Carborhodamine compounds and methods of preparation thereof

An oligonucleotide conjugate comprising:

• a carborhodamine compound having a structure of
• wherein R1 and R2 are independently (C1-C100)alkyl or (C1-C100)heteroalkyl, or R1 and R2 form a ring structure comprising one or more rings,
• R3, R6, R7, and R10 are independently selected from H, (C1-C100)alkyl, (C1-C100)heteroalkyl, (C1-C100)alkoxy, (C1-C100)alkenyl, (C1-C100)alkynyl, aryl, heteroaryl, halo, —OR′, —OC(O)R′, —NR′R″, —SR′, —OC(O) NR′R″, —NR″C(O)R′, —NR″C(O)OR′, —NR′C(O)NR″R′″, and —SO2H, wherein R′, R″ and R′″ are independently selected from H, (C1-C8)alkyl, (C1-C8)heteroalkyl, aryl, and heteroaryl,
• R4, R5, R8, and R9 are independently selected from H, (C1-C100)alkyl, (C1-C100)heteroalkyl, (C1-C100)alkoxy, (C1-C100)alkenyl, (C1-C100)alkynyl, aryl and heteroaryl,
• R11, R12, R13 and R14 are independently selected from H, (C1-C100)alkyl, (C1-C100)heteroalkyl, (C1-C100)alkoxy, (C1-C100)alkenyl, (C1-C100)alkynyl, aryl, heteroaryl, halo, —ORiv, —OSO2Riv, —OC(O) Riv, —NRivRv—SRiv, -—Riv, —CN, —NO2, —CO2Riv, —CONRivRv, —C(O) Riv,—SO2Riv, —SO2NRivRv, —N3, —CH(Ph)2, perfluoro(C1-C4)alkoxy, perfluoro(C1-C4)alkyl, —P(O)(OR15)(OR16) and —R21-R22, wherein Ph is phenyl, wherein Riv and Rv are independently selected from H, (C1-C20)alkyl perfluoro(C1-C4)alkyl, perfluoro(C1-C4)heteroalkyl, aryl and heteroaryl, and wherein aryl and heteroaryl groups are unsubstituted or substituted,
• or
• R3, R4, R5, R6, R7, R8, R9, R10, R11, R12, R13 and R14 form one or more 4- to 7-member ring systems by bridging between one or more of R3, R4, R5, R6, R7, R8, R9, R10, R11, R12, R13 and R14,
• R15 is selected from H—, NH2(CH)4-, NH2(CH2)5-, CF3C(O)NR′(CH2)4-, CF3C(O)NR′(CH2)5, (CH3)3COC(O)NR′(CH2)4-, (CH3)3COC(O)NR′(CH2)5-, tert-butyl, methyl, and aryl, wherein R′ is selected from H- and (C1-C8)alkyl,
• R16 is identical to R15 or R22,
• R21 is a divalent group selected from alkylene, alkenylene, alkynylene, arylene, heteroalkylene, heteroalkenylene, heteroalkynylene, and heteroarylene, where one free valence connects to an aromatic carbon of R11, R12, R13 or R14 and one free valence connects to R22,
• Q is -N(R23)(R24) or OR25,
• R22, R23, R24 are independently selected from (C1-C100)alkyl, aryl, (C1-C100)heteroalkyl, HOSO2(C1-C100)alkyl, heteroaryl or a combination thereof, or
• R23 and R24 together form a saturated ring with 0 to 3 heteroatoms,
• R25 is H or is identical to R23, and
• wherein one of R11, R12, R13 and R14 is —P(O)(OR15)(OR16) and one or more hydrocarbon hydrogens in R16 is replaced with —C(O)R17 or —OR18, wherein R17 is a nitrogen atom of an alkylamino group in an alkylamine-modified oligonucleotide and R18 is a phosphorus atom of a phosphate group in an oligonucleotide;
• an oligonucleotide;
• and
• a quencher.