Nucleic Acid Labeling Compounds

• US 20110082289A1
• Filed: 09/28/2010
• Published: 04/07/2011
• Est. Priority Date: 03/12/2001
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Barone, Anthony D., McGall, Glenn
• Granted Patent: US 8,076,072 B2
• Time in Patent Office: Days
• US Class Current: 536/28.4
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07D 239/47 One nitrogen atom and one oxygen or sulfur atom, e.g. cytosine
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 7/00 Compounds containing non-saccharide radicals linked to saccharide radicals by a carbon-to-carbon bond
• CPC Class Codes: C07H 7/06 Heterocyclic radicals
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence

Abstract

Nucleic acid labeling compounds are disclosed. The compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.

Claims

1-30. -30. (canceled)

31. A nucleic acid labeling compound having the formula:

32. The nucleic acid labeling compound of claim 31, wherein A is H or H₄O₉P₃—

;

L is alkanoyl; and

Q is biotin or a carboxyfluorescein;

M is —

NR₃—

where R₃ is hydrogen or alkyl, and

wherein m is 1 or O.

33. The nucleic acid labeling compound of claim 32,

wherein L is —

C(O)(CH₂)_n—

wherein n is an integer ranging from about 1 to about 10;

M is —

NH—

;

Q is biotin or a carboxyfluorescein.

34. The nucleic acid labeling compound of claim 33, wherein -L-(M)_m- is —

C(O)(CH₂)₆—

NH—

; and

Q is biotin.

35. The nucleic acid labeling compound of claim 33, wherein -L-(M)_m- is —

C(O)(CH.sub.2).sub.6-NH—

; and

Q is carboxyfluorescein.

36. A nucleic acid labeling compound having the formula:

37. The nucleic acid labeling compound of claim 36,

wherein A is H or H₄O₉P₃—

;

X₁ is O;

Y₁ is hydrogen, OR₉,

wherein R₉ is hydrogen, or alkyl, or —

NR₁₆-L-(M)_m-Q;

wherein R₁₆ is hydrogen, alkyl or aryl;

Z, is hydrogen OR₁₀, wherein R₁₀ is hydrogen, or alkyl, or —

NR₁₆-L-(M)_m-Q,

wherein R₁₆ is hydrogen, or alkyl;

L is N-alkyl amido;

R₁₅ is hydrogen or alkyl;

M is —

(CH₂)_nNR₃—

where R₃ is hydrogen or alkyl, and m is from 1 to about 15.

38. The nucleic acid labeling compound of claim 37, wherein Y, is hydrogen or OH;

Z, is —

NH-L-(M)-, -Q;

L is —

(CH₂)_nNHC(O)—

where n is an integer from 1 to about 10;

M is —

NH(CH₂)_p—

where p is an integer from 1 to about 10;

R₁₅ is hydrogen or methyl; and

Q is biotin or a carboxyfluorescein.

39. The nucleic acid labeling compound of claim 38 wherein Y₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

(CH₂)₄NH—

C(O)(CH₂)₅NH—

; and

Q is biotin.

40. The nucleic acid labeling compound of claim 39, wherein Y₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

(CH₂)₄NH—

C(O)(CH₂)₅NH—

; and

Q is a carboxyfluorescein.

41. The nucleic acid labeling compound of claim 39

wherein Y₁ is OH;

R₁₅ is methyl;

-L-(M)_m- is —

(CH₂)₄NH—

C(O)(CH₂)₅NH—

; and

Q is biotin.

42. The nucleic acid labeling compound of claim 39, wherein Y₁ is OH;

R₁₅ is methyl;

-L-(M)_m is —

(CH₂)₄NH—

C(O)(CH₂)₅NH—

; and

Q is a carboxyfluorescein.

43. The nucleic acid labeling compound of claim 37,

wherein Y₁ is —

NH-L-(M)-, -Q;

Z₁ is hydrogen or OH;

L is —

(CH₂)_nNHC(O)—

where n is an integer from 1 to about 10;

M is —

NH(CH₂)_p—

where n is an integer from 1 to about 10;

R.sub.15 is hydrogen or methyl; and

Q is biotin or a carboxyfluorescein.

44. The nucleic acid labeling compound of claim 43, wherein Z₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

(CH₂)₄NH—

C(O)(CH₂)₅NH—

; and

Q is biotin.

45. The nucleic acid labeling compound of claim 43,

wherein Z₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

(CH₂)₄NH—

C(O)(CH₂)₅NH—

; and

Q is a carboxyfluorescein.

46. The nucleic acid labeling compound of claim 43,

wherein Z₁ is OH;

R₁₅ is methyl;

-L-(M)_m, is —

(CH₂)₄NH—

C(O)(CH₂)₅NH—

; and

Q is biotin.

47. The nucleic acid labeling compound of claim 43,

wherein Z₁ is OH;

R₁₅ is methyl;

-L-(M)_m- is —

(CH₂)₄NH—

C(O)(CH₂)₅NH—

; and

Q is a carboxyfluorescein.

48. The nucleic acid labeling compound of claim 37,

wherein A is H or H₄O₉P₃—

;

X₁ is O;

Y₁ is hydrogen, OR₉,

wherein R₉ is hydrogen, or alkyl, or —

O-L-(M)_m-Q;

Z, is hydrogen OR₁₀, wherein R₁₀ is hydrogen, or alkyl, or —

O-L-(M)_m-Q,

or alkyl;

L is alkylene; and

m is from 1 to about 10.

49. The nucleic acid labeling compound of claim 48,

wherein Y₁ is hydrogen or OH;

Z₁ is —

O-L-(M)_m-Q;

L is —

(CH₂)_n—

where n is an integer from 1 to about 12;

M is —

NH—

;

R₁₅ is hydrogen or methyl; and

Q is biotin or a carboxyfluorescein.

50. The nucleic acid labeling compound of claim 49, wherein Y₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

(CH₂)₆—

NH—

; and

Q is biotin.

51. The nucleic acid labeling compound of claim 49, wherein Y₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

(CH₂)₆—

NH—

; and

Q is a carboxyfluorescein.

52. The nucleic acid labeling compound of claim 49, wherein Y.sub.1 is OH;

R₁₅ is methyl;

-L-(M)_m- is —

(CH₂)₆—

NH—

; and

Q is biotin.

53. The nucleic acid labeling compound of claim 49, wherein Y.sub.1 is OH;

R₁₅ is methyl;

-L-(M)_m- is —

(CH₂)₆—

NH—

; and

Q is a carboxyfluorescein.

54. The nucleic acid labeling compound of claim 37, wherein Y₁ is —

O-L-(M)_m-Q;

Z₁ is hydrogen or OH;

L is -(CH₂)_n—

where n is an integer from 1 to about 12;

M is —

NH—

;

R₁₅ is hydrogen or methyl; and

Q is biotin or a carboxyfluorescein.

55. The nucleic acid labeling compound of claim 54,

wherein Z₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

(CH₂)₆—

NH—

; and

Q is biotin.

56. The nucleic acid labeling compound of claim 54, wherein Z₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

(CH₂)₆—

NH—

; and

Q is a carboxyfluorescein.

57. The nucleic acid labeling compound of claim 54, wherein Z₁ is OH;

R₁₅ is methyl;

-L-(M)_m- is —

(CH₂)₆—

NH—

; and

Q is biotin.

58. The nucleic acid labeling compound of claim 54, wherein Z₁ is OH;

R₁₅ is methyl;

-L-(M)_m- is —

(CH₂)₆—

NH—

; and

Q is a carboxyfluorescein.

59. The nucleic acid labeling compound of claim 37, wherein A is H or H₄O₉P₃—

;

X₁ is O;

Y₁ is hydrogen, OR₉, wherein R₉ is hydrogen, or alkyl, or —

S-L-(M)_m-Q;

Z₁ is hydrogen OR₁₀, wherein R.sub.10 is hydrogen, or alkyl, or —

S-L-(M)_m-Q;

L is alkyl thio; and

m is from 1 to about 10.

60. The nucleic acid labeling compound of claim 59, wherein Y₁ is hydrogen or OH;

Z₁ is —

S-L-(M)_m-Q;

L is —

S—

(CH₂)_n—

where n is an integer from 1 to about 10;

M is —

NH—

;

R₁₅ is hydrogen or methyl; and

Q is biotin or a carboxyfluorescein.

61. The nucleic acid labeling compound of claim 60, wherein Y₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

S—

(CH₂)₂—

NH—

; and

Q is biotin.

62. The nucleic acid labeling compound of claim 60, wherein Y₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

S—

(CH₂)₂—

NH—

; and

Q is a carboxyfluorescein.

63. The nucleic acid labeling compound of claim 60,

wherein Y₁ is OH;

R₁₅ is methyl;

-L-(M)_m- is —

S—

(CH.sub.2).sub.2-NH—

; and

Q is biotin.

64. The nucleic acid labeling compound of claim 60,

wherein Y₁ is OH;

R₁₅ is methyl;

-L-(M)_m- is —

S—

(CH₂)₂—

NH—

; and

Q is a carboxyfluorescein.

65. The nucleic acid labeling compound of claim 37, wherein Y₁ is —

S-L-(M)_m-Q;

Z₁ is hydrogen or OH;

L is —

S—

(CH.sub.2).sub.n- where n is an integer from 1 to about 10;

M is —

NH—

;

R₁₅ is hydrogen or methyl; and

Q is biotin or a carboxyfluorescein.

66. The nucleic acid labeling compound of claim 65,

wherein Z₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m is —

S—

(CH₂)₂—

NH—

; and

Q is biotin.

67. The nucleic acid labeling compound of claim 65, wherein Z₁ is OH;

R₁₅ is hydrogen;

-L-(M)_m- is —

S—

(CH₂)₂—

NH—

; and

Q is a carboxyfluorescein.

68. The nucleic acid labeling compound of claim 65,

wherein Z₁ is OH;

R₁₅ is methyl;

-L-(M)_m- is —

S—

(CH₂)₂—

NH—

; and

Q is biotin.

69. The nucleic acid labeling compound of claim 65,

wherein Z₁ is OH;

R₁₅ is methyl;

-L-(M)_m- is —

S—

(CH₂)₂—

NH—

; and

Q is a carboxyfluorescein.

70-81. -81. (canceled)