxyl, oxygen, iminium and amine;
Z.sub.1 is selected from the group consisting of NH, sulfur and
oxygen;
R.sub.11 -R.sub.17 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine, bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, amino, ammonium, amido,
nitrile, alkoxy, phenyl, substituted phenyl, where adjacent
substituents are taken together to form a ring, and combinations
thereof;
R.sub.21 is a C.sub.1-5 alkyl;
R.sub.22 is a substituent selected from the group consisting of an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon;
R.sub.28 includes a functional group which attaches the linker to
the acceptor dye; and
ACCEPTOR is dye which is capable of absorbing excitation energy
emitted by a member of the xanthene class of dyes.
49. The fluorescently labeled reagent according to claim 48 wherein
R.sub.22 is a five or six membered ring selected from the group
consisting of cyclopentene, cyclohexene, cyclopentadiene,
cyclohexadiene, furan, thiofuran, pyrrole, isopyrole, isoazole,
pyrazole, isoimidazole, pyran, pyrone, benzene, pyridine,
pyridazine, pyrimidine, pyrazine oxazine, indene, benzofuran,
thionaphthene, indole and naphthalene.
50. The fluorescently labeled reagent according to claim 48 wherein
the dye has the structure ##STR134## wherein Z.sub.2 is selected
from the group consisting of NH, sulfur and oxygen; and
R.sub.29 is a C.sub.1-5 alkyl.
51. The fluorescently labeled reagent according to claim 48 wherein
the linker has the structure ##STR135##
52. The fluorescently labeled reagent according to claim 48 wherein
the acceptor dye is a member of a class of dyes selected from the
group consisting of xanthene, cyanine, phthalocyanine and squaraine
dyes.
53. The fluorescently labeled reagent according to claim 48 wherein
the donor dye is a member of a class of dyes selected from the
group consisting of fluorescein, rhodamine and asymmetric
benzoxanthene dyes.
54. The fluorescently labeled reagent according to claim 53 wherein
the acceptor dye is a member of a class of dyes selected from the
group consisting of xanthene, cyanine, phthalocyanine and squaraine
dyes.
55. The fluorescently labeled reagent according to claim 48 wherein
the donor dye is selected from the group consisting of
carboxyfluoresceins, 4,7-dichlorofluorescein dyes, asymmetric
benzoxanthene dyes, rhodamine, carboxyrhodamines,
N,N,N',N'-tetramethyl carboxyrhodamines, carboxy R110, and carboxy
R6G.
56. The fluorescently labeled reagent according to claim 48 wherein
the acceptor dye is selected from the group consisting of
4,7-dichlorofluorescein dyes, asymmetric benzoxanthene dyes,
rhodamine, 4,7-dichlororhodamine dyes, carboxyrhodamines,
N,N,N',N'-tetramethyl carboxyrhodamines, carboxy R110, carboxy R6G,
carboxy-X-rhodamines and Cy5.
57. The fluorescently labeled reagent according to claim 48 wherein
the acceptor has the general structure ##STR136## wherein: Y.sub.1
and Y.sub.2 are each independently selected from the group
consisting of hydroxyl, oxygen, iminium and amine;
R.sub.11 -R.sub.16 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine, bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, amino, ammonium, amido,
nitrile, alkoxy, phenyl, substituted phenyl, where adjacent
substituents are taken together to form a ring, and combinations
thereof;
X.sub.1 -X.sub.5 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine, bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, amino, ammonium, amido,
nitrile, alkoxy, where adjacent substituents are taken together to
form a ring, and combinations thereof; and
one of X.sub.3 and X.sub.4 is attached to the R.sub.28 group.
58. The fluorescently labeled reagent according to claim 48 wherein
the acceptor dye has the general structure ##STR137## wherein:
R.sub.1 -R.sub.4 are each independently selected from the group
consisting of hydrogen, and alkyl or where one or more of the
groups of R.sub.1 and R.sub.5, R.sub.2 and R.sub.6, R.sub.3 and
R.sub.7, R.sub.4 and R.sub.8 are taken together to form a ring;
R.sub.5 -R.sub.10 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine, bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, sulfone, amino,
ammonium, amido, nitrile, alkoxy, phenyl, and substituted phenyl,
or where two or more of R.sub.5 -R.sub.10 are taken together to
form one or more rings;
X.sub.1, X.sub.3 and X.sub.4 are each independently selected from
the group consisting of hydrogen, fluorine, chlorine, bromine,
iodine, carboxyl, alkyl, alkene, alkyne, sulfonate, sulfone, amino,
ammonium, amido, nitrile, or alkoxy;
X.sub.2 and X.sub.5 are chlorine; and
one of X.sub.3 and X.sub.4 are attached to R.sub.28.
59. The fluorescently labeled reagent according to claim 58 wherein
R.sub.1 -R.sub.10, X.sub.1, X.sub.3 and X.sub.4 are selected to
correspond to a dye selected from the group consisting of DR110-2,
DR6G-2, DTMR-2, and DROX-2.
60. The fluorescently labeled reagent according to claim 48 wherein
the reagent is selected from the group consisting of
deoxynucleoside, deoxynucleoside monophosphate, deoxynucleoside
diphosphate and deoxynucleoside triphosphate.
61. The fluorescently labeled reagent according to claim 60 wherein
the deoxynucleotides are selected from the group consisting of
deoxycytosine, deoxyadenosine, deoxyguanosine, and
deoxythymidine.
62. The fluorescently labeled reagent according to claim 48 wherein
the reagent is selected from the group consisting of
dideoxynucleoside, dideoxynucleoside monophosphate,
dideoxynucleoside diphosphate and dideoxynucleoside
triphosphate.
63. The fluorescently labeled reagent according to claim 48 wherein
the dideoxynucleotides are selected from the group consisting of
deoxycytosine, deoxyadenosine, deoxyguanosine, and
deoxythymidine.
64. The fluorescently labeled reagent according to claim 48 wherein
the reagent is an oligonucleotide.
65. The fluorescently labeled reagent according to claim 64 wherein
the oligonucleotide has a 3' end which is extendable by using a
polymerase.
66. A fluorescently labeled reagent comprising:
a reagent selected from the group consisting of a nucleoside,
nucleoside monophosphate, nucleoside diphosphate, nucleoside
triphosphate, oligonucleotide and oligonucleotide analog, modified
to be linked to an energy transfer fluorescent dye; and
an energy transfer fluorescent dye attached to the reagent, the
energy transfer fluorescent dye including a dye having the
structure ##STR138## wherein: Y.sub.1, Y.sub.1 ', Y.sub.2 and
Y.sub.2 ' are each independently selected from the group consisting
of hydroxyl, oxygen, iminium and amine,
R.sub.11 -R.sub.16 and R.sub.11 -R.sub.16 ' are each independently
selected from the group consisting of hydrogen, fluorine, chlorine,
bromine, iodine, carboxyl, alkyl, alkene, alkyne, sulfonate, amino,
ammonium, amido, nitrile, alkoxy, phenyl, substituted phenyl, where
adjacent substituents are taken together to form a ring, and
combinations thereof, and
X.sub.1 -X.sub.5 and X.sub.1 '-X.sub.5 ' are each independently
selected from the group consisting of hydrogen, fluorine, chlorine,
bromine, iodine, carboxyl, alkyl, alkene, alkyne, sulfonate, amino,
ammonium, amido, nitrile, alkoxy, where adjacent substituents are
taken together to form a ring, and combinations thereof;
Y.sub.1, Y.sub.2, R.sub.11 -R.sub.16, and X.sub.1 -X.sub.5 are
selected to correspond to a donor dye capable of absorbing light at
a first wavelength and emitting excitation energy in response;
Y.sub.1 ', Y.sub.2 ', R.sub.11 '-R.sub.16 ', and X.sub.1 '-X.sub.5
' are selected to correspond to an acceptor dye which is capable of
absorbing the excitation energy emitted by the donor dye and
fluorescing at a second wavelength in response; and
one of X.sub.3 and X.sub.4 and one of X.sub.3 ' and X.sub.4 ' are
taken together to form a linker linking the donor to the acceptor
dye such that energy is transferred from the donor to the acceptor
dye.
67. The fluorescently labeled reagent according to claim 66 wherein
the linker has a backbone attaching the donor to the acceptor which
is less than 9 atoms in length.
68. The fluorescently labeled reagent according to claim 66 wherein
the linker has the general formula R.sub.25 Z.sub.3 C(O) where
R.sub.25 is a C.sub.1-4 alkyl attached to the donor dye at the
X.sub.3 or X.sub.4 substituent, Z.sub.3 is either NH, O or S, C(O)
is a carbonyl group and the terminal carbonyl group is attached to
the acceptor dye at the X.sub.3 ' or X.sub.4 ' substituent.
69. The fluorescently labeled reagent according to claim 66 wherein
the linker has the general formula R.sub.25 Z.sub.3 C(O)R.sub.26
Z.sub.4 C(O) where R.sub.25 is a C.sub.1-4 alkyl attached to the
donor dye at the X.sub.3 or X.sub.4 substituent, R.sub.26 is a
C.sub.1-4 alkyl, Z.sub.3 and Z.sub.4 are each independently either
NH, O or S, C(O) is a carbonyl group and the terminal carbonyl
group is attached to the acceptor dye at the X.sub.3 ' or X.sub.4 '
substituent.
70. A fluorescently labeled reagent comprising:
a reagent selected from the group consisting of a nucleoside,
nucleoside monophosphate, nucleoside diphosphate, nucleoside
triphosphate, oligonucleotide and oligonucleotide analog, modified
to be linked to an energy transfer fluorescent dye; and
an energy transfer fluorescent dye attached to the reagent, the
energy transfer fluorescent dye being selected from the group
consisting of: 5 or 6 carboxy TMR-B-CF, 5 or 6 carboxy TMR-F-CF, 5
or 6 carboxy TMR-P-CF, 5 or 6 carboxy TMR-P-CF, 5 or 6 carboxy
TMR-A-CF, 5 or 6 carboxy TMR-D-CF, 5 or 6 carboxy TMR-N-CF, 5 or 6
carboxy ROX-CF, CY5-CF, 5 or 6 carboxy TMR-gly-5AMF and 5 or 6
carboxy TMR-5AMF, 5 or 6 carboxy CF-B-TMR-2, 5 or 6 carboxy
CFB-DR110-2, 5 or 6 carboxy CFB-DR6g-2, and 5 or 6 carboxy
CFB-DROX-2.
71. The fluorescently labeled reagent according to claim 70 wherein
the reagent is selected from the group consisting of
deoxynucleoside, deoxynucleoside monophosphate, deoxynucleoside
diphosphate and deoxynucleoside triphosphate.
72. The fluorescently labeled reagent according to claim 71 wherein
the deoxynucleotides are selected from the group consisting of
deoxycytosine, deoxyadenosine, deoxyguanosine, and
deoxythymidine.
73. The fluorescently labeled reagent according to claim 70 wherein
the reagent is selected from the group consisting of
dideoxynucleoside, dideoxynucleoside monophosphate,
dideoxynucleoside diphosphate and dideoxynucleoside
triphosphate.
74. The fluorescently labeled reagent according to claim 70 wherein
the reagent is an oligonucleotide.
75. The fluorescently labeled reagent according to claim 74 wherein
the oligonucleotide has a 3' end which is extendable by using a
polymerase.
76. A method for sequencing a nucleic acid sequence comprising:
forming a mixture of extended labeled primers by hybridizing a
nucleic acid sequence with a fluorescently labeled oligonucleotide
primer in the presence of deoxynucleoside triphosphates, at least
one dideoxynucleoside triphosphate and a DNA polymerase, the DNA
polymerase extending the primer with the deoxynucleoside
triphosphates until a dideoxynucleoside triphosphate is
incorporated which terminates extension of the primer;
separating the mixture of extended primers; and
determining the sequence of the nucleic acid sequence by
fluorescently measuring the mixture of extended primers formed;
the fluorescently labeled oligonucleotide primer including
an oligonucleotide sequence complementary to a portion of the
nucleic acid sequence being sequenced and having a 3' end
extendable by a polymerase, and
an energy transfer fluorescent dye attached to the oligonucleotide,
the energy transfer fluorescent dye having the structure ##STR139##
where DONOR is a dye capable of absorbing light at a first
wavelength and emitting excitation energy in response;
ACCEPTOR is dye which is capable of absorbing the excitation energy
emitted by the donor dye and fluorescing at a second wavelength in
response;
C(O) is a carbonyl group;
Z.sub.1 is selected from the group consisting of NH, sulfur and
oxygen;
R.sub.21 is a C.sub.1-5 alkyl attached to the donor dye;
R.sub.22 is a substituent selected from the group consisting of an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon; and
R.sub.28 includes a functional group which attaches the linker to
the acceptor dye.
77. A method for sequencing a nucleic acid sequence comprising:
forming a mixture of extended labeled primers by hybridizing a
nucleic acid sequence with a fluorescently labeled oligonucleotide
primer in the presence of deoxynucleoside triphosphates, at least
one dideoxynucleoside triphosphate and a DNA polymerase, the DNA
polymerase extending the primer with the deoxynucleoside
triphosphates until a dideoxynucleoside triphosphate is
incorporated which terminates extension of the primer;
separating the mixture of extended primers; and
determining the sequence of the nucleic acid sequence by
fluorescently measuring the mixture of extended primers formed;
the fluorescently labeled oligonucleotide primer including
an oligonucleotide sequence complementary to a portion of the
nucleic acid sequence being sequenced and having a 3' end
extendable by a polymerase, and
an energy transfer fluorescent dye attached to the oligonucleotide,
the energy transfer fluorescent dye having the structure ##STR140##
where C(O) is a carbonyl group;
Y.sub.1 and Y.sub.2 are each independently selected from the group
consisting of hydroxyl, oxygen, iminium and amine;
Z.sub.1 is selected from the group consisting of NH, sulfur and
oxygen;
R.sub.11 -R.sub.17 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine, bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, amino, ammonium, amido,
nitrile, alkoxy, phenyl, substituted phenyl, where adjacent
substituents are taken together to form a ring, and combinations
thereof;
R.sub.21 is a C.sub.1-5 alkyl;
R.sub.22 is a substituent selected from the group consisting of an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon;
R.sub.28 includes a functional group which attaches the linker to
the acceptor dye; and
ACCEPTOR is dye which is capable of absorbing excitation energy
emitted by a member of the xanthene class of dyes.
78. A method for sequencing a nucleic acid sequence comprising:
forming a mixture of extended primers by hybridizing a nucleic acid
sequence with a primer in the presence of deoxynucleoside
triphosphates, at least one fluorescently labeled dideoxynucleoside
triphosphate and a DNA polymerase, the DNA polymerase extending the
primer with the deoxynucleoside triphosphates until a fluorescently
labeled dideoxynucleoside triphosphate is incorporated onto the
extended primer which terminates extension of the primer;
separating the mixture of extended primers; and
determining the sequence of the nucleic acid sequence by detecting
the fluorescently labeled dideoxynucleotide attached to the
separated mixture of extended primers;
the fluorescently labeled dideoxynucleoside triphosphate
including
a dideoxynucleoside triphosphate, and
an energy transfer fluorescent dye attached to the
dideoxynucleoside triphosphate, the energy transfer dye having the
structure ##STR141## where DONOR is a dye capable of absorbing
light at a first wavelength and emitting excitation energy in
response;
ACCEPTOR is dye which is capable of absorbing the excitation energy
emitted by the donor dye and fluorescing at a second wavelength in
response;
C(O) is a carbonyl group;
Z.sub.1 is selected from the group consisting of NH, sulfur and
oxygen;
R.sub.21 is a C.sub.1-5 alkyl attached to the donor dye;
R.sub.22 is a substituent selected from the group consisting of an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon; and
R.sub.28 includes a functional group which attaches the linker to
the acceptor dye.
79. A method for sequencing a nucleic acid sequence comprising:
forming a mixture of extended primers by hybridizing a nucleic acid
sequence with a primer in the presence of deoxynucleoside
triphosphates, at least one fluorescently labeled dideoxynucleoside
triphosphate and a DNA polymerase, the DNA polymerase extending the
primer with the deoxynucleoside triphosphates until a fluorescently
labeled dideoxynucleoside triphosphate is incorporated onto the
extended primer which terminates extension of the primer;
separating the mixture of extended primers; and
determining the sequence of the nucleic acid sequence by detecting
the fluorescently labeled dideoxynucleotide attached to the
separated mixture of extended primers;
the fluorescently labeled dideoxynucleoside triphosphate
including
a dideoxynucleoside triphosphate, and
an energy transfer fluorescent dye attached to the
dideoxynucleoside triphosphate, the dye having the structure
##STR142## where C(O) is a carbonyl group;
Y.sub.1 and Y.sub.2 are each independently selected from the group
consisting of hydroxyl, oxygen, iminium and amine;
Z.sub.1 is selected from the group consisting of NH, sulfur and
oxygen;
R.sub.11 -R.sub.17 are each independently selected from the group
consisting of hydrogen, fluorine, chlorine, bromine, iodine,
carboxyl, alkyl, alkene, alkyne, sulfonate, amino, ammonium, amido,
nitrile, alkoxy, phenyl, substituted phenyl, where adjacent
substituents are taken together to form a ring, and combinations
thereof;
R.sub.21 is a C.sub.1-5 alkyl;
R.sub.22 is a substituent selected from the group consisting of an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon;
R.sub.28 includes a functional group which attaches the linker to
the acceptor dye; and
ACCEPTOR is dye which is capable of absorbing excitation energy
emitted by a member of the xanthene class of dyes.
Description
BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to fluorescent dyes and, more
specifically, energy transfer fluorescent dyes and their use.
2. Description of Related Art
A variety of fluorescent dyes have been developed for labeling and
detecting components in a sample. In general, fluorescent dyes
preferably have a high quantum yield and a large extinction
coefficient so that the dye may be used to detect small quantities
of the component being detected. Fluorescent dyes also preferably
have a large Stokes shift (i.e., the difference between the
wavelength at which the dye has maximum absorbance and the
wavelength at which the dye has maximum emission) so that the
fluorescent emission is readily distinguished from the light source
used to excite the dye.
One class of fluorescent dyes which has been developed is energy
transfer fluorescent dyes. In general, energy transfer fluorescent
dyes include a donor fluorophore and an acceptor fluorophore. In
these dyes, when the donor and acceptor fluorophores are positioned
in proximity with each other and with the proper orientation
relative to each other, the energy emission from the donor
fluorophore is absorbed by the acceptor fluorophore and causes the
acceptor fluorophore to fluoresce. It is therefore important that
the excited donor fluorophore be able to efficiently absorb the
excitation energy of the donor fluorophore and efficiently transfer
the energy to the acceptor fluorophore.
A variety of energy transfer fluorescent dyes have been described
in the literature. For example, U.S. Pat. No. 4,996,143 and WO
95/21266 describe energy transfer fluorescent dyes where the donor
and acceptor fluorophores are linked by an oligonucleotide chain.
Lee, et al., Nucleic Acids Research 20:10 2471-2483 (1992)
describes an energy transfer fluorescent dye which includes
5-carboxy rhodamine linked to 4'-aminomethyl-5-carboxy fluorescein
by the 4'-aminomethyl substituent on fluorescein.
Several diagnostic and analytical assays have been developed which
involve the detection of multiple components in a sample using
fluorescent dyes, e.g. flow cytometry (Lanier, et al., J. Immunol.
132 151-156 (1984)); chromosome analysis (Gray, et al., Chromosoma
73 9-27 (1979)); and DNA sequencing. For these assays, it is
desirable to simultaneously employ a set of two or more spectrally
resolvable fluorescent dyes so that more than one target substance
can be detected in the sample at the same time. Simultaneous
detection of multiple components in a sample using multiple dyes
reduces the time required to serially detect individual components
in a sample. In the case of multi-loci DNA probe assays, the use of
multiple spectrally resolvable fluorescent dyes reduces the number
of reaction tubes that are needed, thereby simplifying the
experimental protocols and facilitating the manufacturing of
application-specific kits. In the case of automated DNA sequencing,
the use of multiple spectrally resolvable fluorescent dyes allows
for the analysis of all four bases in a single lane thereby
increasing throughput over single-color methods and eliminating
uncertainties associated with inter-lane electrophoretic mobility
variations. Connell, et al., Biotechniques 5 342-348 (1987);
Prober, et al., Science 238 336-341 (1987), Smith, et al., Nature
321 674-679 (1986); and Ansorge, et al., Nucleic Acids Research 15
4593-4602 (1989).
There are several difficulties associated with obtaining a set of
fluorescent dyes for simultaneously detecting multiple target
substances in a sample, particularly for analyses requiring an
electrophoretic separation and treatment with enzymes, e.g., DNA
sequencing. For example, each dye in the set must be spectrally
resolvable from the other dyes. It is difficult to find a
collection of dyes whose emission spectra are spectrally resolved,
since the typical emission band half-width for organic fluorescent
dyes is about 40-80 nanometers (nm) and the width of the available
spectrum is limited by the excitation light source. As used herein
the term "spectral resolution" in reference to a set of dyes means
that the fluorescent emission bands of the dyes are sufficiently
distinct, i.e., sufficiently non-overlapping, that reagents to
which the respective dyes are attached, e.g. polynucleotides, can
be distinguished on the basis of the fluorescent signal generated
by the respective dyes using standard photodetection systems, e.g.
employing a system of band pass filters and photomultiplier tubes,
charged-coupled devices and spectrographs, or the like, as
exemplified by the systems described in U.S. Pat. Nos. 4,230,558,
4,811,218, or in Wheeless et al, pgs. 21-76, in Flow Cytometry:
Instrumentation and Data Analysis (Academic Press, New York,
1985).
The fluorescent signal of each of the dyes must also be
sufficiently strong so that each component can be detected with
sufficient sensitivity. For example, in the case of DNA sequencing,
increased sample loading can not compensate for low fluorescence
efficiencies, Pringle et al., DNA Core Facilities Newsletter, 1
15-21 (1988). The fluorescent signal generated by a dye is
generally greatest when the dye is excited at its absorbance
maximum. It is therefore preferred that each dye be excited at
about its absorbance maximum.
A further difficulty associated with the use of a set of dyes is
that the dyes generally do not have the same absorbance maximum.
When a set of dyes are used which do not have the same absorbance
maximum, a trade off is created between the higher cost associated
with providing multiple light sources to excite each dye at its
absorbance maximum, and the lower sensitivity arising from each dye
not being excited at its absorbance maximum.
In addition to the above difficulties, the charge, molecular size,
and conformation of the dyes must not adversely affect the
electrophoretic mobilities of the fragments. The fluorescent dyes
must also be compatible with the chemistry used to create or
manipulate the fragments, e.g., DNA synthesis solvents and
reagents, buffers, polymerase enzymes, ligase enzymes, and the
like.
Because of the multiple constraints on developing a set of dyes for
multicolor applications, particularly in the area of four color DNA
sequencing, only a few sets of fluorescent dyes have been
developed. Connell, et al., Biotechniques 5 342-348 (1987); Prober,
et al., Science 238 336-341 (1987); and Smith, et al., Nature 321
674-679 (1986).
One class of fluorescent dyes that has been found to be useful in
multicolor applications are rhodamine dyes, e.g.,
tetramethylrhodamine (TAMRA), rhodamine X (ROX), rhodamine 6G
(R6G), rhodamine 110 (R110), and the like. U.S. Pat. No. 5,366,860.
Rhodamine dyes are particularly attractive relative to fluorescein
dyes because (1) rhodamines are typically more photostable than
fluoresceins, (2) rhodamine-labeled dideoxynucleotides are better
substrates for thermostable polymerase enzymes, and (3) the
emission spectra of rhodamine dyes is significantly to the red
(higher wavelength) of fluoresceins.
One drawback associated with currently available rhodamine dyes,
particularly in the context of multiplex detection methods, is the
relatively broad emission spectrum of the rhodamine dyes. This
broad emission spectrum limits spectral resolution between
spectrally neighboring dyes, making the multicomponent analysis of
such dye combinations difficult. A second drawback associated with
currently available rhodamine dyes is that their absorption
spectrum does not match the wavelength of currently available solid
state frequency-doubled green diode lasers, e.g., neodymium
solid-state YAG lasers, which have an emission line at
approximately 532 nm. It is highly advantageous to use such lasers
because of their compact size, long useful life, and efficient use
of power.
Energy transfer fluorescent dyes possess several features which
make them attractive for use in the simultaneous detection of
multiple target substances in a sample, such as in DNA sequencing.
For example, a single donor fluorophore can be used in a set of
energy transfer fluorescent dyes so that each dye has strong
absorption at a common wavelength. Then, by varying the acceptor
fluorophore in the energy transfer dye, a series of energy transfer
dyes having spectrally resolvable fluorescence emissions can be
generated.
Energy transfer fluorescent dyes also provide a larger effective
Stokes shift than non-energy transfer fluorescent dyes. This is
because the Stokes shift for an energy transfer fluorescent dye is
based on the difference between the wavelength at which the donor
fluorophore maximally absorbs light and the wavelength at which the
acceptor fluorophore maximally emits light. In general, a need
exists for fluorescent dyes having larger Stokes shifts.
The sensitivity of any assay using a fluorescent dye is dependent
on the strength of the fluorescent signal generated by the
fluorescent dye. A need therefore exists for fluorescent dyes which
have a strong fluorescence signal. With regard to energy transfer
fluorescent dyes, the fluorescence signal strength of these dyes is
dependent on how efficiently the acceptor fluorophore absorbs the
energy emission of the donor fluorophore. This, in turn, depends on
a variety of variables, including the proximity of the donor
fluorophore to the acceptor fluorophore and the orientation of the
donor fluorophore relative to the acceptor fluorophore. A need
therefore exists for energy transfer fluorescent dyes in which the
orientation between the donor and acceptor fluorophore is such that
energy is efficiently transferred between the donor and acceptor
fluorophore.
SUMMARY OF THE INVENTION
The present invention relates to linkers for linking a donor dye to
an acceptor dye in an energy transfer fluorescent dye. The present
invention also relates to energy transfer fluorescent dyes having
enhanced fluorescence. The present invention also relates to
reagents which include the energy transfer dyes of the present
invention, methods for using the dyes and reagents, and kits within
which the dyes and reagents are included.
One linker according to the present invention for linking a donor
dye to an acceptor dye in an energy transfer fluorescent dye has
the general structure R.sub.21 Z.sub.1 C(O)R.sub.22 R.sub.28, as
illustrated below, where R.sub.21 is a C.sub.1-5 alkyl attached to
the donor dye, C(O) is a carbonyl group, Z.sub.1 is either NH,
sulfur or oxygen, R.sub.22 is a substituent attached to the
carbonyl carbon which may be either an alkene, diene, alkyne, a
five or six membered ring having at least one unsaturated bond or a
fused ring structure, and R.sub.28 includes a functional group
which attaches the linker to the acceptor dye. ##STR1##
The R.sub.28 group used in the linker may be any group known in the
art which can be used to attach the R.sub.22 group to an acceptor
dye. Typically, the R.sub.28 group will be attached to a benzene
ring or other aromatic ring structure on the acceptor dye.
Accordingly, R.sub.28 is preferably formed by forming an
electrophilic functional group on the benzene ring or other
aromatic ring structure of the acceptor dye, such as a carboxylic
acids, acid halide, sulfonic acid, ester, aldehyde, thio,
disulfide, isothiocyanate, isocyanate, sulfonyl halide, maleimide,
hydroxysuccinimide ester, haloacetyl, hydroxysulfosuccinimide
ester, imido ester, hydrazine, azidonitrophenyl, and azide. The
R.sub.22 group can then be added to the acceptor dye, either before
or after attachment of the donor dye to the R.sub.22 group, by
reacting the electrophilic agent on the acceptor dye with a
nucleophile, such as an amino, hydroxyl or sulfhydryl
nucleophile.
For example, in the embodiment illustrated below, the linker has
the general structure R.sub.21 Z.sub.1 C(O)R.sub.22 R.sub.29
Z.sub.2 C(O) where R.sub.21 and R.sub.22 are as detailed above,
Z.sub.1 and Z.sub.2 are each independently either NH, sulfur or
oxygen, and R.sub.29 is a C.sub.1-5 alkyl, and the terminal
carbonyl group is attached to the ring structure of the acceptor
dye. In the variation where Z.sub.2 is nitrogen, the C(O)R.sub.22
R.sub.29 Z.sub.2 subunit forms an amino acid subunit. ##STR2## In
this embodiment, the linker may be formed by the reaction of an
activated carbonyl group (NHS ester) with a amine, hydroxyl or
thiol group. It is noted that a wide variety of other mechanisms
for attaching an R.sub.22 group to an acceptor dye are envisaged
and are intended to fall within the scope of the invention.
Particular examples of five or six membered rings which may be used
as R.sub.22 in the linker include, but are not limited to
cyclopentene, cyclohexene, cyclopentadiene, cyclohexadiene, furan,
thiofuran, pyrrole, isopyrole, isoazole, pyrazole, isoimidazole,
pyran, pyrone, benzene, pyridine, pyridazine, pyrimidine, pyrazine
and oxazine. Examples of fused ring structures include, but are not
limited to indene, benzofuran, thionaphthene, indole and
naphthalene.
A preferred embodiment of this linker is where R.sub.21 and
R.sub.29 are methylene, Z.sub.1 and Z.sub.2 are NH, and R.sub.22 is
benzene, as shown below. ##STR3##
One class of energy transfer fluorescent dyes according to the
present invention includes a donor dye which has the following
xanthene ring structure with a 4' ring position ##STR4## where
Y.sub.1 and Y.sub.2 taken separately are either hydroxyl, oxygen,
iminium or amine, the iminium and amine preferably being a tertiary
iminium or amine. R.sub.11 -R.sub.17 may be any substituent which
is compatible with the energy transfer dyes of the present
invention, it being noted that the R.sub.11 -R.sub.17 may be widely
varied in order to alter the spectral and mobility properties of
the dyes.
According to this embodiment, the energy transfer dye also includes
an acceptor dye which absorbs the excitation energy emitted by the
donor dye and fluoresces at a second wavelength in response. The
energy transfer dye also includes a linker which attaches the donor
dye to the acceptor dye.
In one variation of this embodiment of energy transfer dyes, the
linker has the general structure R.sub.21 Z.sub.1 C(O)R.sub.22
R.sub.28, as illustrated above, where R.sub.21 is a C.sub.1-5 alkyl
attached to the 4' position of the xanthene donor dye, C(O) is a
carbonyl group, Z.sub.1 is either NH, sulfur or oxygen, R.sub.22 is
a substituent attached to the carbonyl carbon which may be either
an alkene, diene, alkyne, a five or six membered ring having at
least one unsaturated bond or a fused ring structure, and R.sub.28
includes a functional group which attaches the linker to the
acceptor dye.
In a further variation of this embodiment of energy transfer dyes,
the linker has the general structure R.sub.21 Z.sub.1 C(O)R.sub.22
R.sub.29 Z.sub.2 C(O), as illustrated above, where R.sub.21 and
R.sub.22 are as detailed above, Z.sub.1 and Z.sub.2 are each
independently either NH, sulfur or oxygen, and R.sub.29 is a
C.sub.1-5 alkyl, and the terminal carbonyl group is attached to the
ring structure of the acceptor dye. In the variation where Z.sub.2
is nitrogen, --C(O)R.sub.22 R.sub.29 Z.sub.2 -- forms an amino acid
subunit.
In a further preferred variation of this embodiment of energy
transfer dyes, the linker is where R.sub.21 and R.sub.29 are
methylene, Z.sub.1 and Z.sub.2 are NH, and R.sub.22 is benzene, as
shown below. ##STR5##
The donor dye may optionally be a member of the class of dyes where
R.sub.17 is a phenyl or substituted phenyl. When Y.sub.1 is
hydroxyl and Y.sub.2 is oxygen, and R.sub.17 is a phenyl or
substituted phenyl, the dye is a member of the fluorescein class of
dyes. When Y.sub.1 is amine and Y.sub.2 is iminium, and R.sub.17 is
a phenyl or substituted phenyl, the dye is a member of the
rhodamine class of dyes. Further according to this embodiment, the
acceptor dye may optionally be a member of the xanthene, cyanine,
phthalocyanine and squaraine classes of dyes.
In another embodiment, the energy transfer fluorescent dyes have
donor and acceptor dyes with the general structure ##STR6## where
Y.sub.1 and Y.sub.2 taken separately are either hydroxyl, oxygen,
iminium or amine, the iminium and amine preferably being a tertiary
iminium or amine and R.sub.11 -R.sub.17 are any substituents which
are compatible with the energy transfer dyes of the present
invention.
According to this embodiment, as illustrated below, the linker is
attached to one of X.sub.3 and X.sub.4 substituents of each of the
donor and acceptor dyes, preferably the X.sub.3 substituents of the
donor and acceptor dyes. In this embodiment, the linker is
preferably short and/or rigid as this has been found to enhance the
transfer of energy between the donor and acceptor dyes.
##STR7##
In another embodiment, the energy transfer fluorescent dyes include
a donor dye which is a member of the xanthene class of dyes, an
acceptor dye which is a member of the xanthene, cyanine,
phthalocyanine and squaraine classes of dyes which is capable of
absorbing the excitation energy emitted by the donor dye and
fluorescing at a second wavelength in response, and a linker
attaching the donor dye to the acceptor dye. According to this
embodiment, the acceptor has an emission maximum that is greater
than about 600 nm or at least about 100 nm greater than the
absorbance maximum of the donor dye.
In addition to the above-described novel energy transfer
fluorescent dyes, the present invention also relates to fluorescent
reagents containing the energy transfer fluorescent dyes. In
general, these reagents include any molecule or material to which
the energy transfer dyes of the invention can be attached and used
to detect the presence of the reagent based on the fluorescence of
the energy transfer dye. In one embodiment, a fluorescent reagent
is provided which includes a nucleoside or a mono-, di- or
triphosphate nucletotide labeled with an energy transfer
fluorescent dye. The nucleotide may be a deoxynucleotide which may
be used for example, in the preparation of dye labeled
oligonucleotides. The nucleotide may also be a dideoxynucleoside
which may be used, for example, in dye terminator sequencing. In
another embodiment, the fluorescent reagent includes an
oligonucleotide labeled with an energy transfer fluorescent dye.
These reagents may be used, for example, in dye primer
sequencing.
The present invention also relates to methods which use the energy
transfer fluorescent dyes and reagents of the present invention. In
one embodiment, the method includes forming a series of different
sized oligonucleotides labeled with an energy transfer fluorescent
dye of the present invention, separating the series of labeled
oligonucleotides based on size, detecting the separated labeled
oligonucleotides based on the fluorescence of the energy transfer
dye.
In one embodiment of this method, a mixture of extended labeled
primers is formed by hybridizing a nucleic acid sequence with an
oligonucleotide primer in the presence of deoxynucleotide
triphosphates, and at least one dye labeled dideoxynucleotide
triphosphate and a DNA polymerase. The DNA polymerase serves to
extend the primer with the deoxynucleotide triphosphates until a
dideoxynucleotide triphosphate is incorporated which terminates
extension of the primer. Once terminated, the mixture of extended
primers are separated and detected based on the fluorescence of the
dye on the dideoxynucleoside. In a variation of this embodiment,
four different fluorescently labeled dideoxynucleotide
triphosphates are used, i.e., a fluorescently labeled
dideoxycytosine triphosphate, a fluorescently labeled
dideoxyadenosine triphosphate, a fluorescently labeled
dideoxyguanosine triphosphate, and a fluorescently labeled
dideoxythymidine triphosphate. In an alternate embodiment of this
method, the oligonucleotide primer is fluorescently labeled as
opposed to the deoxynucleotide triphosphate.
The present invention also relates to kits containing the dyes and
reagents for performing DNA sequencing using the dyes and reagents
of present invention.
BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 illustrates the modification of a carboxy substituent on a
energy transfer dye to an activated N-hydroxysuccinimidyl (NHS)
ester which is then reacted with an aminohexyl-oligomer to form a
dye labeled oligonucleotide primer.
FIG. 2 compares the fluorescence emission strength of a series of
energy transfer dyes of the present invention to other energy
transfer dyes and the acceptor dye alone.
FIGS. 3A and 3B show several particularly preferred embodiments of
4,7-dichlororhodamine dye compounds which can be used in the energy
transfer dyes of the present invention.
FIGS. 4A and 4B show preferred generalized synthesis schemes for
the preparation of the 4,7-dichlororhodamine dyes of the
invention.
FIG. 4A shows a generalized synthesis wherein the substituent
X.sub.1 can be other than carboxylate.
FIG. 4B shows a generalized synthesis wherein the substituent
X.sub.1 is carboxylate.
FIG. 5 illustrates a set of four dyes (3-carboxy-R110,
5-carboxy-R6G, 5TMR-B-CF and 5ROX-CF) which are spectrally
resolvable from each other.
FIG. 6 illustrates a set of four dyes (3-carboxy-R110,
5-carboxy-R6G, 5ROX-CF and Cy5-CF) which are spectrally resolvable
from each other.
FIG. 7 is a plot of a mixture of labeled oligonucleotides generated
during dye primer sequencing using 5TMR-CF and 5TMR-B-CF labeled
primers.
FIG. 8 is a four color plot of dye primer sequencing using a four
dye set including 3-carboxy-R110, 5-carboxy-R6G, 5TMR-CF and
5TMR-B-CF.
FIGS. 9A-D compare the fluorescence emission strength of a series
of energy transfer dyes of the present invention to the
corresponding acceptor dye alone.
FIG. 9A provides the overlaid spectra of 6-CFB-DR110-2 and
DR110-2.
FIG. 9B provides an overlaid spectra of 5-CFB-DR6G-2 and
DR6G-2.
FIG. 9C provides an overlaid spectra of 6-CFB-DTMR-2 and
DTMR-2.
FIG. 9D provides an overlaid spectra of 6-CFB-DROX-2 and
DROX-2.
FIG. 10 illustrates a set of four dyes (5-CFB-DR110-2,
5-CFB-DR6G-2, 6-CFB-DTMR-2, and 6-CFB-DROX-2) which are spectrally
resolvable from each other.
FIG. 11 is a plot of a mixture of labeled oligonucleotides
generated during dye primer sequencing using 6-CFB-DTMR-2 and
DTMR-2 labeled primers.
FIG. 12 is a plot of a mixture of labeled oligonucleotides
generated during dye primer sequencing using 5-CF-TMR-2 and
5-CFB-TMR-2 labeled primers.
FIG. 13 is a four color plot of dye primer sequencing using a four
dye set including 5-CFB-DR110-2, 6-CFB-DR6g-2, 5-CFB-DTMR-2, and
5-CFB-DROX-2.
DETAILED DESCRIPTION
I. Energy Transfer Dye Linkers Of The Present Invention
The present invention relates to novel linkers for linking a donor
dye to an acceptor dye in an energy transfer fluorescent dye. The
present invention also relates to energy transfer fluorescent dyes
which incorporate these linkers. These linkers have been found to
faciliate the efficient transfer of energy between a donor and
acceptor dye in an energy transfer dye.
One linker according to the present invention for linking a donor
dye to an acceptor dye in an energy transfer fluorescent dye has
the general structure R.sub.21 Z.sub.1 C(O)R.sub.22 R.sub.28, as
illustrated below, where R.sub.21 is a C.sub.1-5 alkyl attached to
the donor dye, C(O) is a carbonyl group, Z.sub.1 is either NH,
sulfur or oxygen, R.sub.22 is a substituent which includes an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon, and R.sub.28 includes a functional group which
attaches the linker to the acceptor dye. ##STR8##
In one embodiment of this linker, illustrated below, the linker has
the general structure R.sub.21 Z.sub.1 C(O)R.sub.22 R.sub.29
Z.sub.2 C(O) where R.sub.21 and R.sub.22 are as detailed above,
Z.sub.1 and Z.sub.2 are each independently either NH, sulfur or
oxygen, R.sub.29 is a C.sub.1-5 alkyl, and the terminal carbonyl
group is attached to the ring structure of the acceptor dye. In the
variation where Z.sub.2 is nitrogen, the C(O)R.sub.22 R.sub.29
Z.sub.2 subunit forms an amino acid subunit. ##STR9##
Particular examples of five or six membered rings which may be used
as R.sub.22 in the linker include, but are not limited to
cyclopentene, cyclohexene, cyclopentadiene, cyclohexadiene, furan,
thiofuran, pyrrole, isopyrole, isoazole, pyrazole, isoimidazole,
pyran, pyrone, benzene, pyridine, pyridazine, pyrimidine, pyrazine
and oxazine. Examples of fused ring structures include, but are not
limited to indene, benzofuran, thionaphthene, indole and
naphthalene.
A preferred embodiment of this linker is where R.sub.21 and
R.sub.29 are methylene, Z.sub.1 and Z.sub.2 are NH, and R.sub.22 is
benzene, as shown below. ##STR10##
Table 3 illustrates examples of --C(O)R.sub.22 -- subunits of
linkers which may be used in the linkers of the present
invention.
II. Energy Transfer Dyes Of The Present Invention
In general, the energy transfer dyes of the present invention
include a donor dye which absorbs light at a first wavelength and
emits excitation energy in response, an acceptor dye which is
capable of absorbing the excitation energy emitted by the donor dye
and fluorescing at a second wavelength in response, and a linker
which attaches the donor dye to the acceptor dye. With regard to
all of the molecular structures provided herein, it is intended
that these molecular structures encompass not only the exact
electronic structure presented, but also include all resonant
structures and protonation states thereof.
One class of energy transfer fluorescent dyes according to the
present invention includes a donor dye which is a member of the
xanthene class of dyes, an acceptor dye and a linker which is a
member of the group of linkers described in Section I. As used
herein, xanthene dyes include all molecules having the general
structure ##STR11## where Y.sub.1 and Y.sub.2 taken separately are
either hydroxyl, oxygen, iminium or amine, the iminium and amine
preferably being a tertiary iminium or amine. When Y.sub.1 is
hydroxyl and Y.sub.2 is oxygen, and R.sub.17 is a phenyl or
substituted phenyl, the dye is a member of the fluorescein class of
dyes. When Y.sub.1 is amine and Y.sub.2 is iminium, and R.sub.17 is
a phenyl or substituted phenyl, the dye is a member of the
rhodamine class of dyes.
R.sub.11 -R.sub.17 may be any substituent which is compatible with
the energy transfer dyes of the present invention, it being noted
that the R.sub.11 -R.sub.17 may be widely varied in order to alter
the spectral and mobility properties of the dyes. The number
indicated in the ring structure indicates the 4' position on the
xanthene ring structure. For the energy transfer dyes of the
present invention in which the linker is attached to the 4'
position of the xanthene ring structure, the R.sub.14 substituent
corresponds to the linker.
Examples of R.sub.11 -R.sub.17 substituents include, but not
limited to hydrogen, fluorine, chlorine, bromine, iodine, carboxyl,
alkyl, alkene, alkyne, sulfonate, amino, ammonium, amido, nitrile,
alkoxy, phenyl, substituted phenyl, where adjacent substituents are
taken together to form a ring, and combinations thereof.
In one embodiment, R.sub.1 and R.sub.16 are taken together to form
a substituted or unsubstituted benzene ring. This class of xanthene
dyes are referred to herein as asymmetric benzoxanthene dyes and
are described in U.S. application Ser. No. 08/626,085, filed Apr.
1, 1996, entitled Asymmetric Benzoxanthene Dyes, by Scott C.
Benson, et al. which is incorporated herein by reference.
In another embodiment, R.sub.17 is a phenyl or substituted phenyl
having the general formula ##STR12## Substituents X.sub.1 -X.sub.5
on the phenyl ring can include hydrogen, fluorine, chlorine,
bromine, iodine, carboxyl, alkyl, alkene, alkyne, sulfonate, amino,
ammonium, amido, nitrile, alkoxy, where adjacent substituents are
taken together to form a ring, and combinations thereof.
In one embodiment, the donor dye is a member of the class of dyes
where Y.sub.1 is amine, Y.sub.2 is iminium, and X.sub.2 and X.sub.5
are chlorine, referred to herein as 4,7-dichlororhodamine dyes.
Dyes falling within the 4,7-dichlororhodamine class of dyes and
their synthesis are described herein as well as in U.S. application
Ser. No.: 08/672,196; filed: Jun. 27,1996; entitled:
"4,7-DICHLORORHODAMINE DYES" which is incorporated herein by
reference.
As used here, alkyl denotes straight-chain and branched hydrocarbon
moieties, i.e., methyl, ethyl, propyl, isopropyl, tert-butyl,
isobutyl, sec-butyl, neopentyl, tert-pentyl, and the like.
Substituted alkyl denotes an alkyl moiety substituted with any one
of a variety of substituents, including, but not limited to
hydroxy, amino, thio, cyano, nitro, sulfo, and the like. Haloalkyl
denotes a substituted alkyl with one or more halogen atom
substituents, usually fluoro, chloro, bromo, or iodo. Alkene
denotes a hydocarbon wherein one or more of the carbon-carbon bonds
are double bonds, and the non-double bonded carbons are alkyl or
substituted alkyl. Alkyne denotes a hydocarbon where one or more of
the carbons are bonded with a triple bond and where the non-triple
bonded carbons are alkyl or substituted alkyl moieties. Sulfonate
refers to moieties including a sulfur atom bonded to 3 oxygen
atoms, including mono- and di-salts thereof, e.g., sodium
sulfonate, potassium sulfonate, disodium sulfonate, and the like.
Amino refers to moieties including a nitrogen atom bonded to 2
hydrogen atoms, alkyl moieties, or any combination thereof. Amido
refers to moieties including a carbon atom double bonded to an
oxygen atom and single bonded to an amino moiety. Nitrile refers to
moieties including a carbon atom triple bonded to a nitrogen atom.
Alkoxy refers to a moiety including an alkyl moiety single bonded
to an oxygen atom. Aryl refers to single or multiple phenyl or
substituted phenyl, e.g., benzene, naphthalene, anthracene,
biphenyl, and the like.
R.sub.11 -R.sub.17 may also each independently be a linking moiety
which may be used to attach the energy transfer dye to a reagent,
such as a nucleotide, nucleoside or oligonucleotide. Examples of
linking moieties include isothiocyanate, sulfonyl chloride,
4,6-dichlorotriazinylamine, succinimidyl ester, or other active
carboxylate whenever the complementary functionality is amine.
Preferably the linking group is maleimide, halo acetyl, or
iodoacetamide whenever the complementary functionality is
sulfhydryl. See R. Haugland, Molecular Probes Handbook of
Fluorescent Probes and Research Chemicals, Molecular probes, Inc.
(1992). In a particularly preferred embodiment, as illustrated in
FIG. 1, the linking group is an activated NHS ester formed from a
carboxyl group on either the donor or acceptor dye which can be
reacted with an aminohexyl-oligomer to form a dye labeled
oligonucleotide primer.
The energy transfer fluorescent dyes of this embodiment also
include an acceptor dye which is capable of absorbing the
excitation energy emitted by the donor dye and fluorescing at a
second wavelength in response, and a linker which attaches the
donor dye to the acceptor dye. In the first class of energy
transfer dyes, the linker is a member of the class of linkers
described in Section I and is attached to the donor dye at the 4'
position of the xanthene ring structure.
Energy transfer dyes of this first class exhibit enhanced
fluorescent strength as compared to the acceptor fluorophore itself
and energy transfer fluorescent dyes having the same
donor--acceptor pair where the linkage between the donor--acceptor
pair is different.
The present invention also relates to a second class of energy
transfer fluorescent dyes in which the donor and acceptor dyes each
have the general structure ##STR13## where Y.sub.1, Y.sub.2,
R.sub.11 -R.sub.16 and X.sub.1 -X.sub.5 are as specified above.
Within this class of dyes, the linker is attached to the donor and
acceptor dyes by one of X.sub.3 and X.sub.4 substituents of each of
the donor and acceptor dyes. ##STR14##
In a preferred embodiment of this class of dyes, the linker is
attached to the donor and acceptor dyes by the X.sub.3 substituent
of each of the donor and acceptor dyes.
Within this class of dyes, the linker is preferably short and/or
rigid as this has been found to enhance the transfer of energy
between the donor and acceptor dyes.
The present invention also relates to a third class of energy
transfer fluorescent dyes in which the acceptor dye is a member of
the 4,7-dichlororhodamine class of dyes, i.e., dyes having the
general structure ##STR15## where R.sub.1 -R.sub.4 are each
independently hydrogen, alkyl or where R.sub.1 and R.sub.5, R.sub.2
and R.sub.6, R.sub.3 and R.sub.8, R.sub.4 and R.sub.9 are taken
together to form a ring, and combinations thereof;
R.sub.5 -R.sub.10 are each independently hydrogen, fluorine,
chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne,
sulfonate, sulfone, amino, ammonium, amido, nitrile, alkoxy,
phenyl, or substituted phenyl, or where adjacent substituents are
taken together to form a ring, and combinations thereof;
X.sub.1, X.sub.3 and X.sub.4 are each independently hydrogen,
fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile, or
alkoxy, or where adjacent substituents are taken together to form a
ring, and combinations thereof; and
X.sub.2 and X.sub.5 are chlorine.
With regard to R.sub.1 -R.sub.10, X.sub.3 and X.sub.4, R.sub.1 and
R.sub.5, R.sub.2 and R.sub.6, R.sub.3 and R.sub.8, R.sub.4 and
R.sub.9, and X.sub.3 and X.sub.4 may each independently be taken
together to form a 5, 6, or 7 membered ring.
The numbers (4', 5, 6) indicated in the ring structure indicate the
4', 5 and 6 ring positions on the rhodamine ring structure. As will
be discussed herein, the 4' and 5 ring positions are preferred
sites for attachment of the linker used in the energy transfer dyes
of the present invention which attaches the donor to the acceptor
fluorophore. The 4', 5 and 6 ring positions are also preferred
sites for attachment of a biomolecule, such as a nucleotide or
oligonucleotide to the energy transfer dye.
Donor dyes within this class of energy transfer dyes may include
any dye which emits excitation energy which a 4,7-dichlororhodamine
dye is capable of absorbing and producing an energy emission in
response. In one embodiment, the donor dye has a xanthene ring
structure with a 4' ring position where the 4,7-dichlororhodamine
acceptor dye is attached to the donor dye by a linker which is
attached to the 4' ring position of the xanthene dye. The linker is
preferably attached to the 5 or 6 ring positions of the
4,7-dichlororhodamine acceptor dye.
Energy transfer dyes according to this third class of dyes, i.e.,
where 4,7-dichlororhodamine is the acceptor dye, provide the
advantage of having a relatively narrow emission spectrum as
compared to other rhodamine dyes. This narrow emission spectrum
enhances the spectral resolution achievable by a set of these dyes,
thereby facilitating multicomponent analysis using these dyes.
The present invention also relates to a fourth class of energy
transfer fluorescent dyes in which the donor dye is a member of the
xanthene class of dyes, the acceptor dye is a member of the
xanthene, cyanine, phthalocyanine and squaraine classes of dyes,
and the acceptor has an emission maximum that is greater than about
600 nm and/or preferably has an emission maximum that is at least
about 100 nm greater than the absorbance maximum of the donor dye.
Within this class of dyes, the donor is preferably a member of the
fluorescein class of dyes.
The fourth class of energy transfer dyes of the present invention
exhibit unusually large Stoke shifts, as measured by the difference
between the absorbance of the donor and the emission of the
acceptor. In addition, these dyes exhibit efficient energy transfer
in that minimal donor fluorescence is observed.
Described herein in greater detail are the four classes of energy
transfer dyes of the present invention.
TABLE 1
__________________________________________________________________________
##STR16## ##STR17## ##STR18## ##STR19## ##STR20## ##STR21##
##STR22## ##STR23##
__________________________________________________________________________
TABLE 1A
__________________________________________________________________________
##STR24## ##STR25##
__________________________________________________________________________
A. First Class Of Energy Transfer Dyes
As described above, the first class of energy transfer dyes
according to the present invention includes a donor dye which is a
member of the xanthene class of dyes and hence has a xanthene ring
structure with a 4' ring position. Within this class of dyes, the
acceptor dye is a dye which is capable of absorbing the excitation
energy emitted by the donor dye and fluorescing at a second
wavelength in response.
According to this embodiment, the donor may be a member of the
fluorescein, rhodamine or asymmetric benzoxanthene classes of dyes,
these dyes each being members of the broader xanthene class of
dyes. Illustrated below are the general structural formulas for
these xanthene dyes. The substituents illustrated on these dyes may
be selected from the wide variety of substituents which may be
incorporated onto these different classes of dyes since all dyes
having the general xanthene, fluorescein, rhodamine, and asymmetric
benzoxanthene ring structures are intended to fall within the scope
of this invention. ##STR26##
Examples of classes of acceptor dyes which may be used in the
energy transfer fluorescent dye of this embodiment include, but are
not limited to, xanthene dyes, cyanine dyes, phthalocyanine dyes
and squaraine dyes. The general structures of these dyes are
illustrated in Table 1A. The substituents illustrated on these dyes
may be selected from the wide variety of substituents which may be
incorporated onto these different classes of dyes since all dyes
having the general xanthene, fluorescein, rhodamine, asymmetric
benzoxanthene, cyanine, phthalocyanine and squaraine ring
structures are intended to fall within the scope of this
invention.
Examples of donor dyes which may be used in this embodiment
include, but are not limited to fluorescein, isomers of
carboxyfluorescein (e.g., 5 and 6 carboxy), isomers of carboxy-HEX
(e.g., 5 and 6 carboxy), NAN, CI-FLAN, TET, JOE, ZOE, rhodamine,
isomers of carboxyrhodamine (e.g., 5 and 6 carboxy), isomers of
carboxy R110 (e.g., 5 and 6 carboxy), isomers of carboxy R6G (e.g.,
5 and 6 carboxy), 4,7-dichlorofluoresceins (See U.S. Pat. No.
5,188,934), 4,7-dichlororhodamines (See application Ser. No.
08/672,196, filed Jun. 27, 1996), asymmetric benzoxanthene dyes
(See U.S. application Ser. No. 08/626,085, filed Apr. 1, 1996), and
isomers of N,N,N',N'-tetramethyl-carboxyrhodamine (TAMRA) (e.g., 5
and 6 carboxy).
Examples of acceptor dyes which may be used in this embodiment
include, but are not limited to isomers of carboxyfluorescein
(e.g., 5 and 6 carboxy), 4,7-dichlorofluoresceins,
4,7-dichlororhodamines, fluoresceins, asymmetric benzoxanthene
dyes, isomers of carboxy-HEX (e.g., 5 and 6 carboxy), NAN, CI-FLAN,
TET, JOE, ZOE, rhodamine, isomers of carboxyrhodamine (e.g., 5 and
6 carboxy), isomers of carboxy R110 (e.g., 5 and 6 carboxy),
isomers of carboxy R6G (e.g., 5 and 6 carboxy), isomers of
N,N,N',N'-tetramethyl carboxyrhodamine (TAMRA) (e.g., 5 and 6
carboxy), isomers of carboxy-X-rhodamine (ROX) (e.g., 5 and 6
carboxy) and Cy5. Illustrated in Table 2 are the structures of
these dyes.
In the first class of energy transfer dyes according to the present
invention, the linker is attached to the donor dye at the 4'
position of the xanthene ring structure. In one embodiment, the
linker has the general structure R.sub.21 Z.sub.1 C(O)R.sub.22
R.sub.28, as illustrated below, where R.sub.21 is a C.sub.1-5 alkyl
which is attached to the 4' ring position of the donor xanthene
dye, Z.sub.1 is either NH, sulfur or oxygen, C(O) is a carbonyl
group, R.sub.22 is a substituent which includes an alkene, diene,
alkyne, a five and six membered ring having at least one
unsaturated bond or a fused ring structure which is attached to the
carbonyl carbon, and R.sub.28 is a functional group which attaches
the linker to the acceptor dye. ##STR27##
Examples of five or six membered rings which may be used in
R.sub.22 include, but are not limited to cyclopentene, cyclohexene,
cyclopentadiene, cyclohexadiene, furan, thiofuran, pyrrole,
isopyrole, isoazole, pyrazole, isoimidazole, pyran, pyrone,
benzene, pyridine, pyridazine, pyrimidine, pyrazine and oxazine.
Examples of fused ring structures include, but are not limited to
indene, benzofuran, thionaphthene, indole and naphthalene.
In one variation of this embodiment, illustrated below, the linker
has the general structure R.sub.21 Z.sub.1 C(O)R.sub.22 R.sub.29
Z.sub.2 C(O) where R.sub.21 is a C.sub.1-5 alkyl which is attached
to the 4' ring position of the donor xanthene dye, Z.sub.1 and
Z.sub.2 are each independently either NH, sulfur or oxygen, C(O) is
a carbonyl group, R.sub.22 is a substituent which includes an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon, R.sub.29 is a C.sub.1-5 alkyl, and the
terminal carbonyl group is attached to the ring structure of the
acceptor dye. ##STR28##
A preferred embodiment of this linker is where R.sub.21 and
R.sub.29 are methylene, Z.sub.1 and Z.sub.2 are NH, and R.sub.22 is
benzene, as shown below. ##STR29##
TABLE 2 ______________________________________ ##STR30## ##STR31##
##STR32## ##STR33## ##STR34## ##STR35## ##STR36## ##STR37##
##STR38## ##STR39## ##STR40## ##STR41## ##STR42## ##STR43##
##STR44## ______________________________________
TABLE 3 ______________________________________ ##STR45## ##STR46##
##STR47## ##STR48## ##STR49## ##STR50## ##STR51## ##STR52##
##STR53## ##STR54## ##STR55## ##STR56## ##STR57##
______________________________________
As illustrated in Example 4 and FIG. 2, energy transfer dyes such
as 5-TMR-B-CF, which include a donor, acceptor and linker as
specified above exhibit enhanced fluorescence as compared to the
acceptor itself and energy transfer fluorescent dyes having the
same donor--acceptor pair where the linker between the
donor--acceptor pair is different. Without being bound by theory,
the enhanced fluorescence intensity observed is believed to be due
to an improved energy transfer orientation between the donor and
acceptor dye which is achieved and maintained by the relatively
rigid R.sub.22 portion of the linker. As a result, the energy
transfer fluorescent dyes of the present invention exhibit enhanced
fluorescent strength as compared to the acceptor fluorophore itself
and energy transfer fluorescent dyes having the same
donor--acceptor pair where the linkage between the donor--acceptor
pair is different. The enhanced fluorescent strength of these dyes
is particularly evident in the presence of 8M urea which serves to
reduce dye stacking.
In one variation of this embodiment, the acceptor is a member of
the xanthene class of dyes having the general structure ##STR58##
where Y.sub.1, Y.sub.2, R.sub.11 -R.sub.16 and X.sub.1 -X.sub.5 are
as specified above.
According to this variation, it is preferred that a linker, such as
the ones described above, is attached to the acceptor xanthene dye
via the X.sub.3 or X.sub.4 substituent of the acceptor xanthene
dye. In a preferred embodiment, as illustrated below, the linker is
attached to the X.sub.3 substituent of the acceptor xanthene dye.
##STR59##
Table 4 provides examples of the above-described energy transfer
dyes according to this embodiment of the invention. It is noted
that although the dyes illustrated in Table 4 include a
5-carboxyfluorescein donor dye and a TAMRA acceptor dye, it should
be understood that a wide variety of other xanthene dyes can be
readily substituted as the donor dye. It should also be understood
that a wide variety of other xanthene dyes, as well as cyanine,
phthalocyanine and squaraine dyes can be readily substituted for
the TAMRA acceptor dye, as has been described above, all of these
variations with regard to the donor and acceptor dyes falling
within the scope of the invention.
TABLE 4
__________________________________________________________________________
##STR60## ##STR61## ##STR62## ##STR63## ##STR64## ##STR65##
##STR66## ##STR67## ##STR68## ##STR69## ##STR70## ##STR71##
__________________________________________________________________________
B. Second Class Of Energy Transfer Dyes
The present invention also relates to a second class of energy
transfer fluorescent dyes, illustrated below, in which the donor
dye and acceptor each are members of the xanthene class of dyes
having the general structure ##STR72## where Y.sub.1, Y.sub.2,
R.sub.11 -R.sub.16 and X.sub.1 -X.sub.5 are as specified above.
According to this embodiment, the linker is attached to the X.sub.3
or X.sub.4 substituent of both the donor and acceptor dyes, as
illustrated below. ##STR73##
In this embodiment, the linker is preferably short and/or rigid as
this has been found to enhance the transfer of energy between the
donor and acceptor dyes. For example, in one variation of this
embodiment, the linker preferably has a backbone attaching the
donor to the acceptor which is less than 9 atoms in length. In
another variation of this embodiment, the linker includes a
functional group which gives the linker some degree of structural
rigidity, such as an alkene, diene, an alkyne, a five and six
membered ring having at least one unsaturated bond or a fused ring
structure. In yet another variation, the linker has the general
formula R.sub.25 Z.sub.3 C(O) or R.sub.25 Z.sub.3 C(O)R.sub.26
Z.sub.4 C(O) where R.sub.25 is attached to the donor dye, C(O) is a
carbonyl group and the terminal carbonyl group is attached to the
acceptor dye, R.sub.25 and R.sub.26 are each selected from the
group of C.sub.1-4 alkyl, and Z.sub.3 and Z.sub.4 are each
independently either NH, O or S.
Examples of donor and acceptor dyes which may be used in this
embodiment include, but are not limited to fluorescein, 5 or 6
carboxyfluorescein, 5 or 6 carboxy-HEX, NAN, CI-FLAN, TET, JOE,
ZOE, 4,7-dichlorofluoresceins, asymmetric benzoxanthene dyes,
rhodamine, 5 or 6 carboxyrhodamine, 5 or 6 carboxy-R110, 5 or 6
carboxy-R6G, N,N,N',N'-tetramethyl (5 or 6)-carboxyrhodamine
(TAMRA), 5 or 6 carboxy-X-rhodamine (ROX) and
4,7-dichlororhodamines. Illustrated in Table 2 are the structures
of these dyes.
In another variation of this embodiment, the linker includes a
R.sub.27 Z.sub.5 C(O) group where R.sub.27 is a C.sub.1-5 alkyl
attached to the donor dye, Z.sub.5 is either NH, sulfur or oxygen,
and C(O) is a carbonyl group attached to the acceptor dye.
Table 5 provides examples of the second class of energy transfer
dyes according to the present invention. It is noted that although
the dyes illustrated in Table 5 include a 5-aminomethylfluorescein
donor dye, it should be understood that a wide variety of other
xanthene dyes can be readily substituted as the donor dye. It
should also be understood that a wide variety of other xanthene
dyes, as well as cyanine, phthalocyanine and squaraine dyes can be
readily substituted for the TAMRA acceptor dye, as has been
described above, all of these variations with regard to the donor
and acceptor dyes falling within the scope of the invention.
TABLE 5
__________________________________________________________________________
##STR74## ##STR75## ##STR76## ##STR77## ##STR78## ##STR79##
##STR80## ##STR81## ##STR82## ##STR83## ##STR84## ##STR85##
##STR86## ##STR87## ##STR88## ##STR89## ##STR90## ##STR91##
##STR92## ##STR93##
__________________________________________________________________________
C. Third Class Of Energy Transfer Dyes
The third class of energy transfer fluorescent dyes include a
4,7-dichlororhodamine dye as the acceptor dye and a dye which
produces an emission which the 4,7-dichlororhodamine dye can absorb
as the donor dye. These dyes exhibit enhanced fluorescence
intensity as compared to the acceptor dye alone. In addition,
4,7-dichlororhodamine dyes exhibit a narrower emission spectrum
than other rhodamine dyes which facilitates their use in multiple
component analyses.
In a preferred embodiment, these energy transfer dyes include those
dyes according to the first and second classes of dyes in which the
acceptor is a 4,7-dichlororhodamine dye.
1. 4,7-Dichlororhodamine Dyes
4,7-dichlororhodamine dye compounds have the general structure
##STR94## where: R.sub.1 -R.sub.4 are each independently hydrogen,
alkyl or where R.sub.1 and R.sub.5, R.sub.2 and R.sub.6, R.sub.3
and R.sub.8, R.sub.4 and R.sub.9 are taken together to form a ring,
and combinations thereof;
R.sub.5 -R.sub.10 are each independently hydrogen, fluorine,
chlorine, bromine, iodine, carboxyl, alkyl, alkene, alkyne,
sulfonate, sulfone, amino, ammonium, amido, nitrile, alkoxy,
phenyl, or substituted phenyl, or where adjacent substituents are
taken together to form a ring, and combinations thereof;
X.sub.1, X.sub.3 and X.sub.4 are each independently hydrogen,
fluorine, chlorine, bromine, iodine, carboxyl, alkyl, alkene,
alkyne, sulfonate, sulfone, amino, ammonium, amido, nitrile, or
alkoxy, or where adjacent substituents are taken together to form a
ring, and combinations thereof; and
X.sub.2 and X.sub.5 are chlorine.
Dyes falling within the 4,7-dichlororhodamine class of dyes and
their synthesis are described in U.S. application Ser. No.:
08/672,196; filed: Jun. 27, 1996; entitled: "4,7-DICHLORORHODAMINE
DYES" which is incorporated herein by reference.
With regard to R.sub.1 -R.sub.4, alkyl substituents may include
between about 1 to 8 carbon atoms (i.e., methyl, ethyl, propyl,
isopropyl, tertbutyl, isobutyl, sec-butyl, neopentyl, tert-pentyl,
and the like) and may be straight-chain and branched hydrocarbon
moieties. In a preferred embodiment, R.sub.1 -R.sub.4 are each
independently either hydrogen, methyl, or ethyl and more preferably
either hydrogen or methyl.
With regard to R.sub.5 -R.sub.10, alkyl, alkene, alkyne and alkoxy
substituents preferably include between about 1 to 8 carbon atoms
(i.e., methyl, ethyl, propyl, isopropyl, tert-butyl, isobutyl,
sec-butyl, neopentyl, tert-pentyl, and the like) and may be
straight-chain and branched hydrocarbon moieties.
With regard to R.sub.1 -R.sub.10, R.sub.1 and R.sub.5, R.sub.2 and
R.sub.6, R.sub.3 and R.sub.8, R.sub.4 and R.sub.9 may each
independently be taken together to form a 5, 6, or 7 membered
ring.
In one embodiment, R.sub.6 and R.sub.7 is benzo, and/or, R.sub.9
and R.sub.10 is benzo. In a preferred embodiment, R.sub.5 -R.sub.10
are each independently either hydrogen, methyl, or ethyl and more
preferably either hydrogen or methyl.
With regard to X.sub.1, X.sub.3 and X.sub.4, X.sub.1 is preferably
a carboxylate and one of X.sub.3 and X.sub.4 may include a
substituent which is used to link the 4,7-dichlororhodamine
acceptor dye to a donor dye or to link a nucleotide or an
oligonucleotide to the energy transfer dye. The R.sub.8 substituent
at the 4' ring position may also be used to link the acceptor to
either the donor dye or to a biomolecule such as a nucleotide or
oligonucleotide.
In one particularly preferred acceptor dye that may be used in the
present invention, referred to herein as DR110-2, R.sub.1 -R.sub.10
taken separately are hydrogen, X.sub.1 is carboxylate, and one of
X.sub.3 and X.sub.4 is a linking group (L), the other being
hydrogen. The structure of DR110-2 is shown below. ##STR95##
In a second particularly preferred acceptor dye that may be used in
the present invention, referred to herein as DR6G-2, one of R.sub.1
and R.sub.2 is ethyl, the other being hydrogen, one of R.sub.3 and
R.sub.4 is ethyl, the other being hydrogen, R.sub.5 and R.sub.8
taken separately are methyl, R.sub.6, R.sub.7, R.sub.9, and
R.sub.10 are hydrogen, X.sub.1 is carboxylate, and one of X.sub.3
and X.sub.4 is a linking group, the other being hydrogen. The
structure of DR6G-2 is shown below. ##STR96##
In a third particularly preferred acceptor dye that may be used in
the present invention, referred to herein as DTMR, R.sub.1 -R.sub.6
taken separately are hydrogen, Y.sub.1 -Y.sub.4 taken separately
are methyl, X.sub.1 is carboxylate, and one of X.sub.2 and X.sub.3
is linking group, the other being hydrogen. The structure of DTMR
is shown below. ##STR97##
In a fourth particularly preferred acceptor dye that may be used in
the present invention, referred to herein as DROX, R.sub.1 and
R.sub.6 are taken together to form a six membered ring, R.sub.2 and
R.sub.5 are taken together to form a six membered ring, R.sub.3 and
R.sub.7 are taken together to form a six membered ring, R.sub.4 and
R.sub.8 are taken together to form a six membered ring, R.sub.5 and
R.sub.6 are hydrogen, X.sub.1 is carboxylate, and one of X.sub.3
and X.sub.4 is a linking group, the other being hydrogen. The
structure of DROX is shown below. ##STR98##
FIGS. 3A and 3B show several additional preferred embodiments of
4,7-dichlororhodamine dyes which can be used in the energy transfer
dyes of the present invention.
In compound 3a, one of R.sub.1 and R.sub.2 is ethyl, the other
being hydrogen, R.sub.3 and R.sub.4 taken separately are hydrogen,
R.sub.5 is methyl, R.sub.6 -R.sub.10 taken separately are hydrogen,
X.sub.1 is carboxylate, and one of X.sub.3 and X.sub.4 is a linking
group, the other being hydrogen.
In compound 3b, one of R.sub.1 and R.sub.2 is ethyl, the other
being hydrogen, R.sub.3 and R.sub.4 taken separately are methyl,
R.sub.5 is methyl, R.sub.6 -R.sub.10 taken separately are hydrogen,
X.sub.1 is carboxylate, and, one of X.sub.3 and X.sub.4 is a
linking group, the other being hydrogen.
In compound 3c, R.sub.1 and R.sub.2 taken separately are methyl,
R.sub.3 and R.sub.7 taken together form a six membered ring,
R.sub.4 and R.sub.8 taken together form a six membered ring,
R.sub.5, R.sub.6, R.sub.9, and R.sub.10 taken separately are
hydrogen, X.sub.1 is carboxylate, and, one of X.sub.3 and X.sub.4
is a linking group, the other being hydrogen.
In compound 3d, R.sub.1 and R.sub.2 taken separately are hydrogen,
R.sub.3 and R.sub.7 taken together form a six membered ring,
R.sub.4 and R.sub.8 taken together form a six membered ring,
R.sub.5, R.sub.6, R.sub.9, and R.sub.10 taken separately are
hydrogen, X.sub.1 is carboxylate, and one of X.sub.3 and X.sub.4 is
a linking group, the other being hydrogen.
In compound 3e, one of R.sub.1 and R.sub.2 is ethyl, the other
being hydrogen, R.sub.3 and R.sub.7 taken together form a six
membered ring, R.sub.4 and R.sub.8 taken together form a six
membered ring, R.sub.5 is methyl, R.sub.6, R.sub.9 and R.sub.10
taken separately are hydrogen, X.sub.1 is carboxylate, and, one of
X.sub.3 and X.sub.4 is a linking group, the other being
hydrogen.
In compound 3f, R.sub.1 and R.sub.2 taken separately are hydrogen,
R.sub.3 and R.sub.4 taken separately are methyl, R.sub.5 -R.sub.10
taken separately are hydrogen, X.sub.1 is carboxylate, and, one of
X.sub.3 and X.sub.4 is linking group, the other being hydrogen.
FIGS. 4A and 4B show preferred generalized synthesis schemes for
the preparation of 4,7-dichlororhodamine dyes used in the energy
transfer dyes of this invention. The variable substituents
indicated in each figure are as previously defined.
FIG. 4A shows a generalized synthesis wherein the substituent
X.sub.1 can be other than carboxylate. In the figure, X' indicates
moieties which are precursors to X.sub.1. In the method illustrated
in FIG. 4A, two equivalents of a 3-aminophenol derivative 4a/4b,
such as 3-dimethylaminophenol, is reacted with one equivalent of a
dichlorobenzene derivative 4c, e.g.,
4-carboxy-3,6,dichloro-2-sulfobenzoic acid cyclic anhydride, i.e.,
where the X.sub.1 ' moieties of 4c taken together are,
##STR99##
The reactants are then heated for 12 h in a strong acid, e.g.,
polyphosphoric acid or sulfuric acid, at 180 .degree. C. The crude
dye 4d is precipitated by addition to water and isolated by
centrifugation. To form a symmetrical product, the substituents of
reactants 4a and 4b are the same, while to form an asymmetrical
product, the substituents are different.
FIG. 4B shows a generalized synthesis wherein the substituent
X.sub.1 is carboxylate. In the method of FIG. 4B, two equivalents
of a 3-aminophenol derivative 4a/4b, such as 3-dimethylaminophenol,
is reacted with one equivalent of a phthalic anhydride derivative
4e, e.g. 3,6-dichlorotrimellitic acid anhydride. The reactants are
then heated for 12 h in a strong acid, e.g., polyphosphoric acid or
sulfuric acid, at 180.degree. C. The crude dye 4d is precipitated
by addition to water and isolated by centrifugation. To form a
symmetrical product, the substituents of reactants 4a and 4b are
the same, while to form an asymmetrical product, the substituents
are different.
2. Energy Transfer Dyes With 4,7-Dichlororhodamine As The
Acceptor
In general, the energy transfer dyes of the present invention
include a donor dye which absorbs light at a first wavelength and
emits excitation energy in response, a 4,7-dichlororhodamine
acceptor dye which is capable of absorbing the excitation energy
emitted by the donor dye and fluorescing at a second wavelength in
response, and a linker which attaches the donor dye to the acceptor
dye. Prefered examples of this class of dyes which use a
4,7-dichlororhodamine dye as the acceptor dye is illustrated in
Table 1.
Examples of acceptor dyes which may be used in this class of dyes
include, but are not limited to DR110-2, DR6G-2, DTMR, DROX, as
illustrated above, as well as the dyes illustrated in FIGS.
3A-3B.
One subclass of these energy transfer fluorescent dyes are the dyes
according to the first class of dyes of the present invention in
which the acceptor dye is a 4,7-dichlororhodamine dye. The general
structure of these dyes is illustrated below. ##STR100##
Table 4 provides examples of the energy transfer dyes belonging to
the first class of dyes in which a 4,7 dichlororhodamine is used as
the acceptor dye. It is noted that although the dyes illustrated in
Table 4 include a 5-carboxyfluorescein donor dye and a 5 or 6
carboxy DTMR as the acceptor dye, it should be understood that a
wide variety of other xanthene dyes can be readily substituted as
the donor dye and a wide variety of other 4,7-dichlororhodamine
dyes can be readily substituted for the DTMR acceptor dye, all of
these variations with regard to the donor and acceptor dyes being
intended to fall within the scope of the invention.
Another subclass of these energy transfer fluorescent dyes are the
dyes according to the second class of dyes of the present invention
in which the acceptor dye is a 4,7-dichlororhodamine dye. The
general structure of these dyes where the donor xanthene dye and
acceptor 4,7-dichlororhodamine dye are linked to each other at
either the five or six ring positions of the donor and acceptor
dyes is illustrated below. ##STR101##
As described above, in this embodiment, the linker attaching the
donor to the acceptor dye is preferably short and/or rigid as this
has been found to enhance the transfer of energy between the donor
and acceptor dyes. The substituent labels shown above correspond to
the same groups of substituents as has been specified with regard
to the other dyes.
Table 5 provides examples of the second class of energy transfer
dyes according to the present invention in which 4,7
dichlororhodamine is used as the acceptor dye. It is noted that
although the dyes illustrated in Table 5 include a
5-aminomethylfluorescein donor dye, it should be understood that a
wide variety of other xanthene dyes can be readily substituted as
the donor dye. It should also be understood that a wide variety of
other 4,7-dichlororhodamine dyes can be readily substituted for the
acceptor dye shown in Table 5 since, as has been described above,
all of these variations with regard to the donor and acceptor dyes
are intended to fall within the scope of the invention.
D. Fourth Class Of Energy Transfer Dyes
The present invention also relates to a fourth class of energy
transfer fluorescent dyes in which the donor dye is a member of the
xanthene class of dyes, and the acceptor dye is a member of the
xanthene, cyanine, phthalocyanine or squaraine classes of dyes.
Within this class of energy transfer dyes, it is preferred that the
donor be a member of the fluorescein class of dyes and the acceptor
dye have an emission maximum that is greater than about 600 nm
and/or an emission maximum that is at least about 100 nm greater
than the absorbance maximum of the donor dye.
The fourth class of dyes of the present invention exhibit unusually
large Stoke shifts, as measured by the difference between the
absorbance of the donor and the emission of the acceptor. In
addition, these dyes exhibit efficient energy transfer in that
minimal donor fluorescence is observed. Interestingly, energy is
transfered from the donor to the acceptor in some of the dyes
belonging to this class even though the absorbance spectrum of the
acceptor dye does not overlap with the emission spectrum of the
donor dye.
Examples of acceptor dyes which may be used in this embodiment
include, but are not limited to 5-carboxy-X-rhodamine (ROX) and
Cy5.
The energy transfer dyes of this embodiment also include a linker
which attaches the donor to the acceptor. The linker used to attach
the donor to the acceptor dye may be any linker according to the
first and second classes of dyes. However, it is foreseen that
alternate linkers may be used in this class of dyes.
In one embodiment of this class of dyes, the linker is attached to
the 4' position of the donor dye's xanthene ring structure. The
linker preferably has a general structure R.sub.21 Z.sub.1
C(O)R.sub.22 R.sub.28, as described above where R.sub.21 is a
C.sub.1-5 alkyl which is attached to the 4' ring position of the
donor xanthene dye, Z.sub.1 is either NH, sulfur or oxygen, C(O) is
a carbonyl group, R.sub.22 is a substituent which includes an
alkene, diene, alkyne, a five and six membered ring having at least
one unsaturated bond or a fused ring structure which is attached to
the carbonyl carbon, and R.sub.28 is a functional group which
attaches the linker to the acceptor dye. In cases where the
acceptor dye is a member of the xanthene class of dyes, the linker
is preferably attached to acceptor at the 5 position of the
xanthene ring structure.
Table 6 provides examples of the above-described energy transfer
dyes according to the present invention. It is noted that although
the dyes illustrated in Table 6 include a 5-carboxyfluorescein
donor dye it should be understood that a wide variety of other
xanthene dyes can be readily substituted as the donor dye. It
should also be understood that a wide variety of other xanthene
dyes, as well as cyanine, phthalocyanine and squaraine dyes can be
readily substituted for the 5-carboxy ROX and Cy5 acceptor dyes, as
has been described above, all of these variations with regard to
the donor and acceptor dyes falling within the scope of the
invention.
The energy transfer dyes of this embodiment exhibit unusually large
Stoke shifts which make these dyes particularly well suited for use
with dyes having smaller Stoke shifts in four dye DNA sequencing.
For example, FIGS. 5 and 6 illustrate two sets of four dyes which
are spectrally resolvable from each other. Within FIG. 5, 5ROX-CF
is a dye falling within the scope of the fourth class of dyes
described above. Meanwhile, FIG. 6 includes 5ROX-CF and Cy5-CF
which both fall within the scope of the fourth class of dyes
described above.
As can be seen from the emission spectra of 5ROX-CF and Cy5-CF
illustrated in FIG. 6, very little fluorescence from the donor dye
(5-carboxyfluorescein, 520 nm) is observed in these dyes. This is
an unexpected result in view of the large difference between the
emission maximum of the donor dye (fluorescein) and the absorbance
maximum of the acceptor dyes (ROX, 590 nm, Cy5, 640 nm).
TABLE 6
__________________________________________________________________________
##STR102## ##STR103##
__________________________________________________________________________
II. Reagents Including Energy Transfer Dyes Of The Present
Invention
The present invention also relates to fluorescent reagents which
incorporate an energy transfer fluorescent dye according to the
present invention. As described in greater detail in Section III,
these reagents may be used in a wide variety of methods for
detecting the presence of a component in a sample.
The fluorescent reagents of the present invention include any
molecule or material to which the energy transfer dyes of the
invention can be attached and used to detect the presence of the
reagent based on the fluorescence of the energy transfer dye. Types
of molecules and materials to which the dyes of the present
invention may be attached to form a reagent include, but are not
limited to proteins, polypeptides, polysaccharides, nucleotides,
nucleosides, oligonucleotides, oligonucleotide analogs (such as a
peptide nucleic acid), lipids, solid supports, organic and
inorganic polymers, and combinations and assemblages thereof, such
as chromosomes, nuclei, living cells, such as bacteria, other
microorganisms, mammalian cells, and tissues.
Preferred classes of reagents of the present invention are
nucleotides, nucleosides, oligonucleotides and oligonucleotide
analogs which have been modified to include an energy transfer dye
of the invention. Examples of uses for nucleotide and nucleoside
reagents include, but are not limited to, labeling oligonucleotides
formed by enzymatic synthesis, e.g., nucleoside triphosphates used
in the context of PCR amplification, Sanger-type oligonucleotide
sequencing, and nicktranslation reactions. Examples of uses for
oligonucleotide reagents include, but are not limited to, as DNA
sequencing primers, PCR primers, oligonucleotide hybridization
probes, and the like.
One particular embodiment of the reagents are labeled nucleosides
(NTP), such as cytosine, adenosine, guanosine, and thymidine,
labeled with an energy transfer fluorescent dye of the present
invention. These reagents may be used in a wide variety of methods
involving oligonucleotide synthesis. Another related embodiment are
labeled nucleotides, e.g., mono-, di- and triphosphate nucleoside
phosphate esters. These reagents include, in particular,
deoxynucleoside triphosphates (dNTP), such as deoxycytosine
triphosphate, deoxyadenosine triphosphate, deoxyguanosine
triphosphate, and deoxythymidine triphosphate, labeled with an
energy transfer fluorescent dye of the present invention. These
reagents may be used, for example, as polymerase substrates in the
preparation of dye labeled oligonucleotides. These reagents also
include labeled dideoxynucleoside triphosphates (ddNTP), such as
dideoxycytosine triphosphate, dideoxyadenosine triphosphate,
dideoxyguanosine triphosphate, and dideoxythymidine triphosphate,
labeled with an energy transfer fluorescent dye of the present
invention. These reagents may be used, for example, in dye
termination sequencing.
Another embodiment of reagents are oligonucleotides which includes
an energy transfer fluorescent dye of the present invention. These
reagents may be used, for example, in dye primer sequencing.
As used herein, "nucleoside" refers to a compound consisting of a
purine, deazapurine, or pyrimidine nucleoside base, e.g., adenine,
guanine, cytosine, uracil, thymine, deazaadenine, deazaguanosine,
and the like, linked to a pentose at the 1' position, including
2'-deoxy and 2'-hydroxyl forms, e.g. as described in Kornberg and
Baker, DNA Replication, 2nd Ed. (Freeman, San Francisco, 1992). The
term "nucleotide" as used herein refers to a phosphate ester of a
nucleoside, e.g., mono, di and triphosphate esters, wherein the
most common site of esterification is the hydroxyl group attached
to the C-5 position of the pentose. "Analogs" in reference to
nucleosides include synthetic nucleosides having modified base
moieties and/or modified sugar moieties, e.g. described generally
by Scheit, Nucleotide Analogs (John Wiley, New York, 1980). The
terms "labeled nucleoside" and "labeled nucleotide" refer to
nucleosides and nucleotides which are covalently attached to an
energy transfer dye through a linkage.
As used herein, the term "oligonucleotide" refers to linear
polymers of natural or modified nucleoside monomers, including
double and single stranded deoxyribonucleosides, ribonucleosides,
.alpha.-anomeric forms thereof, and the like. Usually the
nucleoside monomers are linked by phosphodiester linkages, where as
used herein, the term "phosphodiester linkage" refers to
phosphodiester bonds or analogs thereof including phosphorothioate,
phosphorodithioate, phosphoroselenoate, phosphorodiselenoate,
phosphoroanilothioate, phosphoranilidate, phosphoramidate, and the
like, including associated counterions, e.g., H, NH.sub.4, Na, and
the like if such counterions are present. The oligonucleotides
range in size form a few monomeric units, e.g. 8-40, to several
thousands of monomeric units. Whenever an oligonucleotide is
represented by a sequence of letters, such as "ATGCCTG," it will be
understood that the nucleotides are in 5'.fwdarw.3' order from left
to right and that "A" denotes deoxyadenosine, "C" denotes
deoxycytidine, "G" denotes deoxyguanosine, and "T" denotes
thymidine, unless otherwise noted.
Nucleoside labeling can be accomplished using any of a large number
of known nucleoside labeling techniques using known linkages,
linking groups, and associated complementary functionalities. The
linkage linking the dye and nucleoside should (i) be stable to
oligonucleotide synthesis conditions, (ii) not interfere with
oligonucleotide-target hybridization, (iii) be compatible with
relevant enzymes, e.g., polymerases, ligases, and the like, and
(iv) not quench the fluorescence of the dye.
Preferably, the dyes are covalently linked to the 5-carbon of
pyrimidine bases and to the 7-carbon of 7-deazapurine bases.
Several suitable base labeling procedures have been reported that
can be used with the invention, e.g. Gibson et al, Nucleic Acids
Research, 15 6455-6467 (1987); Gebeyehu et al, Nucleic Acids
Research, 15 4513-4535 (1987); Haralambidis et al, Nucleic Acids
Research, 15 4856-4876 (1987); Nelson et al., Nucleosides and
Nucleotides, 5(3) 233-241 (1986); Bergstrom, et al., JACS, 111
374-375 (1989); U.S. Pat. Nos. 4,855,225, 5,231,191, and 5,449,767,
each of which is incorporated herein by reference.
Preferably, the linkages are acetylenic amido or alkenic amido
linkages, the linkage between the dye and the nucleotide base being
formed by reacting an activated N-hydroxysuccinimide (NHS) ester of
the dye with an alkynylamino-, alkynylethoxyamino- or
alkenylamino-derivatized base of a nucleotide. More preferably, the
resulting linkage is proargyl-1-ethoxyamido
(3-(amino)ethoxy-1-propynyl), 3-(carboxy)amino-1-propynyl or
3-amino-1-propyn-1-yl.
Several preferred linkages for linking the dyes of the invention to
a nucleoside base are shown below. ##STR104## where R.sub.1 and
R.sub.2 taken separately are H, alkyl, a protecting group or a
fluorescent dye.
The synthesis of alkynylamino-derivatized nucleosides is taught by
Hobbs et al. in European Patent Application No. 87305844.0, and
Hobbs et al., J. Org. Chem., 54 3420 (1989), which is incorporated
herein by reference. Briefly, the alkynylamino-derivatized
nucleotides are formed by placing the appropriate
halodideoxynucleoside (usually 5-iodopyrimidine and
7-iodo-7-deazapurine dideoxynucleosides as taught by Hobbs et al.
(cited above)) and Cu(I) in a flask, flushing with argon to remove
air, adding dry DMF, followed by addition of an alkynylamine,
triethyl-amine and Pd(0). The reaction mixture can be stirred for
several hours, or until thin layer chromatography indicates
consumption of the halodideoxynucleoside. When an unprotected
alkynylamine is used, the alkynylaminonucleoside can be isolated by
concentrating the reaction mixture and chromatographing on silica
gel using an eluting solvent which contains ammonium hydroxide to
neutralize the hydrohalide generated in the coupling reaction. When
a protected alkynylamine is used, methanol/methylene chloride can
be added to the reaction mixture, followed by the bicarbonate form
of a strongly basic anion exchange resin. The slurry can then be
stirred for about 45 minutes, filtered, and the resin rinsed with
additional methanol/methylene chloride. The combined filtrates can
be concentrated and purified by flash-chromatography on silica gel
using a methanol-methylene chloride gradient. The triphosphates are
obtained by standard techniques.
The synthesis of oligonucleotides labeled with an energy transfer
dye of the present invention can be accomplished using any of a
large number of known oligonucleotide labeling techniques using
known linkages, linking groups, and associated complementary
functionalities. For example, labeled oligonucleotides may be
synthesized enzymatically, e.g., using a DNA polymerase or ligase,
e.g., Stryer, Biochemistry, Chapter 24, W. H. Freeman and Company
(1981), or by chemical synthesis, e.g., by a phosphoramidite
method, a phosphite-triester method, and the like, e.g., Gait,
Oligonucleotide Synthesis, IRL Press (1990). Labels may be
introduced during enzymatic synthesis utilizing labeled nucleoside
triphosphate monomers, or introduced during chemical synthesis
using labeled non-nucleotide or nucleotide phosphoramidites, or may
be introduced subsequent to synthesis.
Generally, if the labeled oligonucleotide is made using enzymatic
synthesis, the following procedure may be used. A template DNA is
denatured and an oligonucleotide primer is annealed to the template
DNA. A mixture of deoxynucleoside triphosphates is added to the
reaction including dGTP, dATP, dCTP, and dTTP where at least a
fraction of one of the deoxynucleotides is labeled with a dye
compound of the invention as described above. Next, a polymerase
enzyme is added under conditions where the polymerase enzyme is
active. A labeled polynucleotide is formed by the incorporation of
the labeled deoxynucleotides during polymerase strand synthesis. In
an alternative enzymatic synthesis method, two primers are used
instead of one, one primer complementary to the +strand and the
other complementary to the--strand of the target, the polymerase is
a thermostable polymerase, and the reaction temperature is cycled
between a denaturation temperature and an extension temperature,
thereby exponentially synthesizing a labeled complement to the
target sequence by PCR, e.g., PCR Protocols, Innis et al. eds.,
Academic Press (1990).
Generally, if the labeled oligonucleotide is made using a chemical
synthesis, it is preferred that a phosphoramidite method be used.
Phosphoramidite compounds and the phosphoramidite method of
polynucleotide synthesis are preferred in synthesizing
oligonucleotides because of the efficient and rapid coupling and
the stability of the starting materials. The synthesis is performed
with the growing oligonucleotide chain attached to a solid support,
so that excess reagents, which are in the liquid phase, can be
easily removed by filtration, thereby eliminating the need for
purification steps between cycles.
In view of the utility of phosphoramidite reagents in labeling
nucleosides and oligonucleotides, the present invention also
relates to phosphoramidite compounds which include an energy
transfer dye of the present invention.
Detailed descriptions of the chemistry used to form
oligonucleotides by the phosphoramidite method are provided in
Caruthers et al., U.S. Pat. No. 4,458,066; Caruthers et al., U.S.
Pat. No. 4,415,732; Caruthers et al., Genetic Engineering, 4 1-17
(1982); Users Manual Model 392 and 394 Polynucleotide Synthesizers,
pages 6-1 through 6-22, Applied Biosystems, Part No. 901237 (1991),
each of which are incorporated by reference in their entirety.
The following briefly describes the steps of a typical
oligonucleotide synthesis cycle using the phosphoramidite method.
First, a solid support including a protected nucleotide monomer is
treated with acid, e.g., trichloroacetic acid, to remove a
5'-hydroxyl protecting group, freeing the hydroxyl for a subsequent
coupling reaction. An activated intermediate is then formed by
simultaneously adding a protected phosphoramidite nucleoside
monomer and a weak acid, e.g., tetrazole, to the reaction. The weak
acid protonates the nitrogen of the phosphoramidite forming a
reactive intermediate. Nucleoside addition is complete within 30 s.
Next, a capping step is performed which terminates any
polynucleotide chains that did not undergo nucleoside addition.
Capping is preferably done with acetic anhydride and
1-methylimidazole. The internucleotide linkage is then converted
from the phosphite to the more stable phosphotriester by oxidation
using iodine as the preferred oxidizing agent and water as the
oxygen donor. After oxidation, the hydroxyl protecting group is
removed with a protic acid, e.g., trichloroacetic acid or
dichloroacetic acid, and the cycle is repeated until chain
elongation is complete. After synthesis, the polynucleotide chain
is cleaved from the support using a base, e.g., ammonium hydroxide
or t-butyl amine. The cleavage reaction also removes any phosphate
protecting groups, e.g., cyanoethyl. Finally, the protecting groups
on the exocyclic amines of the bases and the hydroxyl protecting
groups on the dyes are removed by treating the polynucleotide
solution in base at an elevated temperature, e.g., 55.degree.
C.
Any of the phosphoramidite nucleoside monomers may be dye-labeled
phosphoramidites. If the 5'-terminal position of the nucleotide is
labeled, a labeled non-nucleotidic phosphoramidite of the invention
may be used during the final condensation step. If an internal
position of the oligonucleotide is to be labeled, a labeled
nucleotidic phosphoramidite of the invention may be used during any
of the condensation steps.
Subsequent to their synthesis, oligonucleotides may be labeled at a
number of positions including the 5'-terminus. See Oligonucleotides
and Analogs, Eckstein ed., Chapter 8, IRL Press (1991) and Orgel et
al., Nucleic Acids Research 11(18) 6513 (1983); U.S. Pat. No.
5,118,800, each of which are incorporated by reference
Oligonucleotides may also be labeled on their phosphodiester
backbone (Oligonucleotides and Analogs, Eckstein ed., Chapter 9) or
at the 3'-terminus (Nelson, Nucleic Acids Research 20(23)
6253-6259, and U.S. Pat. Nos. 5,401,837 and 5,141,813, both patents
hereby incorporated by reference. For a review of oligonucleotide
labeling procedures see R. Haugland in Excited States of
Biopolymers, Steiner ed., Plenum Press, New York (1983).
In one preferred post-synthesis chemical labeling method an
oligonucleotide is labeled as follows. A dye including a carboxy
linking group is converted to the n-hydroxysuccinimide ester by
reacting with approximately 1 equivalent of
1,3-dicyclohexylcarbodiimide and approximately 3 equivalents of
n-hydroxysuccinimide in dry ethyl acetate for 3 hours at room
temperature. The reaction mixture is washed with 5% HCl, dried over
magnesium sulfate, filtered, and concentrated to a solid which is
resuspended in DMSO. The DMSO dye stock is then added in excess
(10-20.times.) to an aminohexyl derivatized oligonucleotide in
0.25M bicarbonate/carbonate buffer at pH 9.4 and allowed to react
for 6 hours, e.g., U.S. Pat. No. 4,757,141. The dye labeled
oligonucleotide is separated from unreacted dye by passage through
a size-exclusion chromatography column eluting with buffer, e.g.,
0.1 molar triethylamine acetate (TEM). The fraction containing the
crude labeled oligonucleotide is further purified by reverse phase
HPLC employing gradient elution.
III. Methods Employing Dyes And Reagents Of The Present
Invention
The energy transfer dyes and reagents of the present invention may
be used in a wide variety of methods for detecting the presence of
a component in a sample by labeling the component in the sample
with a reagent containing the dye. In particular, the energy
transfer dyes and reagents of the present invention are well suited
for use in methods which combine separation and fluorescent
detection techniques, particularly methods requiring the
simultaneous detection of multiple spatially-overlapping analytes.
For example, the dyes and reagents are particularly well suited for
identifying classes of oligonucleotides that have been subjected to
a biochemical separation procedure, such as electrophoresis, where
a series of bands or spots of target substances having similar
physiochemical properties, e.g. size, conformation, charge,
hydrophobicity, or the like, are present in a linear or planar
arrangement. As used herein, the term "bands" includes any spatial
grouping or aggregation of analytes on the basis of similar or
identical physiochemical properties. Usually bands arise in the
separation of dye-oligonucleotide conjugates by
electrophoresis.
Classes of oligonucleotides can arise in a variety of contexts. In
a preferred category of methods referred to herein as "fragment
analysis" or "genetic analysis" methods, labeled oligonucleotide
fragments are generated through template-directed enzymatic
synthesis using labeled primers or nucleotides, e.g., by ligation
or polymerase-directed primer extension; the fragments are
subjected to a size-dependent separation process, e.g.,
electrophoresis or chromatography; and, the separated fragments are
detected subsequent to the separation, e.g., by laser-induced
fluorescence. In a particularly preferred embodiment, multiple
classes of oligonucleotides are separated simultaneously and the
different classes are distinguished by spectrally resolvable
labels.
One such fragment analysis method is amplified fragment length
polymorphisim detection (AmpFLP) and is based on amplified fragment
length polymorphisms, i.e., restriction fragment length
polymorphisms that are amplified by PCR. These amplified fragments
of varying size serve as linked markers for following mutant genes
through families. The closer the amplified fragment is to the
mutant gene on the chromosome, the higher the linkage correlation.
Because genes for many genetic disorders have not been identified,
these linkage markers serve to help evaluate disease risk or
paternity. In the AmpFLPs technique, the polynucleotides may be
labeled by using a labeled oligonucleotide PCR primer, or by
utilizing labeled nucleotide triphosphates in the PCR.
Another fragment analysis method is nick translation. Nick
translation involves a reaction to replace unlabeled nucleotide
triphosphates in a double-stranded DNA molecule with labeled ones.
Free 3'-hydroxyl groups are created within the unlabeled DNA by
"nicks" caused by deoxyribonuclease I (DNAase I) treatment. DNA
polymerase I then catalyzes the addition of a labeled nucleotide to
the 3'-hydroxyl terminus of the nick. At the same time, the 5' to
3'-exonuclease activity of this enzyme eliminates the nucleotide
unit from the 5'-phosphoryl terminus of the nick. A new nucleotide
with a free 3'-OH group is incorporated at the position of the
original excised nucleotide, and the nick is shifted along by one
nucleotide unit in the 3' direction. This 3' shift will result in
the sequential addition of new labeled nucleotides to the DNA with
the removal of existing unlabeled nucleotides. The nick-translated
polynucleotide is then analyzed using a separation process, e.g.,
electrophoresis.
Another exemplary fragment analysis method is based on variable
number of tandem repeats, or VNTRs. VNTRs are regions of
double-stranded DNA that contain adjacent multiple copies of a
particular sequence, with the number of repeating units being
variable. Examples of VNTR loci are pYNZ22, pMCT118, and Apo B. A
subset of VNTR methods are those methods based on the detection of
microsatellite repeats, or short tandem repeats (STRs), i.e.,
tandem repeats of DNA characterized by a short (2-4 bases) repeated
sequence. One of the most abundant interspersed repetitive DNA
families in humans is the (dC-dA)n--(dG-dT)n dinucleotide repeat
family (also called the (CA)n dinucleotide repeat family). There
are thought to be as many as 50,000 to 100,000 (CA)n repeat regions
in the human genome, typically with 15-30 repeats per block. Many
of these repeat regions are polymorphic in length and can therefore
serve as useful genetic markers. Preferably, in VNTR or STR
methods, label is introduced into the polynucleotide fragments by
using a dye-labeled PCR primer.
Another exemplary fragment analysis method is DNA sequencing. In
general, DNA sequencing involves an extension/termination reaction
of an oligonucleotide primer. Included in the reaction mixture are
deoxynucleoside triphosphates (dNTPs) which are used to extend the
primer. Also included in the reaction mixture is at least one
dideoxynucleoside triphosphate (ddNTP) which when incorporated onto
the extended primer prevents the further extension of the primer.
After the extension reaction has been terminated, the different
termination products that are formed are separated and analyzed in
order to determine the positioning of the different
nucleosides.
Fluorescent DNA sequencing may generally be divided into two
categories, "dye primer sequencing" and "dye terminator
sequencing". In dye primer sequencing, a fluorescent dye is
incorporated onto the primer being extended. Four separate
extension/termination reactions are then run in parallel, each
extension reaction containing a different dideoxynucleoside
triphosphate (ddNTP) to terminate the extension reaction. After
termination, the reaction products are separated by gel
electrophoresis and analyzed. See, for example, Ansorge et al.,
Nucleic Acids Res. 15 4593-4602 (1987).
In one variation of dye primer sequencing, different primers are
used in the four separate extension/termination reactions, each
primer containing a different spectrally resolvable dye. After
termination, the reaction products from the four
extension/termination reactions are pooled, electrophoretically
separated, and detected in a single lane. See, for example, Smith
et al., Nature 321 674-679 (1986). Thus, in this variation of dye
primer sequencing, by using primers containing a set of spectrally
resolvable dyes, products from more than one extension/termination
reactions can be simultaneously detected.
In dye terminator sequencing, a fluorescent dye is attached to each
of the dideoxynucleoside triphosphates. An extension/termination
reaction is then conducted where a primer is extended using
deoxynucleoside triphosphates until the labeled dideoxynucleoside
triphosphate is incorporated into the extended primer to prevent
further extension of the primer. Once terminated, the reaction
products for each dideoxynucleoside triphosphate are separated and
detected. In one embodiment, separate extension/termination
reactions are conducted for each of the four dideoxynucleoside
triphosphates. In another embodiment, a single
extension/termination reaction is conducted which contains the four
dideoxynucleoside triphosphates, each labeled with a different,
spectrally resolvable fluorescent dye.
Thus according to one aspect of the invention, a method is provided
for conducting dye primer sequencing using one or more
oligonucleotide reagents of the present invention. According to
this method, a mixture of extended labeled primers are formed by
hybridizing a nucleic acid sequence with a fluorescently labeled
oligonucleotide primer in the presence of deoxynucleoside
triphosphates, at least one dideoxynucleoside triphosphate and a
DNA polymerase. The fluorescently labeled oligonucleotide primer
includes an oligonucleotide sequence complementary to a portion of
the nucleic acid sequence being sequenced, and an energy transfer
fluorescent dye attached to the oligonucleotide.
According to the method, the DNA polymerase extends the primer with
the deoxynucleoside triphosphates until a dideoxynucleoside
triphosphate is incorporated which terminates extension of the
primer. After termination, the mixture of extended primers are
separated. The sequence of the nucleic acid sequence is then
determined by fluorescently detecting the mixture of extended
primers formed.
In a further embodiment of this method, four dye primer sequencing
reactions are run, each primer sequencing reaction including a
different fluorescently labeled oligonucleotide primer and a
different dideoxynucleoside triphosphate (ddATP, ddCTP, ddGTP and
ddTTP). After the four dye primer sequencing reactions are run, the
resulting mixtures of extended primers may be pooled. The mixture
of extended primers may then be separated, for example by
electrophoresis and the fluorescent signal from each of the four
different fluorescently labeled oligonucleotide primers detected in
order to determine the sequence of the nucleic acid sequence.
According to a further aspect of the invention, a method is
provided for conducting dye terminator sequencing using one or more
dideoxynucleoside triphosphates labeled with an energy transfer dye
of the present invention. According to this method, a mixture of
extended primers are formed by hybridizing a nucleic acid sequence
with an oligonucleotide primer in the presence of deoxynucleoside
triphosphates, at least one fluorescently labeled dideoxynucleotide
triphosphate and a DNA polymerase. The fluorescently labeled
dideoxynucleotide triphosphate includes a dideoxynucleoside
triphosphate labeled with an energy transfer fluorescent dye of the
present invention.
According to this method, the DNA polymerase extends the primer
with the deoxynucleoside triphosphates until a fluorescently
labeled dideoxynucleoside triphosphate is incorporated into the
extended primer. After termination, the mixture of extended primers
are separated. The sequence of the nucleic acid sequence is then
determined by detecting the fluorescently labeled dideoxynucleoside
attached to the extended primer.
In a further embodiment of this method, the step of forming a
mixture of extended primers includes hybridizing the nucleic acid
sequence with four different fluorescently labeled
dideoxynucleoside triphosphates, i.e., a fluorescently labeled
dideoxycytosine triphosphate, a fluorescently labeled
dideoxyadenosine triphosphate, a fluorescently labeled
dideoxyguanosine triphosphate, and a fluorescently labeled
dideoxythymidine triphosphate.
In each of the above-described fragment analysis methods, the
labeled oligonucleotides are preferably separated by
electrophoretic procedures, e.g. Gould and Matthews, cited above;
Rickwood and Hames, Eds., Gel Electrophoresis of Nucleic Acids: A
Practical Approach, (IRL Press Limited, London, 1981); or Osterman,
Methods of Protein and Nucleic Acid Research, Vol. 1
Springer-Verlag, Berlin, 1984). Preferably the type of
electrophoretic matrix is crosslinked or uncrosslinked
polyacrylamide having a concentration (weight to volume) of between
about 2-20 weight percent. More preferably, the polyacrylamide
concentration is between about 4-8 percent. Preferably in the
context of DNA sequencing in particular, the electrophoresis matrix
includes a strand separating, or denaturing, agent, e.g., urea,
formamide, and the like. Detailed procedures for constructing such
matrices are given by Maniatis et al., "Fractionation of Low
Molecular Weight DNA and RNA in Polyacrylamide Gels Containing 98%
Formamide or 7M Urea," in Methods in Enzymology, 65 299-305 (1980);
Maniatis et al., "Chain Length Determination of Small Double- and
Single-Stranded DNA Molecules by Polyacrylamide Gel
Electrophoresis," Biochemistry, 14 3787-3794 (1975); Maniatis et
al., Molecular Cloning: A Laboratory Manual (Cold Spring Harbor
Laboratory, New York, 1982), pgs. 179-185; and ABI PRISM.TM. 377
DNA Sequencer User's Manual, Rev. A, January 1995, Chapter 2 (p/n
903433, The Perkin-Elmer Corporation, Foster City, Calif.), each of
which are incorporated by reference. The optimal polymer
concentration, pH, temperature, concentration of denaturing agent,
etc. employed in a particular separation depends on many factors,
including the size range of the nucleic acids to be separated,
their base compositions, whether they are single stranded or double
stranded, and the nature of the classes for which information is
sought by electrophoresis. Accordingly application of the invention
may require standard preliminary testing to optimize conditions for
particular separations. By way of example, oligonucleotides having
sizes in the range of between about 20-300 bases have been
separated and detected in accordance with the invention in the
following matrix: 6 percent polyacrylamide made from 19 parts to 1
part acrylamide to bis-acrylamide, formed in a Tris-borate EDTA
buffer at pH 8.3.
After electrophoretic separation, the dye-oligonucleotide
conjugates are detected by measuring the fluorescence emission from
the dye labeled polynucleotides. To perform such detection, the
labeled polynucleotides are illuminated by standard means, e.g.
high intensity mercury vapor lamps, lasers, or the like. Preferably
the illumination means is a laser having an illumination beam at a
wavelength between 488 and 550 nm. More preferably, the
dye-polynucleotides are illuminated by laser light generated by an
argon ion laser, particularly the 488 and 514 nm emission lines of
an argon ion laser, or an the 532 emission line of a neodymium
solid-state YAG laser. Several argon ion lasers are available
commercially which lase simultaneously at these lines, e.g.
Cyonics, Ltd. (Sunnyvale, Calif.) Model 2001, or the like. The
fluorescence is then detected by a light-sensitive detector, e.g.,
a photomultiplier tube, a charged coupled device, or the like.
IV. Kits Incorporating The Energy Transfer Dyes
The present invention also relates to kits having combinations of
energy transfer fluorescent dyes and/or reagents. In one
embodiment, the kit includes at least two spectrally resolvable
energy transfer dyes according to the present invention. In this
kit, the energy transfer dyes preferably include the same donor dye
so that a single light source is needed to excite the dyes.
In another embodiment, the kit includes dideoxycytosine
triphosphate, dideoxyadenosine triphosphate, dideoxyguanosine
triphosphate, and dideoxythymidine triphosphate, each
dideoxynucleotide triphosphate labeled with an energy transfer dye
according to the present invention. In one embodiment, each energy
transfer dye is spectrally resolvable from the other energy
transfer dyes attached to the other dideoxynucleotide
triphosphates. In this kit, the energy transfer dyes preferably
include the same first xanthene dye.
In yet another embodiment, the kit includes at least two
oligonucleotides, each oligonucleotide including an energy transfer
dye according to the present invention. In one embodiment, each
oligonucleotide contains an energy transfer dye which is spectrally
resolvable from the energy transfer dyes attached to the other
oligonucleotides. In another embodiment, the kit includes at least
four oligonucleotides which each contain a spectrally resolvable
energy transfer dye.
The energy transfer fluorescent dyes and their use in DNA
sequencing is illustrated by the following examples. Further
objectives and advantages other than those set forth above will
become apparent from the examples.
Examples
1. Synthesis of 5TMR-B-CF ##STR105##
5TMR-B-CF was synthesized from 5-TMR NHS and
4'-aminomethyl-5-carboxyfluorescein according to the reaction
sequences described in Examples 1A-C. 5TMR-B-CF was then converted
to 5TMR-B-CF-NHS according to the reaction sequence described in 1D
so that the dye could be coupled to a nucleoside, nucleotide or
oligonucleotide primer.
A. Synthesis of 5-TMR-B ##STR106##
A mixture of 4-aminomethylbenzoic acid (3 mg, 19 .mu.mol), 5-TMR
NHS (5 mg, 9 .mu.mol) and triethylamine (20 .mu.L) was suspended in
dimethylformamide (DMF, 200 .mu.L) in a 1.5-mL eppendorf tube. The
mixture was heated to 60.degree. C. for 10 minutes. Reaction
progress was monitored by thin layer chromatography (TLC) on silica
gel with elution with a 400/30/10 mixture of dichloromethane,
methanol and acetic acid. The insoluble 4-aminomethylbenzoic acid
was separated by centrifugation and the DMF solution was decanted
into 5% HCl (1 mL). The insoluble 5TMR-B was separated by
centrifugation, washed with 5% HCl (2.times.1 mL) and dried in a
vacuum centrifuge. The product was dissolved in DMF (200 .mu.L) and
used to prepare 5TMR-B-NHS.
B. Synthesis of 5-TMR-B-NHS ##STR107##
A solution of 5TMR-B in DMF (125 .mu.L), diisopropylethylamine (10
.mu.L) and disuccinimidylcarbonate (10 mg) was combined in a 1.5-mL
eppendorf tube and heated to 60.degree. C. The reaction progress
was monitored by TLC on silica gel with elution with a 600/60/16
mixture of dichloromethane, methanol and acetic acid. After five
minutes, the reaction appeared to be complete. The solution was
diluted into methylene chloride (3 mL) and washed with 250 mM
carbonate/bicarbonate buffer (pH 9, 4.times.1 mL), dried (Na.sub.2
SO.sub.4) and concentrated to dryness on a vacuum centrifuge. The
solid was dissolved in DMF (100 .mu.L). The yield was determined by
diluting an aliquot into pH 9 buffer and measuring the absorbance
at 552 nm. Using an extinction coefficient of 50,000 cm.sup.-1
M.sup.-1, the concentration of 5TMR-B-NHS was 4.8 mM. Yield from
5TMR NHS was 8%.
C. Synthesis of 5TMR-B-CF ##STR108##
A solution of 5TMR-B-NHS (1 .mu.mol in 250 .mu.L DMF) was combined
with a solution of 4'-aminomethyl-5-carboxyfluorescein (CF, 2.2
.mu.mol in 100 .mu.L DMSO) and triethylamine (20 .mu.L) in a 1.5-mL
eppendorf tube. The reaction was monitored by HPLC using a C8
reverse-phase column with a gradient elution of 15% to 35%
acetonitrile vs. 0.1M triethylammonium acetate. HPLC analysis
indicated the 5TMR-B-NHS was consumed, leaving the excess,
unreacted CF. The reaction was diluted with 5% HCl (1 mL) and the
product separated by centrifugation, leaving the unreacted CF in
the aqueous phase. The solid was washed with 5% HCl (4.times.1 mL),
dried in a vacuum centrifuge and taken up in DMF (300 .mu.L). The
yield was quantitative.
D. Synthesis of 5-TMR-B-CF-NHS ##STR109##
A solution of 5TTMR-B-CF (0.6 .mu.mol in 100 .mu.l DMF),
1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (DEC, 2
mg) and N-hydroxysuccinimide (4 mg) were combined in a 1.5-mL
eppendorf tube. The mixture was sonicated briefly and heated to
60.degree. C. The reaction was monitored by TLC on silica gel with
elution with a 600/60/16 mixture of dichioromethane, methanol and
acetic acid. The reaction was complete in 30 minutes and diluted
with 5% HCl. The product was separated by centrifugation and dried
in a vacuum centrifuge. The activated dye was dissolved in DMF (20
.mu.L).
2. Synthesis of 5ROX-CF ##STR110##
A solution of 5ROX NHS (2 .mu.mol in 100 .mu.L DMSO) was mixed with
CF (2 .mu.mol in 100 .mu.L DMSO) and triethylamine (10 .mu.L). The
reaction was followed by HPLC on a C8 reverse phase column using a
gradient elution of 20% to 40% acetonitrile vs. 0.1M TEAA. The
reaction was diluted into 5% HCl (1 mL) and the product collected
by centrifugation, washed with 5% HCl (1.times.1 mL) and dried in a
vacuum centrifuge. The product was taken up in DMF (200 .mu.L).
3. Synthesis of Cy5-CF ##STR111##
A solution of CF (0.4 .mu.mol in 20 .mu.L CMSO) and triethylamine
(2 .mu.L) was added to monoCy5 NHS (approximately 0.3 .mu.mol). The
reaction was followed by HPLC on a C8 reverse phase column using a
gradient elution of 10% to 30% acetonitrile vs. 0.1M TEAA. The
reaction was diluted into 5% HCl (1 mL) and the product collected
by centrifugation, washed with 5% HCl (1.times.1 mL) and dried in a
vacuum centrifuge. The product was taken up in DMF (100 .mu.L).
4. Comparison Of Fluorescence Strength of Energy Transfer Dyes
The following example compares the fluorescence emission strength
of a series of energy transfer dyes according to the present
invention. Dye solutions of 5TMR, 6TMR-CF, 5TMR-gly-CF, 5TMR-CF,
5TMR-B-CF, 5TMR-gly-5AMF, 5TMR-5AMF and 5TMR-lys-5FAM were measured
in 1.times.TBE/8M urea. Each dye solution had an optical density of
0.1 at 560 nm and was excited at 488 nm.
TABLE 7
__________________________________________________________________________
##STR112## ##STR113## ##STR114## ##STR115## ##STR116##
__________________________________________________________________________
The structures of each of these dyes is illustrated in Table 7.
FIG. 2 provides a bar graph of the relative fluorescence of each of
these dyes.
As can be seen from FIG. 2, energy transfer dyes where the linker
is attached to the acceptor at the 5 ring position (5TMR-CF and
5-TMR-B-CF were found to exhibit significantly stronger
fluorescence than the acceptor dye itself or when the acceptor dye
is linked at the 6 ring position (6TMR-CF). As also can be seen
from FIG. 2, energy transfer dyes where the linker has the formula
R.sub.1 XC(O)R.sub.2 where R.sub.2 is benzene (5TMR-B-CF) were
found to have significantly enhanced fluorescence as compared to
the dye where the linker has the formula --CH.sub.2 NHCO--
(5TMR-CF) or --CH.sub.2 NHCOCH.sub.2 NHCO-- (5TMR-gly-5AMF).
As can also be seen from FIG. 2, energy transfer dyes where the
linker is attached to both the donor and acceptor at the 5 ring
position (5TMR-5AMF and 5TMR-gly-5AMF) were found to have
significant fluorescence. Interestingly, the use of a lysine linker
was found not to result in appreciable energy transfer between the
donor and acceptor.
5. Dye Primer Sequencing Using Energy Transfer Dye
In this example, dye primer sequencing was performed on M13 (SEQ.
ID. NO.: 1) in order to compare the relative brightness of 5TMR-CF
and 5TMR-B-CF labeled oligonucelotides. In this example, dye primer
sequencing was performed according to the ABI PRISM.TM. 377 DNA
Sequencer User's Manual, Rev. B, January 1995, Chapter 2 (p/n
402114, The Perkin-Elmer Corporation, Foster City, Calif.). 5TMR-CF
and 5TMR-B-CF were each attached to the 5' end of M13-21 primer
(SEQ. ID. NO.: 2). Equimolar solutions of each primer were mixed
with the M13 (SEQ. ID. NO.: 1) and sequenced with a single dideoxy
nucleotide mixture (ddA/dNTP) and Taq FS. A plot of the resulting
mixture of oligonucleotides that were detected using 5TMR-CF and
5TMR-B-CF labeled primers is presented in FIG. 7. As can be seen
from FIG. 7, oligonucleotides labeled with 5TMR-B-CF are brighter
than oligonucleotides labeled with 5TMR-CF. As can also be seen
from FIG. 7, the mobility of oligonucleotides labeled with
5TMR-B-CF are about one nucleotide slower than the oligonucleotides
labeled with 5TMR-CF.
6. Dye Primer Sequencing Using Four Dyes
Dye primer sequencing was performed on the M13 (SEQ. ID. NO.: 1)
using a set of four dyes attached to the M13-21 primer (SEQ. ID.
NO. 2) as described in Example 5. FIG. 8 is a four color plot of
the dye labeled oligonucleotides produced from the sequencing. The
peak for cytosine corresponds to the fluorescence of
5-carboxy-R110. The peak for adenosine corresponds to the
fluorescence of 5-carboxy-R6G. The peak for guanosine corresponds
to the fluorescence of TMR-B-CF. The peak for thymidine corresponds
to the fluorescence of ROX-CF.
As can be seen from FIG. 8, each of the dye labeled
oligonucleotides exhibit significant fluorescence intensity. In
addition, the different dye labeled oligonucleotides exhibit
sufficiently similar mobility so that good resolution of the series
of peaks is achieved.
7. Synthesis of 6-CFB-DTMR-2-NHS ##STR117##
6-CFB-DTMR-2 was synthesized from DTMR-2 and 6-CFB according to the
reaction sequences described in Examples 1A-B. 6CFB-DTMR-2 was then
converted to 6-CFB-DTMR-2-NHS according to the reaction sequence
described in 1C so that the dye could be coupled to a nucleoside,
nucleotide or oligonucleotide primer.
A. Synthesis of DTMR-2-NHS ##STR118##
A solution of DTMR-2 in DMF, N-hydroxysuccinimide and
1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride were
combined in an eppendorf tube and heated to 60.degree. C. The
reaction progress was monitored by TLC on silica gel. After the
reaction appeared to be complete, the solution was diluted into
methylene chloride and washed with 250 mM carbonate/bicarbonate
buffer (pH 9, 4.times.1 mL), and then with an HCl solution (5%,
1.times.1 mL), dried (Na.sub.2 SO.sub.4) and concentrated to
dryness on a vacuum centrifuge.
B. Synthesis of 6-CF-B-DTMR-2 ##STR119##
A solution of 6-CFB in dimethylsulfoxide (100 .mu.L, 11 mM) was
combined with a solution of DTMR-2 succidimidyl ester in
dimethylformamide (100 .mu.L, 22 mM) and triethylamine (20 .mu.L).
The reaction was added to a solution of hydrochloric acid (5%, 1
mL) and the solid separated by centrifugation. The red solid was
dissolved in carbonate/bicarbonate buffer (250 mM, pH 9, 100 .mu.L)
and reprecipitated with dilute HCl. The solid was dried in a vacuum
centrifuge and dissolved in dimethylformamide (200 .mu.L). The
concentration of the dye solution was determined by diluting an
aliquot into 40% acetonitrile/0.1M triethylammonium acetate buffer
(pH 7). Assuming an extinction coefficient of 80,000 cm.sup.-1
m.sup.-1 for fluorescein, the 6-CF-B-DTMR-2 solution was found to
be 4 mM (70% yield).
C. Synthesis of 6-CF-B-DTMR-NHS ##STR120##
A solution of 6-CF-B-DTMR-2 in dimethylformamide (200 .mu.L, 4 mM)
was added N-hydroxysuccinimide (10 mg) and
1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (5
.mu.g). Additional N-hydroxysuccinimide (10 mg) was added. The
reaction progress was monitored by thin-layer chromatography on
silica gel with elution with dichloromethane: methanol : acetic
acid in a 600:60:16 mixture. When the reaction was complete, dilute
HCl (5%, 1 mL) was added and the product separated by
centrifugation. The solid was dried in a vacuum centrifuge and
dissolved in dimethylformamide (100 .mu.L). The concentration of
the dye solution was determined by diluting an aliquot into 40%
acetonitrile/0.1M triethylammonium acetate buffer (pH 7). Assuming
an extinction coefficient of 80,000 cm.sup.-1 m.sup.-1 for
fluorescein, the 6-CF-B-DTMR-NHS solution was found to be 5.4 mM
(68% yield).
8. Comparison Of Fluorescence Strength of Dyes
The following example compares the fluorescence emission strength
of a series of energy transfer dyes according to the present
invention to the corresponding acceptor dye. According to this
example, each dye was attached to a 21 primer sequence
(5'-TGTAAAACGACGGCCAGT) (SEQ. ID. NO.: 1) with an aminohexyl
linkage at the 5' end. The oligonucleotides were quantitated based
on the absorbance at 260 nm, assuming an extinction coefficient of
180,000 cm.sup.-1 M.sup.-1. Spectra were obtained at a primer
concentration of 0.4 .mu.M in 8M urea, 1.times. Tris/Borate/EDTA
(TBE) buffer with 488 nm excitation. FIG. 9A provides the overlaid
spectra of 5-CFB-DR110-2 and DR110-2. FIG. 9B provides the overlaid
spectra of 5-CFB-DR6G-2 and DR6G-2. FIG. 9C provides the overlaid
spectra of 6-CFB-DTMR-2 and DTMR-2. FIG. 9D provides the overlaid
spectra of 6-CFB-DROX-2 and DROX-2.
The structures of each of these dyes is illustrated in Table 1. As
can be seen from FIGS. 9A-D, energy transfer dyes were found to
exhibit significantly stronger fluorescence than the acceptor dye
itself.
FIG. 10 shows the normalized fluorescence emission spectra of four
dye-labeled oligonucleotides. Spectra were obtained at a primer
concentration of 0.4 .mu.M in 8M urea, 1.times. Tris/Borate/EDTA
(TBE) buffer with 488 nm excitation. The dyes shown in FIG. 10
include 5-CFB-DR110-2, 5-CFB-DR6G-2, 6-CFB-DTMR-2, and
6-CFB-DROX-2. As can be seen from FIG. 10, all four energy transfer
dyes are well resolved relative to each other.
9. Dye Primer Sequencing Using Energy Transfer Dye
In this example, dye primer sequencing was performed on M13 (SEQ.
ID. NO.: 2) using 5-CF-TMR-2, 5-CF-B-TMR-2, 6-CF-B-DTMR-2 and
DTMR-2 labeled primers. In this example, dye primer sequencing was
performed according to the ABI PRISM.TM. 377 DNA Sequencer User's
Manual, Rev. B, January 1995, Chapter 2 (p/n 402114, The
Perkin-Elmer Corporation, Foster City, Calif.). The dye was
attached to the 5' end of M13-21 primer (SEQ. ID. NO.: 3).
Equimolar solutions of each primer were mixed with the M13 (SEQ.
ID. NO.: 2) and sequenced with a single dideoxy nucleotide mixture
(ddA/dNTP) and Taq FS. Plots of the resulting mixtures of
oligonucleotides that were detected using 5-CF-TMR-2 and
5-CF-B-TMR-2 labeled primers are presented in FIG. 11. As can be
seen from this figure, 5-CF-B-TMR-2 provides a significantly
stronger signal than 5-CF-TMR-2, showing the fluorescence
enhancement provided by the linker used in 5-CF-B-TMR-2.
Plots of the resulting mixtures of oligonucleotides that were
detected using 6-CF-B-DTMR-2 and DTMR-2 labeled primers are
presented in FIG. 12. As can be seen from this figure,6-CF-B-DTMR-2
provides a significantly stronger signal than DTMR-2, showing the
fluorescence enhancement provided by the energy transfer dye.
10. Dye Primer Sequencing Using Four Dyes
Dye primer sequencing was performed on the pGEM(SEQ ID. NO.: 3)
using a set of four dyes attached to the M13-21 primer (SEQ. ID.
NO.: 2) as described in Example 5. FIG. 13 is a four color plot of
the dye labeled oligonucleotides produced from the sequencing. The
peak for cytosine corresponds to the fluorescence of 5-CFB-DR1
10-2. The peak for adenosine corresponds to the fluorescence of
6-CFB-DR6g-2. The peak for guanosine corresponds to the
fluorescence of 5-CFB-DTMR-2. The peak for thymidine corresponds to
the fluorescence of 5-CFB-DROX-2.
As can be seen from FIG. 13, each of the dye labeled
oligonucleotides exhibit significant fluorescence intensity. In
addition, the different dye labeled oligonucleotides exhibit
sufficiently similar mobility so that good resolution of the series
of peaks is achieved.
The foregoing description of preferred embodiments of the invention
has been presented for purposes of illustration and description. It
is not intended to be exhaustive or to limit the invention to the
precise forms disclosed. Obviously, many modifications and
variations will be apparent to practitioners skilled in this art
and are intended to fall within the scope of the invention.
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SEQUENCE LISTING (1) GENERAL INFORMATION: (iii) NUMBER OF
SEQUENCES: 3 (2) INFORMATION FOR SEQ ID NO: 1: (i) SEQUENCE
CHARACTERISTICS: (A) LENGTH: 1217 nucleotides (B) TYPE: nucleic
acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (xi) SEQUENCE
DESCRIPTION: SEQ ID NO: 1:
GCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCC40
CGGGTACCGAGCTCGAATTCGTAATCATGGTCATAGCTGT80
TTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAA120
CATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCC160
TAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCAC200
TGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCA240
TTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGT280
ATTGGGCGCCAGGGTGGTTTTTCTTTTCACCAGTGAGACG320
GGCAACAGCTGATTGCCCTTCACCGCCTGGCCCTGAGAGA360
GTTGCAGCAAGCGGTCCACGCTGGTTTGCCCCAGCAGGCG400
AAAATCCTGTTTGATGGTGGTTCCGAAATCGGCAAAATCC440
CTTATAAATCAAAAGAATAGCCCGAGATAGGGTTGAGTGT480
TGTTCCAGTTTGGAACAAGAGTCCACTATTAAAGAACGTG520
GACTCCAACGTCAAAGGGCGAAAAACCGTCTATCAGGGCG560
ATGGCCCACTACGTGAACCATCACCCAAATCAAGTTTTTT600
GGGGTCGAGGTGCCGTAAAGCACTAAATCGGAACCCTAAA640
GGGAGCCCCCGATTTAGAGCTTGACGGGGAAAGCCGGCGA680
ACGTGGCGAGAAAGGAAGGGAAGAAAGCGAAAGGAGCGGG720
CGCTAGGGCGCTGGCAAGTGTAGCGGTCACGCTGCGCGTA760
ACCACCACACCCGCCGCGCTTAATGCGCCGCTACAGGGCG800
CGTACTATGGTTGCTTTGACGAGCACGTATAACGTGCTTT840
CCTCGTTGGAATCAGAGCGGGAGCTAAACAGGAGGCCGAT880
TAAAGGGATTTTAGACAGGAACGGTACGCCAGAATCTTGA920
GAAGTGTTTTTATAATCAGTGAGGCCACCGAGTAAAAGAG960
TCTGTCCATCACGCAAATTAACCGTTGTAGCAATACTTCT1000
TTGATTAGTAATAACATCACTTGCCTGAGTAGAAGAACTC1040
AAACTATCGGCCTTGCTGGTAATATCCAGAACAATATTAC1080
CGCCAGCCATTGCAACAGGAAAAACGCTCATGGAAATACC1120
TACATTTTGACGCTCAATCGTCTGAAATGGATTATTTACA1160
TTGGCAGATTCACCAGTCACACGACCAGTAATAAAAGGGA1200 CATTCTGGCCAACAGAG1217
(2) INFORMATION FOR SEQ ID NO: 2: (i) SEQUENCE CHARACTERISTICS: (A)
LENGTH: 18 nucleotides (B) TYPE: nucleic acid (C) STRANDEDNESS:
single (D) TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO:
2: TGTAAAACGACGGCCAGT18 (2) INFORMATION FOR SEQ ID NO: 3: (i)
SEQUENCE CHARACTERISTICS: (A) LENGTH: 738 nucleotides (B) TYPE:
nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (xi)
SEQUENCE DESCRIPTION: SEQ ID NO: 3:
ATACGACTCACTATAGGGCGAATTCGAGCTCGGTACCCGG40
GGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGAGT80
ATTCTATAGTGTCACCTAAATAGCTTGGCGTAATCATGGT120
CATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAAT160
TCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCC200
TGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGT240
TGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTG280
CCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGC320
GGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTG360
ACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATC400
AGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCA440
GGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGC480
AAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTT520
TTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAAT560
CGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTAT600
AAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCG640
CTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCC680
GCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCT720 CACGCTGTAGGTATCTCA738
__________________________________________________________________________
* * * * *