Pyrimidine derivatives for labeled binding partners

A compound having the structure:

• ##STR20## wherein R.sup.1 is a polymer, H or a linker group selected from the group consisting of:
• E--CHR.sup.7 R.sup.11 --(CH.sub.2).sub.m1 --C(R.sup.8)((CH.sup.2).sub.m1 (R.sup.9))--(CH.sub.2).sub.m1 --R.sup.10 --(CH.sub.2).sub.m1 --,
• E--O--C.sub. H.sub.4 --CH.sub.2 --;
• E--CHR.sup.7 --O--CHR.sup.7 --O--CHR.sup.7 --,
• E--CHR.sup.7 --(CHR.sup.13)--.sub.m1 --CHR.sup.14 --R.sup.10 --,
• H(CH.sub.2).sub.m1 CH(COOR.sup.20)(CH.sub.2).sub.m1 -- ##STR21## D is an oligonucleotide coupling group;
• D.sup.1 is independently F, H, O--alkyl, S--alkyl or an oligonucleotide coupling group, but only one D.sup.1 is a coupling group;
• O is independently --C(R.sup.12).sub.2 --CH.sub.2 --C(R.sup.12).sub.2 --O--, --CR.sup.12 .dbd.CR.sup.12 --, or --C.tbd.C--;
• R.sup.7 is independently H or C.sub.1 -C.sub.4 alkyl;
• R.sup.8 is H or C.sub.1 -C.sub.4 alkyl, C.sub.2 -C.sub.4 alkenyl or azidomethyl;
• R.sup.9 is halo, H or OR.sup.20
• R.sup.10 is O, CH.sub.2 or a covalent bond;
• R.sup.11 is O, S, CH.sub.2, CHR or CF.sub.2 ;
• R.sup.12 is independently H or halogen;
• R.sup.13 is H, halogen, OR.sup.20,CH.sub.3, CH.sub.2 OR.sup.20 or C.sub.3 -C.sub.6 alcyloxyalkyl;
• R.sup.13 is H, halogen, OR.sup.20,CH.sub.3, CH.sub.2 OR.sup.20, C.sub.3 -C.sub.6 acyloxymethyl, or C.sub.2 -C.sub.6 acyloxy,
• R.sup.15 is CH.sub.2, CHF or O;
• R.sup.16 is CH or S, provided that when R.sup.19 is O or S, or R.sup.15 is CH, then R.sup.16 is not S;
• R.sup.17 is H, OR.sup.20,halogen, N.sub.3, C.sub.1 -C.sub.4 alkyl or C.sub.1 -C.sub.4 alkoxy or is absent when R.sup.16 is S;
• R.sup.18 is H OR.sup.20, halogen, N.sub.3, C.sub.1 -C.sub.4 alkyl or C.sub.1 -C.sub.4 alkoxy;
• R.sup.19 is O, S, CH.sub.2, CHR or CF.sub.2 ;
• R.sup.20 is H or a protecting group;
• m1 is independently 0 or an integer from 1 to 4;
• and
• E is OH, OR.sup.20, --PO.sub.2 or --OP(O).sub.2 ;
• a and b are 0;
• A is independently N or C;
• X is independently S, 0, --C(0)--, NH or NCH.sub.2 R.sup.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.sup.6 or .dbd.O;
• R.sup.6 is independently H, C.sub.1 -C.sub.6 alkyl, C.sub.2 -C.sub.6 alkenyl, C.sub.2 -C.sub.6 alkynyl, NO.sub.2, N(R.sup.3).sub.2, C.tbd.N or halo, or an R.sup.6 is taken together with an adjacent R.sup.6 to complete a ring selected from the group consisting of cyclopentyl, cyclohexyl, cyclopentenyl, cyclohexenyl, phenyl, thiazolyl, imidozolyl, oxazolyl, pyridinyl and pyrimidinyl;
• R.sup.3 is a protecting group or H;
• and tautomers, solvates and salts thereof;
• and provided that where a is 0, b is 1, and R.sup.1 is ##STR22## in which D.sup.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.sup.3 is H or OH;
• then Z is not unsubstituted phenyl.