Purines and pyrimidines linked to a quencher
First Claim
Patent Images
1. A derivatized pyrimidine or purine compound having the following structure:
-
wherein, L is a linker group selected from the group consisting of —
CH═
CH—
C(O)—
NH—
(CH2)n—
NH—
, —
CH═
CH—
C(O)—
NH—
CH2—
CH2(O—
CH2—
CH2)m—
NH—
, —
C C—
C(O)—
(CH2)n—
NH—
, —
CH═
CH—
C(O)—
NH—
(CH2)n—
CO2—
, —
CH═
CH—
C(O)—
NH—
(CH2)n—
NH—
, —
(CH2)n—
NH—
, and —
NH—
(CH2)n—
NH—
, wherein n is an integer from 2 to 12, and m is 1 or 2, and Q is a quencher group selected from the group consisting of radicals of azo dyes and triphenyl methane dyes;
P represents a pyrimidine selected from the group consisting of uridine, thymidine and cytosine or the purine adenine;
substituted with a linker L at the 4 position, when P is a pyrimidine and at the 8 position when P is a purine;
wherein said pyrimidine is linked to the sugar at the 1-position nitrogen and said guanine is linked to the sugar at the 9-position nitrogen and either;
x is an activated phosphorus group capable of bonding to a 3′
-hydroxyl group of a nucleotide or polynucleotide selected from the group consisting of HO—
P(═
O)(—
OH)—
O—
, HO—
P(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
, HO—
P—
(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
, (HO)2P(═
S)—
O—
, (HO)2P(═
O)—
O—
(HO)P(═
O)—
O—
(HO)P(═
S)—
O—
, —
O—
P(OCH3)(N(iso-propyl)2), —
O—
P(OCH2CH2CN)(N(isopropyl)2) and —
O—
P(CH3)(N(iso-propyl)2);
or x is NH2, H, OH or a protected hydroxyl;
y is a protected hydroxyl group, OH, H or NH2, and z is —
H, —
OH, —
F, —
OCH3, —
O-allyl, a protected hydroxyl group, —
NH2 or a protected amine group;
or y is an activated phosphorus group capable of bonding to a 5′
hydroxyl group of a nucleotide or polynucleotide selected from the group consisting of HO—
P(═
O)(—
OH)—
O—
, HO—
P(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
, HO—
P—
(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
, (HO)2P(═
S)—
O—
, (HO)2P(═
O)—
O—
(HO)P(═
O)—
O—
(HO)P(═
S)—
O—
, —
O—
P(OCH3)(N(iso-propyl)2), —
O—
P(OCH2CH2CN)(N(isopropyl)2) and —
O—
P(CH3)(N(iso-propyl)2);
or y is NH2, H, OH or a protected hydroxyl;
x is a protected hydroxyl group, OH, H or NH2, and z is —
H, —
OH, —
F, —
OCH3, —
O-allyl, a protected hydroxyl group, NH2 or a protected amine group.
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Abstract
Compounds are described comprising purines substituted at the C-8 position and pyrimidines substituted at the C-4 position with a linker and quencher. These compounds, when incorporated into hairpin oligonucleotides quench the fluorescence of fluorophores linked to the 5′-terminus of the oligonucleotide. These nucleotide-quencher compounds are also easily incorporated into oligonucleotides using conventional or automated oligonucleotide synthetic techniques.
54 Citations
20 Claims
-
1. A derivatized pyrimidine or purine compound having the following structure:
-
wherein, L is a linker group selected from the group consisting of —
CH═
CH—
C(O)—
NH—
(CH2)n—
NH—
, —
CH═
CH—
C(O)—
NH—
CH2—
CH2(O—
CH2—
CH2)m—
NH—
, —
C C—
C(O)—
(CH2)n—
NH—
, —
CH═
CH—
C(O)—
NH—
(CH2)n—
CO2—
, —
CH═
CH—
C(O)—
NH—
(CH2)n—
NH—
, —
(CH2)n—
NH—
, and —
NH—
(CH2)n—
NH—
, wherein n is an integer from 2 to 12, and m is 1 or 2, and Q is a quencher group selected from the group consisting of radicals of azo dyes and triphenyl methane dyes;
P represents a pyrimidine selected from the group consisting of uridine, thymidine and cytosine or the purine adenine;
substituted with a linker L at the 4 position, when P is a pyrimidine and at the 8 position when P is a purine;
wherein said pyrimidine is linked to the sugar at the 1-position nitrogen and said guanine is linked to the sugar at the 9-position nitrogen and either;
x is an activated phosphorus group capable of bonding to a 3′
-hydroxyl group of a nucleotide or polynucleotide selected from the group consisting of HO—
P(═
O)(—
OH)—
O—
, HO—
P(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
, HO—
P—
(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
, (HO)2P(═
S)—
O—
, (HO)2P(═
O)—
O—
(HO)P(═
O)—
O—
(HO)P(═
S)—
O—
, —
O—
P(OCH3)(N(iso-propyl)2), —
O—
P(OCH2CH2CN)(N(isopropyl)2) and —
O—
P(CH3)(N(iso-propyl)2);
or x is NH2, H, OH or a protected hydroxyl;
y is a protected hydroxyl group, OH, H or NH2, and z is —
H, —
OH, —
F, —
OCH3, —
O-allyl, a protected hydroxyl group, —
NH2 or a protected amine group;
ory is an activated phosphorus group capable of bonding to a 5′
hydroxyl group of a nucleotide or polynucleotide selected from the group consisting of HO—
P(═
O)(—
OH)—
O—
, HO—
P(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
, HO—
P—
(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
P(═
O)(—
OH)—
O—
, (HO)2P(═
S)—
O—
, (HO)2P(═
O)—
O—
(HO)P(═
O)—
O—
(HO)P(═
S)—
O—
, —
O—
P(OCH3)(N(iso-propyl)2), —
O—
P(OCH2CH2CN)(N(isopropyl)2) and —
O—
P(CH3)(N(iso-propyl)2);
or y is NH2, H, OH or a protected hydroxyl;
x is a protected hydroxyl group, OH, H or NH2, and z is —
H, —
OH, —
F, —
OCH3, —
O-allyl, a protected hydroxyl group, NH2 or a protected amine group.- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)
T is — - NH—
, —
SO2—
, —
O—
, —
S—
, —
C(O)—
S—
, —
C(O)—
, —
C(O)—
NH—
, —
C(O)—
O—
, —
C(S)—
NH—
, or —
C(S)—
O—
,
a, a′
, b, b′
, c, c′
, d, d′
, and e′
are each —
H, —
Cl, —
Br, —
F, —
OCH3, —
OH, —
CH3, SO3, diazophenyl, diazo-1-naphthyl, NO2, —
CO2R, or —
N(R)2, andR is —
H, —
CH3, or —
CH2—
CH3.
-
-
16. The compound of claim 15, wherein T is —
- SO2—
;
a, a′
, b, b′
, c, c′
, d, and d′
each are H; and
e′
is —
N—
(CH3)2 or —
N—
(CH2—
CH3)2.
- SO2—
-
17. The compound of claim 16, wherein e′
- is —
N—
(CH3)2.
- is —
-
18. The compound of claim 16, wherein e′
- is —
N—
(CH2—
CH3)2.
- is —
-
19. A method for producing a compound containing at least two nucleotides, wherein the method comprises linking the compound of claim 1 to another compound containing at least one nucleotide.
-
20. The method of claim 19, wherein the compound containing at least two nucleotides is an oligonucleotide.
Specification