Dye-labeled ribonucleotide triphosphates

• US 20070293662A1
• Filed: 05/04/2007
• Published: 12/20/2007
• Est. Priority Date: 06/22/2001
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Khan, Shaheer, Vatta, Paolo, Fisher, Peter
• Granted Patent: US 7,678,892 B2
• Time in Patent Office: Days
• US Class Current: 536/23.1
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical

Abstract

The invention provides novel dye-labeled ribonucleotide analogs and methods for synthesizing those analogs. The compounds of the invention are especially useful for DNA sequencing by the polymerase chain reaction.

Claims

1. A compound having the formula:

2. The compound according to claim 1, wherein the linker is an propargyl-ethyl-oxide-amino linker.

3. The compound according to claim 1, wherein the linker is a propargyl linker.

4. The compound according to claim 1, wherein the linker is a benzylamine linker.

5. The compound according to claim 1, wherein the linker is a phosphate linker.

6. The compound according to claim 1, wherein the linker is a rigid linker.

7. The compound according to claim 1, wherein the linker is a tuned linker.

8. The compound according to claim 1, wherein the linker is a heterocycle linker.

9. The compound according to claim 1, wherein the dye is a fluorescein-type dye, a rhodamine type dye, an energy transfer dye pair, or a cyanine-type dye.

10. The compound according to claim 9, wherein Dye is selected from a rhodamine dye and a fluorescein dye.

11. The compound according to claim 10, wherein the rhodamine dye is a 4,7-dichlorophenyl-rhodamine dye.

12. The compound according to claim 11, wherein the 4,7-dichlorophenyl-rhodamine dye is selected from dTAMRA, dROX, dR6G, and dR110.

13. The compound according to claim 1, wherein the nucleobase is selected from cytosine, adenine, uracil, guanine, 7-deazaadenine, and 7-deazaguanine.

14-21. -21. (canceled)

22. A compound of the formula II:

23. The compound according to claim 22, wherein the linker is a propargyl-ethyl-oxide-amino linker, a propargylamino linker, a propargyl-propyl-oxide-amino linker, a benzylamine linker, a phosphate linker, a rigid linker, or a multimer thereof.

24. The compound according claim 22, wherein the linker is an propargyl-ethyl-oxide-amino linker.

25. The compound according to claim 22, wherein the linker is a propargylamino linker.

26-77. -77. (canceled)

78. A compound having the formula:

79. The compound according to claim 78, wherein B is uracil;

L is propargyl-ethyl-oxide-amino; and

Dye is TAMRA.

80. The compound according to claim 78, wherein B is uracil;

L is propargylamino; and

Dye is TAMRA.

81. The compound according to claim 78, wherein B is uracil;

L is propargyl-ethyl-oxide-amino; and

Dye is dTAMRA.

82. The compound according to claim 78, wherein B is uracil;

L is propargylamino; and

Dye is dTAMRA.

83. The compound according to claim 78, wherein B is cytosine;

L is propargyl-ethyl-oxide-amino; and

Dye is ROX.

84. The compound according to claim 78, wherein B is cytosine;

L is propargylamino; and

Dye is ROX.

85. The compound according to claim 78, wherein B is cytosine;

L is propargyl-ethyl-oxide-amino; and

Dye is dROX.

86. The compound according to claim 78, wherein B is cytosine;

L is propargylamino; and

Dye is dROX.

87. The compound according to claim 78, wherein B is 7-deazaadenine;

L is propargyl-ethyl-oxide-amino; and

Dye is R6G.

88. The compound according to claim 78, wherein B is 7-deazaadenine;

L is propargylamino; and

Dye is R6G.

89. The compound according to claim 78, wherein B is 7-deazaadenine;

L is propargyl-ethyl-oxide-amino; and

Dye is dR6G.

90. The compound according to claim 78, wherein B is 7-deazaadenine;

L is propargylamino; and

Dye is dR6G.

91. The compound according to claim 78, wherein B is 7-deazaguanine;

L is propargyl-ethyl-oxide-amino; and

Dye is R110.

92. The compound according to claim 78, wherein B is 7-deazaguanine;

L is propargylamino; and

Dye is R110.

93. The compound according to claim 78, wherein B is 7-deazaguanine;

L is propargyl-ethyl-oxide-amino; and

Dye is dR110.

94. The compound according to claim 78, wherein B is 7-deazaguanine;

L is propargylamino; and

Dye is dR110.

95. The compound according to claim 78, wherein Dye is an energy transfer dye pair comprised of a fluorescein dye and a rhodamine dye wherein the fluorescein dye is attached to the nucleobase through a propargyl-ethyl-oxide-amino or propargylamino linker, and the fluorescein dye is attached to the rhodamine dye by a second linker.

96. The compound according to claim 95, wherein the fluorescein dye is 4-aminomethyl FAM and the rhodamine dye is a 4,7-dichlororhodamine dye.

97. The compound according to claim 96, wherein the 4,7-dichlororhodamine dye is dTAMRA.

98. The compound according to claim 96, wherein the 4,7-dichlororhodamine dye is dROX.

99. The compound according to claim 96, wherein the 4,7-dichlororhodamine dye is dR6G.

100. The compound according to claim 96, wherein the 4,7-dichlororhodamine dye is dR110.

101-123. -123. (canceled)