Reagents Useful for Synthesizing Rhodamine-Labeled Oligonucleotides

A reagent useful for labeling an oligonucleotide, comprising a label moiety that comprises an N-protected NH-rhodamine moiety, in which the N-protected NH-rhodamine moiety comprises a structure selected from structural formulae (IIIc), (IIIb) and (IIIc):

• wherein:
• R′ is selected from R3′ and hydrogen;
• R″ is selected from R6′ and hydrogen;
• R9 is an aryl group of the formula —C(O)R10, where R10 is selected from hydrogen, lower alkyl, methyl, —CX3, —CHX2, —CH2X, —CH2—ORd and phenyl optionally mono-substituted with a lower alkyl, methyl, —X, —ORd, cyano or nitro group, where Rd is selected from lower alkyl, phenyl and pyridyl, and each X is a halo group, typically fluoro, or chloro;
• R1′, R2′, R2″, R4′, R4″, R5′, R5″, R7′, R7″, R8′, R4, R5, R6, and R7, when taken alone, are each, independently of one another, selected from hydrogen, lower alkyl, (C6-C14) aryl, (C7-C20) arylalkyl, 5-14 membered heteroaryl, 6-20 membered heteroarylalkyl, —Rb and —(CH2)x—Rb, where x is an intger ranging from 1 to 10 and Rb is selected from —X, —OH, —ORa, —SH, —SRa, —NH2, —NHR1, —NRcRc, —N+RcRcRc, perhalo lower alkyl, trihalomethyl, trifluoromethyl, —B(OH)3, —B(ORa)3, —B(OH)O−, —B(ORa)2O−, —B(OH)(O−)2, —B(ORa)(O−)2, —P(OH)2, —O (OH)O−, —P(ORa)2, —P(ORa)O−, —P(O)(OH)2, —P(O)(OH)O−, —P(O)(O−)2, —P(O)(ORa)2, —P(O)(ORa)O−, —P(O)(OH)(ORa), —OP(OH)2, —OP(OH)O−, —OP(ORa)2, —OP(ORa)O−, —OP(O)(OH)2, —OP(O)(OH)O−, —O P(O)(O−)2, —OP(O)(ORa)2, —OP(O)(ORa)O−, —OP(O)(ORa)(OH), —S(O)2O−, —S(O)2OH, —S(O)2Ra, —C(O) H, —C(O)Ra, —C(S)X, —C(O)O−, —C(O)OH, —C(O)NH2, —C(O)NHRa, —C(O)NRcRc, —C(S)NH2, —C(O)N HRa, —C(O)NRcRc, —C(NH)NH2, —C(NH)NHRa, and —C(NH)NRcRc, where X is halo, each Ra is, independently of the others, selected from lower alkyl, (C6-C14) aryl, (C7-C20) arylalkyl, 5-14 membered heteroaryl and 6-20 membered heteroarylalkyl, and each Rc is, independently of the others, an Ra, or, alternatively, two Rc bonded to the same nitrogen atom may be taken together with that nitrogen atom to form a 5- to 8-membered saturated or unsaturated ring that may optionally include one or more of the same or different ring heteroatoms, which are typically selected from O, N and S
• or, alternatively, R1′ and R2′ or R7′ and R8′ are taken together with the carbon atoms to which they are bonded to form an optionally substituted (C6-C14) aryl bridge and/or R4′ and R4″ and/or R5′ and R5″ are taken together with the carbon atoms to which they are bonded to form a benzo group;
• and
• R3′ and R6′, when taken alone, are each, independently of one another, selected from lower alkyl, (C6-C14) aryl, (C7-C20) arylalkyl, 5-14 membered heteroaryl and 6-20 membered heteroarylalkyl, or alternatively, R3′ and R2′ or R4′ and/or R6′ and R5′ or R7′ in the compounds of structural formula (IIIa), R3′ and R2′ or R4′ and/or R6′ and R5′ or R7″ in the compounds of structural formula (III6), or R3′ and R2″ or R4′ and/or R6′ and R5′ or R7″ in the compounds of structural formula (IIIc) are taken together with the atoms to which they are bonded to form a 5- or 6-membered saturated or unsaturated ring which is optionally substituted with one or more of the same or different lower alkyl, benzo or pyrido groups,
• with the proviso that at least one of R2′, R4′, R5′, R7′, R5 or R6 in the compounds structural formula (IIIa), at least one of R2′, R4′, R5′, R7″, R5 or R6 in the compounds of structural formula (IIIb) and at least one of R2″, R4′, R5′, R7″, R5 or R6 in the compounds of structural formula (IIIc) comprises a group of the formula —Y—, where Y represents a portion of a linkage contributed by a functional group Fy.