WO1997017076B1 - Fluorescent dna-intercalating cyanine dyes including a positively charged benzothiazole substituent - Google Patents
Fluorescent dna-intercalating cyanine dyes including a positively charged benzothiazole substituentInfo
- Publication number
- WO1997017076B1 WO1997017076B1 PCT/US1996/017942 US9617942W WO9717076B1 WO 1997017076 B1 WO1997017076 B1 WO 1997017076B1 US 9617942 W US9617942 W US 9617942W WO 9717076 B1 WO9717076 B1 WO 9717076B1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- alkyl
- group
- positively charged
- independently selected
- cyanine dye
- Prior art date
Links
- ANRHNWWPFJCPAZ-UHFFFAOYSA-M CHEMBL593252 Chemical compound [Cl-].C1=CC(N)=CC2=[S+]C3=CC(N)=CC=C3N=C21 ANRHNWWPFJCPAZ-UHFFFAOYSA-M 0.000 title claims abstract 23
- 239000000975 dye Substances 0.000 title abstract 5
- IOJUPLGTWVMSFF-UHFFFAOYSA-N Benzothiazole Chemical group C1=CC=C2SC=NC2=C1 IOJUPLGTWVMSFF-UHFFFAOYSA-N 0.000 title abstract 2
- 238000009830 intercalation Methods 0.000 title abstract 2
- 150000007523 nucleic acids Chemical class 0.000 claims abstract 10
- 229910052739 hydrogen Inorganic materials 0.000 claims 29
- 125000000008 (C1-C10) alkyl group Chemical group 0.000 claims 19
- 125000000027 (C1-C10) alkoxy group Chemical group 0.000 claims 14
- UHOVQNZJYSORNB-UHFFFAOYSA-N benzene Chemical compound C1=CC=CC=C1 UHOVQNZJYSORNB-UHFFFAOYSA-N 0.000 claims 14
- 125000000217 alkyl group Chemical group 0.000 claims 11
- 229920001850 Nucleic acid sequence Polymers 0.000 claims 9
- 125000004103 aminoalkyl group Chemical group 0.000 claims 9
- 125000004433 nitrogen atoms Chemical group N* 0.000 claims 9
- 125000004169 (C1-C6) alkyl group Chemical group 0.000 claims 7
- 125000004414 alkyl thio group Chemical group 0.000 claims 7
- 239000001257 hydrogen Substances 0.000 claims 7
- 125000004435 hydrogen atoms Chemical class [H]* 0.000 claims 7
- 229910052717 sulfur Inorganic materials 0.000 claims 7
- 125000004429 atoms Chemical group 0.000 claims 4
- 125000004122 cyclic group Chemical group 0.000 claims 4
- 229910052760 oxygen Inorganic materials 0.000 claims 2
- 125000001424 substituent group Chemical group 0.000 claims 2
- 125000003118 aryl group Chemical group 0.000 claims 1
- 238000002372 labelling Methods 0.000 abstract 1
- 108020004707 nucleic acids Proteins 0.000 abstract 1
Abstract
New intercalating cyanine dyes are provided in which the benzothiazole portion of the cyanine dye has been modified to produce dyes with improved properties for labelling nucleic acids. This class of fluorescent cyanine dyes are represented by general formula (1) where the definitions for the variables can be found in the claims.
Claims
1. A fluorescent cyanine dye having the general formula
wherein:
n is 0, 1 or 2;
Y is selected from the group consisting of S and
O;
R12 is a positively charged alkyl substituent;
R13, R14 and R15 are each independently selected from the group consisting of hydrogen, C1 - C10 alkyl, C1 -C10 alkoxy, and C1 - C10 alkylthio;
R16 is a C1 - C50 alkyl;
R17 and R18 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 member ring, R19 and R20 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring;
R17 and R18 or R19 and R20 are each H; and
R21 is selected from the group consisting of H, C1-6 alkyl, C1 - C10 alkoxy and a fused benzene.
2. A fluorescent cyanine dye having the general formula
Y is selected from the group consisting of S and O;
R12 is a positively charged alkyl substituent selected from the group consisting of an aminoalkyl chain containing a backbone of 3-42 carbons and 1-5 positively charged nitrogen atoms, a positively charged cyclic aminoalkyl group having 1-5 positively charged nitrogen atoms, and a substituent having the general formula -R28N(R29R30R31) where R28 is a C1-5 alkyl and R29, R30, and R31 are each independently a C1-10 alkyl;
R13, R14 and R15 are each independently selected from the group consisting of hydrogen, C1 - C10 alkyl, C1 -C10 alkoxy, and C1 - C10 alkylthio;
R16 is a C1 - C50 alkyl;
R17 and R18 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring;
R19 and R20 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring; and
R21 is selected from the group consisting of H, C1-6 alkyl, C1 - C10 alkoxy and a fused benzene.
3. A fluorescent cyanine dye having the general formula
Y is selected from the group consisting of S and
O;
R12 is a positively charged alkyl substituent and includes an aminoalkyl chain containing a backbone of 3-42 carbons and 1-5 positively charged nitrogen atoms;
R13, R14 and R15 are each independently selected from the group consisting of hydrogen, C1 - C10 alkyl, C1 -C10 alkoxy, and C1 - C10 alkylthio;
R16 is a C1 - C50 alkyl;
R17 and R18 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 member ring, R19 and R20 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring;
R17 and R18 or R19 and R20 are each H and are taken together to form a 6 membered aromatic ring;
R19 and R20 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring; and
R21 is selected from the group consisting of H, C1-6 alkyl, C1 - C10 alkoxy and a fused benzene.
4. A fluorescent cyanine dye having the general formula
n is 0, 1 or 2;
Y is selected from the group consisting of S and O;
R12 and R13 represent the atoms necessary to form a 5, 6, 7 or 8 membered ring;
R14 and R15 are each independently selected from the group consisting of hydrogen, C1 - C10 alkyl, C1 - C10 alkoxy, and C1 - C10 alkylthio;
R16 is a C1 - C50 alkyl;
R17 and R18 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring;
R19 and R20 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring;
R21 is selected from the group consisting of H, C1-6 alkyl, C1 - C10 alkoxy and a fused benzene; and
R27 is a positively charged alkyl substituent which may be attached to any of the atoms forming the 5, 6, 7 or 8 membered ring as represented by R12 and R13.
5. The fluorescent cyanine dye of claim 4 wherein R27 includes an aminoalkyl chain containing a backbone of 3-42 carbons and 1-5 positively charged nitrogen atoms.
6. The fluorescent cyanine dye of claim 4 wherein R27 is a positively charged cyclic aminoalkyl group having 1-5 positively charged nitrogen atoms.
7. The fluorescent cyanine dye of claim 4 wherein R27 has the general formula -R28N (R29R30R31) where R28 is a C1-5 alkyl and R29, R30, and R31 are each independently a C1-10 alkyl.
8. A method for detecting a nucleic acid sequence comprising:
contacting a nucleic acid sequence with a fluorescent cyanine dye to form a noncovalently bound dye-nucleic acid composition, the fluorescent cyanine dye having the general formula
n is 0, 1 or 2;
Y is selected from the group consisting of S and
O;
R12 is a positively charged alkyl substituent;
R13, R,4 and R15 are each independently selected from the group consisting of hydrogen, C1 - C10 alkyl, C1 -C10 alkoxy, and C1 - C10 alkylthio;
R16 is a C1 - C50 alkyl;
R17 and R18 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring;
R19 and R20 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring; R21 is selected from the group consisting of H, C1-6 alkyl, C1 - C10 alkoxy and a fused benzene;
exposing the fluorescent cyanine dye bound to the nucleic acid sequence to light, the fluorescent cyanine dye absorbing the light and producing a fluorescence emission; and
detecting the fluorescence emission.
9. The method of claim 8 wherein R12 is a positively charged alkyl substituent and includes an aminoalkyl chain containing a backbone of 3-42 carbons and 1-5 positively charged nitrogen atoms.
10. The method of claim 8 wherein R12 is a positively charged cyclic aminoalkyl group having 1-5 positively charged nitrogen atoms.
11. The method of claim 8 wherein R12 has the general formula -R28N (R29R30R31) where R28 is a C1-5 alkyl and R29, R30, and R31 are each independently a C1-10 alkyl.
12. A method for detecting a nucleic acid sequence comprising:
contacting a nucleic acid sequence with a fluorescent cyanine dye to form a noncovalently bound dye-nucleic acid composition, the fluorescent cyanine dye having the general formula
Y is selected from the group consisting of S and
O;
R12 is a positively charged alkyl substituent selected from the group consisting of an aminoalkyl chain containing a backbone of 3-42 carbons and 1-5 positively charged nitrogen atoms, a positively charged cyclic aminoalkyl group having 1-5 positively charged nitrogen atoms, and a substituent having the general formula -R28N(R29R30R31) where R28 is a C1-5 alkyl and R29, R30, and R31 are each independently a C1-10 alkyl;
R13, R14 and R15 are each independently selected from the group consisting of hydrogen, C1 - C10 alkyl, C1 -C10 alkoxy, and C1 - C10 alkylthio;
R16 is a C1 - C50 alkyl;
R17 and R18 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring;
R19 and R20 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring; and
R21 is selected from the group consisting of H, C1-6 alkyl, C1 - C10 alkoxy and a fused benzene;
exposing the fluorescent cyanine dye bound to the nucleic acid sequence to light, the fluorescent cyanine dye absorbing the light and producing a fluorescence emission; and
detecting the fluorescence emission.
13. A method for detecting a nucleic acid sequence comprising:
contacting a nucleic acid sequence with a fluorescent cyanine dye to form a noncovalently bound dye-nucleic acid composition, the fluorescent cyanine dye having the general formula
wherein:
n is 0, 1 or 2;
Y is selected from the group consisting of S and
O;
R12 and R13 represent the atoms necessary to form a 5, 6, 7 or 8 membered ring;
R14 and R15 are each independently selected from the group consisting of hydrogen, C1 - C10 alkyl, C1 - C10 alkoxy, and C1 - C10 alkylthio;
R16 is a C1 - C50 alkyl;
R17 and R18 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring;
R19 and R20 are each independently selected from the group consisting of H and C1-10 alkyl, or are taken together to form a 5 or 6 membered ring;
R21 is selected from the group consisting of H, C1-6 alkyl, C1 - C10 alkoxy and a fused benzene; and
R27 is a positively charged alkyl substituent which may be attached to any of the atoms forming the 5, 6, 7 or 8 membered ring as represented by R12 and R13;
exposing the fluorescent cyanine dye bound to the nucleic acid sequence to light, the fluorescent cyanine dye absorbing the light and producing a fluorescence emission; and
detecting the fluorescence emission.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| AU11177/97A AU1117797A (en) | 1995-11-09 | 1996-11-08 | Fluorescent dna-intercalating cyanine dyes including a positively charged benzothiazole substituent |
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US08/555,529 | 1995-11-09 | ||
| US08/555,529 US5734058A (en) | 1995-11-09 | 1995-11-09 | Fluorescent DNA-Intercalating cyanine dyes including a positively charged benzothiazole substituent |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| WO1997017076A1 WO1997017076A1 (en) | 1997-05-15 |
| WO1997017076B1 true WO1997017076B1 (en) | 1997-06-26 |
Family
ID=24217608
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/US1996/017942 WO1997017076A1 (en) | 1995-11-09 | 1996-11-08 | Fluorescent dna-intercalating cyanine dyes including a positively charged benzothiazole substituent |
Country Status (3)
| Country | Link |
|---|---|
| US (1) | US5734058A (en) |
| AU (1) | AU1117797A (en) |
| WO (1) | WO1997017076A1 (en) |
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| US6937330B2 (en) | 1999-04-23 | 2005-08-30 | Ppd Biomarker Discovery Sciences, Llc | Disposable optical cuvette cartridge with low fluorescence material |
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| US6617137B2 (en) | 2001-10-15 | 2003-09-09 | Molecular Staging Inc. | Method of amplifying whole genomes without subjecting the genome to denaturing conditions |
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| US20040035793A1 (en) * | 2001-11-05 | 2004-02-26 | Transgenomic, Inc. | Methods, systems, and kits for analysis of polynucleotides |
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| US7419511B2 (en) * | 2004-09-13 | 2008-09-02 | L'oreal, S.A. | Compositions comprising at least one substituted carbocyanin derivative, processes for treating keratin fibers using them, device therefor and uses thereof |
| US7425221B2 (en) * | 2004-09-13 | 2008-09-16 | L'oreal S.A. | Composition comprising at least one substituted derivative of carbocyanine, method for treating keratin fibers using it, device and use |
| EP1762627A1 (en) | 2005-09-09 | 2007-03-14 | Qiagen GmbH | Method for the activation of a nucleic acid for performing a polymerase reaction |
| CN101801185A (en) | 2007-03-22 | 2010-08-11 | 耶鲁大学 | Methods and compositions related to riboswitches that control alternative splicing |
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| SG182365A1 (en) | 2010-01-12 | 2012-08-30 | Univ Yale | Structured rna motifs and compounds and methods for their use |
| US8628914B2 (en) | 2010-05-26 | 2014-01-14 | Qiagen Gaithersburg, Inc. | Quantitative helicase assay |
| WO2012021554A1 (en) | 2010-08-09 | 2012-02-16 | Yale University | Cyclic di-gmp-ii riboswitches, motifs, and compounds, and methods for their use |
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-
1995
- 1995-11-09 US US08/555,529 patent/US5734058A/en not_active Expired - Lifetime
-
1996
- 1996-11-08 WO PCT/US1996/017942 patent/WO1997017076A1/en active Application Filing
- 1996-11-08 AU AU11177/97A patent/AU1117797A/en not_active Abandoned
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US9403985B2 (en) | 2003-12-05 | 2016-08-02 | Life Technologies Corporation | Methine-substituted cyanine dye compounds |
| US8865904B2 (en) | 2005-05-11 | 2014-10-21 | Life Technologies Corporation | Fluorescent chemical compounds having high selectivity for double stranded DNA, and methods for their use |
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