Patent ID: 6781001
Filing Date: 2004-08-24
Classification: C07D,C07H,C09B,C12Q,Y10S,Y10T

Abstract:
A labelled nucleic acid compound having the formula:NUCâ€”Lâ€”D whereinNUC is a nucleic acid compound selected from the group consisting of a nucleoside, a nucleotide, a polynucleotide and analogs thereof; L is a linkage; wherein if NUC comprises a purine base, the linkage is attached to the 8-position of the purine, if NUC comprises a 7-deazapurine base, the linkage is attached to the 7-position of the 7-deazapurine, and if NUC comprises a pyrimidine base, the linkage is attached to the 5-position of the pyrimidine; and D is an extended rhodamine dye comprising one of the following structures: whereinR1, R2, R3, R4, R5, R6, R7, R9, R10, R11, and R13 when taken alone are each independently selected from the group consisting of â€”H, alkyl, alkyl independently substituted with one or more Z1, heteroalkyl, heteroalkyl independently substituted with one or more Z1, aryl, aryl independently substituted with one or more Z1, heteroaryl, heteroaryl independently substituted with one or more Z1, arylalkyl, arylalkyl independently substituted with one or more Z1, heteroarylalkyl, heteroarylalkyl independently substituted with one or more Z1, halogen, â€”OS(O)2OR, â€”S(O)2OR, â€”S(O)2R, â€”S(O)2NR, â€”S(O)R, â€”OP(O)O2RR, â€”P(O)O2RR, â€”C(O)O R, â€”NR2, â€”NR3, â€”NC(O)R, â€”C(O)R, â€”C(O)NR2, â€”CN, and â€”OR, wherein each R is independently selected from the group consisting of â€”H, alkyl, heteroalkyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl and linking group; or R1 taken together with R2, Y1, or Y2; and/or R4 taken together with R3, Y3, or Y4; and/or R5 taken together with R6, Y3, or Y4; and/or R6 taken together with R7, Y3, or Y4; and/or R10 taken together with R9 or R11; and/or R11 taken together with Y1, or Y2; and/or R13 taken together with Y3 or Y4 are selected from the group consisting of alkyleno, alkyleno independently substituted with one or more Z1, heteroalkyleno, heteroalkyleno independently substituted with one or more Z1, aryleno, aryleno independently substituted with one or more Z1, heteroaryleno, and heteroaryleno independently substituted with one or more Z1; R8 is selected from the group consisting of â€”H, alkyl, alkyl independently substituted with one or more Z1, heteroalkyl, heteroalkyl independently substituted with one or more Z1, aryl, aryl independently substituted with one or more Z1, heteroaryl, heteroaryl independently substituted with one or more Z1, arylalkyl, arylalkyl independently substituted with one or more Z1, heteroarylalkyl, and heteroarylalkyl independently substituted with one or more Z1; Y1, Y2, Y3, Y4 when taken alone are independently selected from the group consisting of â€”H, alkyl, alkyl independently substituted with one or more Z1, heteroalkyl, heteroalkyl independently substituted with one or more Z1, aryl, aryl independently substituted with one or more Z1, heteroaryl, heteroaryl independently substituted with one or more Z1, arylalkyl, arylalkyl independently substituted with one or more Z1, heteroarylalkyl, and heteroarylalkyl independently substituted with one or more Z1; or Y1 taken together with R1, R11 or Y2; or Y2 taken together with R1, R11 or Y1; or Y3 taken together with R4, R5, R6, R13 or Y4; or Y4 taken together with R4, R5, R6, R13 or Y3 are selected from the group consisting of alkyleno, alkyleno independently substituted with one or more Z1, heteroalkyleno, heteroalkyleno independently substituted with one or more Z1, aryleno, aryleno independently substituted with one or more Z1, heteroaryleno, and heteroaryleno independently substituted with one or more Z1; and each Z1 is independently selected from the group consisting of â€”R, halogen, â€”OS(O)2OR, â€”SO2OR, â€”SO2R, â€”SO2NR, â€”S(O)R, â€”OP(O)O2RR, â€”P(O)O2RR, â€”CO2 R, â€”NR2, â€”NR3, â€”NC(O)R, â€”C(O)R, â€”C(O)NR2, â€”CN, â€”O and â€”OR, wherein R is independently selected from the group consisting of â€”H, alkyl, heteroalkyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl and linking group.