Pyrimidine derivatives for labeled binding partners

Details Pyrimidine derivatives for labeled binding partners Pyrimidine derivatives for labeled binding partners

1999-12-21

2003-09-09

Carr, Deborah D. (Department: 1623)

Organic compounds -- part of the class 532-570 series

Organic compounds

Carbohydrates or derivatives

C536S026600, C536S028500, C536S028510, C536S028520, C514S04400A, C435S091200

Reexamination Certificate

active

06617437

ABSTRACT:

BACKGROUND OF THE INVENTION
This invention relates to the field of labels, particularly labels for diagnostic use. In particular, it relates to oligonucleotides that are modified to enhance the binding affinity of the oligonucleotides for complementary sequences and that in addition bear a readily detectable characteristic.
Sequence specific binding of oligonucleotides both to single stranded RNA and DNA and to duplex DNA is widely known. This phenomenon has been harnessed for a great variety of diagnostic, preparative and therapeutic purposes. Previously, one objective of research in this field has been to increase the affinity of such oligonucleotides for their complementary sequences. For example, Froehler et al. have described oligonucleotides containing 5-substituted pyrimidine bases that substantially increase the Tm for oligonucleotide binding to complementary bases (International Publication No. 92/10115).
Fluorescent cytosine derivatives are known for use in preparing labeled DNA probes. See Inoue et al., Jpn Kokai JP 62059293, (1987). In addition, fluorescent labeled nucleotides have been employed in DNA sequencing. See Prober et al., “Science” 238:336-341 (1987).
1,3-Dihydro-2H-imidazo[4,5-b]-quinolin-2-one derivatives as phosphodiesterase inhibitors are disclosed by Raeymaekers et al. (EP 541,153).
OBJECTS OF THE INVENTION
An object of this invention is to increase the affinity of oligonucleotides for their complementary sequences.
Another object of this invention is to provide improved detectable labels for use in diagnostic assays.
A further object of this invention is to enhance diagnostic assays which employ oligonucleotides.
A still further object of this invention is to improve the therapeutic efficacy of oligonucleotides.
These and other objects of the invention will be apparent from consideration of the specification as a whole.
Structural Formulas
Structural formulas are designated as parenthetical numerals. It will be understood that designation of aromaticity with respect to carbocycles and heterocycles herein includes any highly resonant unsaturated ring structures Alternatively, placement of double bonds, where indicated, represents one potential structure for the depicted compound but will be understood to include other resonant states of the compound as well as protonated and charged species, only one of which may be shown.
SUMMARY OF THE INVENTION
In accordance with the objects, provided herein is a compound having the structure
wherein
R
1
is a binding partner, a linker or H;
a and b are 0 or 1, provided that the total of a and b is 0 or 1;
A is N or C;
X is S, O, —C(O)—, NH or NCH
2
R
6
;
Y is —C(O)—,
Z is taken together with A to form an aryl or heteroaryl ring structure comprising 5 or 6 ring atoms wherein the heteroaryl ring comprises a single O ring heteroatom, a single N ring heteroatom, a single S ring heteroatom, a single O and a single N ring heteroatom separated by a carbon atom, a single S and a single N ring heteroatom separated by a carbon atom, 2 N ring heteroatoms separated by a carbon atom, or 3 N ring heteroatoms at least two of which are separated by a carbon atom, and wherein the aryl or heteroaryl ring carbon atoms are unsubstituted with other than H or at least 1 nonbridging ring carbon atom is substituted with R
6
or ═O;
R
3
is a protecting group or H;
R
6
is independently H, C
1
-C
6
alkyl, C
2
-C
6
alkenyl, C
2
-C
6
alkynyl, NO
2
, N(R
3
)
2
, C≡N or halo, or an R
6
is taken together with an adjacent R
6
to complete a ring containing 5 or 6 ring atoms, and tautomers, solvates and salts thereof; and
provided that where a is 0, b is 1, and R
1
is
 in which
D
2
is independently hydroxyl, blocked hydroxyl, mono, di or triphosphate, or an oligodeoxyribonucleotide otherwise containing only the bases A, G, T and C; and
D
3
is H or OH;
then Z is not unsubstituted phenyl.
When the binding partner R
1
is an oligomer, embodiments of the compounds of this invention have structure (8)
wherein
D is OH or blocked OH;
D
1
is an oligonucleotide coupling group or OH
X
1
is independently a phosphodiester linkage or a phosphodiester substitute linkage bonded to the 2′ or 3′ position of a furanose ring and the remaining 2′ or 3′ position is substituted with R
21
;
R
21
is H, OH, F, —O-alkyl (C
1
-C
12
), —S-alkyl (C
1
-C
12
), OC
3
H
5
, or SC
3
H
5
;
n is an integer from 0 to 98; and
B is a purine or pyrimidine base or analogue thereof provided that at least one B has the structure
wherein a, b, A, X, Y, Z, and the proviso are the same as for structure (1).
The compounds of structure (1) are made through several novel intermediates. The 4-pyridones are obtained from an intermediate having structure (2)
wherein
R
1
is H or a linker group;
J is an aryl or heteroaryl ring structure comprising 5 or 6 ring atoms wherein the heteroaryl ring comprises a single O ring heteroatom, a single N ring heteroatom, a single S ring heteroatom, a single O and a single N ring heteroatom separated by a carbon atom, a single S and a single N ring heteroatom separated by a carbon atom, or 2 N ring heteroatoms separated by a carbon atom, and wherein the aryl or heteroaryl ring carbon atoms are unsubstituted with other than H or at least 1 nonbridging ring carbon atom is substituted with R
6
; and
R
6
is defined above;
and tautomers, salts and solvates thereof.
The 2-pyridones are synthesized from the intermediates of structures (3) and (6):
wherein
R
1
is H or a linker group;
R
22
is C
1
-C
3
alkyl; and
J′ is an aryl or heteroaryl ring structure comprising 5 or 6 ring atoms wherein the heteroaryl ring comprises a single O ring heteroatom, a single N ring heteroatom, a single S ring heteroatom, a single O and a single N ring heteroatom separated by a carbon atom, a single S and a single N ring heteroatom separated by a carbon atom, or 2 N ring heteroatoms separated by a carbon atom, and wherein the aryl or heteroaryl ring carbon atoms are unsubstituted with other than H or at least 1 nonbridging ring carbon atom is substituted with C
1
-C
6
alkyl, C
2
-C
6
alkenyl, C
2
-C
6
alkynyl, NO
2
, N(R
3
)
2
, or halo;
R
3
is a protecting group or H;
and tautomers, solvates and salts thereof.
wherein
A is independently S, O, N or CR
6
;
R
6
is defined above; and
R
26
is C
1
-C
4
alkyl; and tautomers, salts and solvates thereof.
Phenoxazines and oxadiazines also are made from novel intermediate (5), as are pyridinopyrrolines, thiazines and oxazines.
wherein
R
1
is H or a linker group;
R
24
is independently halo or C
1
-C
2
haloalkyl;
R
25
is independently —SH, —OH, ═S or ═O;
A is independently N or C; and
M, taken together with the radical —A—C(—R
25
), completes an aryl or heteroaryl ring structure comprising 5 or 6 ring atoms wherein the heteroaryl ring comprises a single O ring heteroatom, a single N ring heteroatom, a single S ring heteroatom, a single O and a single N ring heteroatom separated by a carbon atom, a single S and a single N ring heteroatom separated by a carbon atom, 2 N ring heteroatoms separated by a carbon atom, or 3 N ring heteroatoms at least two of which are separated by a carbon atom, and wherein the aryl or heteroaryl ring carbon atoms are unsubstituted with other than H or at least 1 nonbridging ring carbon atom is substituted with R
6
; and
R
6
is defined above,
and tautomers, solvates and salts thereof.
The phenopyrrolines are made by the use of the intermediate of structure (4)
wherein
R
1
is H or a linker group;
J is an aryl or heteroaryl ring structure comprising 5 or 6 ring atoms wherein the heteroaryl ring comprises a single O ring heteroatom, a single N ring heteroatom, a single S ring heteroatom, a single O and a single N ring heteroatom separated by a carbon atom, a single S and a single N ring heteroatom separated by a carbon atom, or 2 N ring heteroatoms separated by a carbon atom, and wherein the aryl or heteroaryl ring carbon atoms are unsubstituted with other than H or at least 1 nonbridging ring carbon atom is substituted with R

Affiliated with

Also associated with

Rating

Pyrimidine derivatives for labeled binding partners does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Pyrimidine derivatives for labeled binding partners, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Pyrimidine derivatives for labeled binding partners will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-3089261