Reagents useful for synthesizing rhodamine-labeled oligonucleotides

An oligonucleotide comprising a label moiety produced by reacting an oligonucleotide attached to a solid support with a reagent having a structure of formula (VII):

• LM-L-PEP (VII)
• wherein PEP is a phosphate ester precursor group, L is an optional linker linking the label moiety to the phosphate ester precursor group and LM comprises an N-protected NH-rhodamine moiety selected from the group consisting
• of structures having formulae (IIIa), (IIIb) and (IIIc):
• wherein:
• R′ is selected from the group consisting of R3′ and hydrogen;
• R″ is selected from the group consisting of R6′ and hydrogen;
• R9 is a protecting group having a structure of the formula —C(O)R10, wherein R10 is selected from the group consisting of hydrogen, a lower alkyl, —CX3,—CHX2, —CH2X, —CH2—ORd and phenyl optionally mono-substituted with a lower alkyl, —X, —ORd, cyano or nitro group, wherein Rd is selected from the group consisting of a lower alkyl, phenyl and pyridyl, and each X is a halo group;
• each of R1′, R2′, R2″, R4′, R4″, R5′, R5″, R7′, R7″, R8′, R4, R5, R6, and R7, when taken alone, is independently selected from the group consisting of hydrogen, a lower alkyl, a (C6-C14) aryl, a (C7-C20) arylalkyl, a 5-14 membered heteroaryl, a 6-20 membered heteroarylalkyl, —Rb and —(CH2)x—Rb, wherein x is an integer having the value between 1 and 10 and Rb is selected from the group consisting of —X, —OH, —ORa, —SH, —SRa, —NH2, —NHRa, —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, —P(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−, —OP(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)NHRa, —C(O)NRcRc, —C(NH)NH2, —C(NH)NHRa, and —C(NH)NRcRc, wherein X is halo, each Ra is independently selected from the group consisting of a lower alkyl, a (C6-C14) aryl, a (C7-C20) arylalkyl, a 5-14 membered heteroaryl and a 6-20 membered heteroarylalkyl, and each Rc is independently 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 selected from the group consisting of 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
• each of R3′ and R6′, when taken alone, is independently selected from the group consisting of a lower alkyl, a (C6-C14) aryl, a (C7-C20) arylalkyl, a 5-14 membered heteroaryl and a 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 of structural formula (IIIa), at least one of R2′, R4′, R5′, R7″, R5 or R6 in the compounds of structural formula (IIIb) or 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—, wherein Y is selected from the group consisting of —C(O)—, —S(O)2—, —S— and —NH—.