N8-and c8-linked purine based and structurally related heterocycles as universal nucleosides used oligonucleotides hybridization

A nucleic acid binding compound comprising a backbone, said backbone having attached heterocyclic groups wherein at least one of said heterocyclic groups has the formula I

• 25
• wherein
• X1 is independently from X4, X5 and X6 selected from the group of N and
• CR1, and X1 is CR1 if each of X2 and X3 is N,
• X2 is independently from X4, X5 and X6 selected from the group of N and
• CR2, and X2 is CR2 if each of X1 and X3 is N,
• X3 is independently from X4, X5 and X6 selected from the group of N and
• CR3, and X3 is CR3if each of X1 and X2 is N,
• X4 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR4,
• if X5is C and X6 is NR35,then X4is CR4 or N,
• if X5 is C and X6 is N, then X4 is NR35, and
• if X5is C and X6 is CR34,then X4is NR35, and
• if X5is N, then X4is N or CR4,
• X5 is independently from X1, X2, X3, X4 and X6 selected from the group of N and C,
• X6 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR34,
• if X5 is C and X4 is NR35, then X6 is CR34 or N,
• if X5 is C and X4 is N, then X6 is NR35,
• if X5 is C and X4 is CR4, then X6 is NR35, and
• if X5 is N, then X6 is N or CR34,
• R1, R2, R3, R4 and R34 are independently selected from the group consisting of —H, -halogen, —OR13, —SR19, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —NO2, —NR5R6, -cyano, and —C(═O)R11,
• R11 is selected from the group consisting of —OH, —(C1-C6)-alkoxy, —(C6-C22)-aryloxy, and NHR12,
• R5, R6, R12, R13, R19 and R35 are selected independently from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkinyl, —(C6-C22)-aryl, a protecting group and a reporter group,
• r and s are independently of each other an integer of from 1 to 18,
• D is the position of attachment of the group to the rest of the nucleic acid binding compound,
• said alkyl, alkenyl and alkynyl being unsubstituted or substituted by one or more moieties selected from the group consisting of -halogen, —SH, —S—(C1-C6)-alkyl, —(C1-C6)-alkoxy, —OH, —NR5R6, —COR11, —NH—CONR5R6, —NH—CSNR5R6 and —[O—(CH2)r]s—NR5R6
• and wherein said nucleic acid binding compound contains at least one reporter group
• with the proviso that
• if X4, X5, X6 of the heterocyclic group of the general formula I are N and X1 is CR1, X2 is N and X3 is CR3, R1 and R3 are not H, OH, NH2 or protected NH2.

A compound of the formula VI

• 26
• wherein
• A is selected from the group consisting of O, S, CH2 and N—(C1-C6)-alkyl,
• R14 is selected from the group consisting of —H, —OH, —(C1-C10)-alkoxy, O-protecting group, S-protecting group, NH-protecting group, —(C2-C10)-alkenyloxy, -halogen, -azido, —SH, —(C1-C6)-alkylmercapto, O-reporter group, O-solid phase and —NH2,
• R15 and R16 are independently selected from the group consisting of —H, —(C1-C8)-alkyl, —(C2-C18)-alkenyl, —(C2-C18)-alkynyl, —(C2-C18)-alkyl-carbonyl, —(C3-C19)-alkenyl-carbonyl, —(C3-C19)-alkynyl-carbonyl, —(C6-CI14)-aryl-(C1-C8)-alkyl, a protecting group or a compound of formula IV,
• with the proviso that R15 or R16 is a group of formula IV,
• 27
• wherein
• T is selected from the group consisting of oxo, thioxo and selenoxo,
• U is selected from the group consisting of —OH, —SH, —SeH, —(C1-C10)-alkoxy, —(C1-C10)-alkyl, —(C6-C22)-aryl, —(C6-C14)-aryl-(C1-C10)-alkyl, —NR23R24, and —O—(C1-C10)-alkyl-O—(C1-C10)-alkyl-R25, or wherein NR23R24 can together with N be a 5-6-membered heterocyclic ring,
• R23 and R24 are independently selected from the group consisting of —(C1-C10)-alkyl, —(C1-C20)-aryl, —(C6-C14)-aryl-(C1-C10)-alkyl, —(C1-C6)-alkyl-[NH(CH2)C]d—NR26R27,
• R25 is selected from the group consisting of —H, —OH, -halogen, amino, —(C1-C18)-alkylamino, —COOH, —CONH2 and COO(C1-C4)-alkyl,
• R26 and R27 are independently selected from the group consisting from —H, —(C1-C6)-alkyl, and —(C1-C4)-alkoxy-(C1-C6)-alkyl,
• R29 is selected from the group consisting of —OR30 and —SR30,
• R30 is selected from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C6-C22)-aryl, a protecting group, a phosphate, a diphosphate and a reporter group, and
• M and M′ are independently selected from the group consisting of oxy, sulfanediyl, —NR22, —(C1-C10)-alkyl, or —O—(C1-C10)-alkyl-O—, and —S—(C1-C10)-alkyl-O— and —NR22—(C1-C6)-alkyl-O—,
• R22 is selected from the group of —H and —(C1-C10)-alkyl, and
• c is an integer from 2 to 6,
• d is an integer from 0 to 6, and
• B has the formula I,
• 28
• wherein
• X1 is independently from X4, X5 and X6 selected from the group of N and
• CR1, and X1 is CR1 if each of X2 and X3 is N,
• X2 is independently from X4, X5 and X6 selected from the group of N and
• CR2, and X2 is CR2 if each of X1 and X3 is N,
• X3 is independently from X4, X5 and X6 selected from the group of N and
• CR3, and X3 is CR3 if each of X1 and X2 is N,
• X4 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR4,
• if X5 is C and X6 is NR35, then X4 is CR4 or N,
• if X5 is C and X6 is N, then X4 is NR35, and
• if X5 is C and X6 is CR34, then X4 is NR35, and
• if X5 is N, then X4 is N or CR4,
• X5 is independently from X1, X2, X3, X4 and X6 selected from the group of N and C,
• X6 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR34,
• if X5 is C and X4 is NR35, then X6 is CR34 or N.
• if X5 is C and X4 is N, then X6 is NR35,
• if X5 is C and X4 is CR4, then X6 is NR35, and
• if X5 is N, then X6 is N or CR34,
• R1, R2, R3, R4 and R34 are independently selected from the group consisting of —H. -halogen, —OR13, —SR19, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —NO2, —NR5R6, -cyano, and —C(═O)R11,
• R11 is selected from the group consisting of —OH, —(C1-C6)-alkoxy, —(C6-C22)-aryloxy, and NHR12,
• R5, R6, R12, R13, R19 and R35 are selected independently from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkinyl, —(C6-C22)-aryl, a protecting group and a reporter group,
• D is the position of attachment of the group to the rest of the nucleic acid binding compound,
• wherein any alkyl, alkenyl and alkynyl can be substituted or unsubstituted by one or more moieties selected from the group consisting of -halogen, —SH, —S—(C1-C6)-alkyl, —(C1-C6)-alkoxy, —OH, —NR5R6, —COR11, —NH—CONR5R6, —NH—CSNR5R6 and
• —[O—(CH2)r]s—NR5R6,
• r and s are independently of each other an integer of from 1 to 18, and
• with the proviso that
• said compound is not 8-aza-7-deaza-7-H-adenine-N8-β-D-ribofuranosyl-5′-monophosphate or 8-aza-7-deaza-7-H-adenine-N8-β-D-ribofuranosyl-5′-diphosphate,
• if A is O and B is a group of formula I with X4=X5=X6 =N and X1 is CR1, X2 is N and X3 is CR3, R1 and R3are not H, OH, NH2 or protected NH2,
• said compound is not 8-aza-7-deaza-N6-methyl-adenine-N8-β-D-ribofuranoside and its 5′-dimethoxytrityl-protected derivative, 8-aza-7-deaza-6-methoxy-purine-N8-3′,5′-di-toluoyl-β-D-ribofuranoside, 8-aza-7-deaza-adenine-N8-β-D-ribofuranoside and its N6-dimethylacetamido-, N6-benzoyl- or N6-benzoyl-5′-O-dimethoxytrityl-protected derivate,
• said compound is not 8-aza-9-deaza-9-methyl-2-mercapto-6-hydroxy-guanine-β-D-ribofuranoside, 8-aza-9-deaza-9-methyl-guanine-β-D-ribofuranoside and its N2-isobutyryl, and N2-isobutyryl-5′-O-dimethoxytrityl-protected derivative.

A compound of the formula VII

• 29
• wherein
• A is selected from the group consisting of O, S, CH2 and N—(C1-C6)-alkyl,
• M and M′ are independently selected from the group consisting of oxy, sulfanediyl, —NR22, —(C1-C10)-alkyl, or —O—(C1-C10)-alkyl-O—, and —S—(C1-C10)-alkyl-O— and —NR22—(C1-C6)-alkyl-O—,
• R22 is selected from the group of —H and —(C1-C10)-alkyl,
• R14 is selected from the group consisting of —H, —OR31, —(C1-C10)-alkoxy, —(C2-C10)-alkenyloxy, —(C2-C10)-alkynyloxy, -halogen, -azido NHR31, SR31, O-reporter group and —NH2,
• R31 is a protecting group or a reporter group,
• R32 and R17 are independently selected from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C6-C22)-aryl, or wherein NR32R17 can form together with N a 5-6-membered heterocyclic ring,
• R18 is selected from the group consisting of —(C2-C6)-alkenyloxy, substituted or unsubstituted —(C1-C6)-alkyl, unsubstituted —(C1-C6)-alkoxy or —(C1-C6)-alkoxy substituted one or more times by a group selected from the group consisting of -halogen, p-nitroaryloxy and -cyano, and
• B has the formula I
• 30
• wherein
• X1 is independently from X4, X5 and X6 selected from the group of N and
• CR1, and X1 is CR1 if each of X2 and X3 is N,
• X2 is independently from X4, X5 and X6 selected from the group of N and
• CR2, and X2 is CR2 if each of X1 and X3 is N,
• X3 is independently from X4, X5 and X6 selected from the group of N and
• CR3, and X3 is CR3 if each of X1 and X2 is N,
• X4 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR4,
• if X5 is C and X6 is NR35, then X4 is CR4 or N,
• if X5 is C and X6 is N, then X4 is NR35, and
• if X5 is C and X6 is CR34, then X4 is NR35, and
• if X5 is N, then X4 is N or CR4,
• X5 is independently from X1, X2, X3, X4 and X6 selected from the group of N and C,
• X6 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR34,
• if X5 is C and X4 is NR35, then X6 is CR34 or N,
• if X5 is C and X is N, then X6 is NR35,
• if X5 is C and X4 is CR4, then X6 is NR35, and
• if X5 is N, then X6 is N or CR34,
• R1, R2, R3, R4 and R34 are independently selected from the group consisting of —H. -halogen, —OR13, —SR19, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —NO2, —NR5R6, -cyano, and —C(═O)R11,
• R11 is selected from the group consisting of —OH, —(C1-C6)-alkoxy, —(C6-C22)-aryloxy, and NHR12,
• R5, R6, R12, R13, R19 and R35 are selected independently from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkinyl, —(C6-C22)-aryl, a protecting group and a reporter group,
• r and s are independently of each other an integer of from 1 to 18,
• D is the position of attachment of the group to the rest of the nucleic acid binding compound,
• said alkyl, alkenyl and alkynyl being unsubstituted or substituted by one or more moieties selected from the group consisting of -halogen, —SH, —S—(C1-C6)-alkyl, —(C1-C6)-alkoxy, —OH, —NR5R6, —COR11, —NH—CONR5R6, —NH—CSNR5R6 and —[O—(CH2)r]s—NR5R6, with the proviso that
• said compound is not 2-[2′-Deoxy-5′-O—(4,4′-dimethoxytrityl)-β-D-erythro-pentofuranosyl]4-(methylamino)-1H-pyrazolo[3,4-d]-pyrimidine 3 ′-[Methyl N,N-Diisopropylphosphoramidite]-4-(Benzoylamino)-2-[2′-deoxy-5′-O—(dimethoxytrityl)-β-D-erythro-pentofuranosyl]-2H-pyrazolo[3,4-d]-pyrimidine 3 ′-[Methyl N,N-Diisopropylphosphoramidite] or N-[2-[5-O-[Bis(4-Methoxyphenyl)phenylmethyl]-2-deoxy-β-D-ribofuranosyl]-3-methyl-7-oxo-2H-pyrazolo[4,3-d]pyrimidin-5-yl]-2-methyl-propanamide-3′-[(2-cyanoethyl)N,N-Diisopropylphosphoramidite],
• if A is O and B is a group of formula I with X4=X5=X6 =N and X1 is CR1, X2 is N and X3 is CR3, R1 and R3 are not H, OH, NH2 or protected NH2.

A compound of the formula VIII

• 31
• wherein
• PPP is a triphosphate group,
• R14 is selected from the group consisting of —H, —OH, —(C1-C10)-alkoxy, —(C2-C10)-alkenyloxy, —(C2-C10)-alkynyloxy halogen, -azido and NH2,
• R36 is selected from the group of —H and —OH, and
• B has the formula I.
• 32
• wherein
• X1 is independently from X4, X5 and X6 selected from the group of N and
• CR1, and X1 is CR1 if each of X2 and X3 is N,
• X2 is independently from X4, X5 and X6 selected from the group of N and
• CR2, and X2 is CR2 if each of X1 and X3 is N,
• X3 is independently from X4, X5 and X6 selected from the group of N and
• CR3, and X3 is CR3 if each of X1 and X2 is N,
• X4 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR4,
• if X5 is C and X6 is NR35, then X4 is CR4 or N,
• if X5 is C and X6 is N, then X4 is NR35, and
• if X5 is C and X6 is CR34,then X4 is NR35, and
• if X5 is N, then X4 is N or CR4,
• X5 is independently from X1, X2, X3, X4 and X6 selected from the group of N and C,
• X6 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR34,
• if X5 is C and X4 is NR35, then X6 is CR3 or N.
• if X5 is C and X4 is N then X6 is NR35,
• if X5 is C and X4 is CR4, then X6 is NR35, and
• if X5 is N, then X6 is N or CR34,
• R1, R2, R3, R4 and R34 are independently selected from the group consisting of —H, -halogen, —OR13, —SR19, —(C1-C10)-alkyl, —(C2-C 1)-alkenyl, —(C2-C10)-alkynyl, —NO2, —NR5R6, -cyano, and —C(═O)R11,
• R11 is selected from the group consisting of —OH, —(C1-C6)-alkoxy, —(C6-C22)-aryloxy, and NHR12,
• R5, R6, R12, R13, R19 and R35 are selected independently from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkinyl, —(C6-C22)-aryl, a protecting group and a reporter group,
• r and s are independently of each other an integer of from 1 to 18,
• D is the position of attachment of the group to the rest of the nucleic acid binding compound,
• said alkyl, alkenyl and alkynyl being unsubstituted or substituted by one or more moieties selected from the group consisting of -halogen, —SH, —S—(C1-C6)-alkyl, —(C1-C6)-alkoxy, —OH, —NR5R6, —COR11, —NH—CONR5R6, —NH—CSNR5R6 and —[O—(CH2)r]s—NR5R6,
• with the proviso that,
• said compound is not 8-aza-guanosine-N8-β-D-2′-3′-didesoxy-glyceropentofuranosyl.

A compound of the formula IX

• 33
• wherein
• A is selected from the group consisting of O, S, CH2 and N—(C1-C6)-alkyl,
• M and M′ are independently selected from the group consisting of oxy, sulfanediyl, —NR22, —(C1-C10)-alkyl, or —O—(C1-C10)-alkyl-O—, and —S—(C1-C10)-alkyl-O— and —NR22—(C1-C6)-alkyl-O—,
• R22 is selected from the group of —H and —(C1-C10)-alkyl,
• R14 is selected from the group consisting of —H, —OR31, —(C1-C10)-alkoxy, —(C2-C10)-alkenyloxy, —(C2-C10)-alkynyloxy, -halogen, -azido NHR31, SR31, O-reporter group and —NH2,
• R31 is a protecting group or a reporter group,
• R32 and R17 are independently selected from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C6-C22)-aryl, or wherein NR32R17 can form together with N a 5-6-membered heterocyclic ring,
• R18 is selected from the group consisting of —(C2-C6)-alkenyloxy, substituted or unsubstituted —(C1-C6)-alkyl, unsubstituted —(C1-C6)-alkoxy or —(C1-C6)-alkoxy substituted one or more times by a group selected from the group consisting of -halogen, p-nitroaryloxy and -cyano, and
• B has the formula I
• 34
• wherein
• X1 is independently from X4, X5 and X6 selected from the group of N and
• CR1, and X1 is CR1 if each of X2 and X3 is N,
• X2 is independently from X4, X5 and X6 selected from the group of N and
• CR2, and X2 is CR2 if each of X1 and X3 is N,
• X3 is independently from X4, X5 and X6 selected from the group of N and
• CR3, and X3 is CR3 if each of X1 and X2 is N,
• X4is independently from X1, X2 and X3 selected from the group of N, NR35 and CR4,
• if X5 is C and X6 is NR35, then X4 is CR4 or N,
• if X5 is C and X6 is N, then X4 is NR35, and
• if X5 is C and X6 is CR34, then X4 is NR35, and
• if X5 is N, then X4 is N or CR4,
• X5 is independently from X1, X2, X3, X4 and X6 selected from the group of N and C,
• X6 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR34,
• if X5 is C and X4 is NR35, then X6 is CR34 or N,
• if X5 is C and X4 is N then X6 is NR35,
• if X5 is C and X4 is CR4, then X6 is NR35, and
• if X5 is N, then X6 is N or CR34,
• R1, R2, R3, R4 and R34 are independently selected from the group consisting of —H, -halogen, —OR13, —SR19, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —NO2, —NR5R6, -cyano, and —C(═O)R11,
• R11 is selected from the group consisting of —OH, —(C1-C6)-alkoxy, —(C6-C22)-aryloxy, and NHR12,
• R5, R6, R12, R13, R19 and R35 are selected independently from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkinyl, —(C6-C22)-aryl, a protecting group and a reporter group,
• r and s are independently of each other an integer of from 1 to 18,
• D is the position of attachment of the group to the rest of the nucleic acid binding compound,
• said alkyl, alkenyl and alkynyl being unsubstituted or substituted by one or more moieties selected from the group consisting of -halogen, —SH, —S—(C1-C6)-alkyl, —(C1-C6)-alkoxy, —OH, —NR5R6, —COR11, —NH—CONR5R6, —NH—CSNR5R6 and —[O—(CH2)r]s—NR5R6.

A compound of the formula X

• 35
• wherein
• M and M′ are independently selected from the group consisting of oxy, sulfanediyl, —NR22, —(C1-C10)-alkyl, or —O—(C1-C10)-alkyl-O—, and —S—(C1-C10)-alkyl-O— and —NR22—(C1-C6)-alkyl-O—,
• R22 is selected from the group of —H and —(C1-C10)-alkyl,
• R14 is selected from the group consisting of —H, —OR31, —(C1-C10)-alkoxy, —(C2-C10)-alkenyloxy, —(C2-C10)-alkynyloxy, -halogen, -azido NHR31, SR31, O-reporter and —NH2,
• R31 is a protecting group or a reporter group,
• B has the formula I
• 36
• wherein
• X1 is independently from X4, X5 and X6 selected from the group of N and
• CR1, and X1 is CR1 if each of X2 and X3 is N,
• X2 is independently from X4, X5 and X6 selected from the group of N and
• CR2, and X2 is CR2 if each of X1 and X3 is N,
• X3 is independently from X4, X5 and X6 selected from the group of N and
• CR3, and X3 is CR3 if each of X1 and X2 is N,
• X4 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR4,
• if X5 is C and X6 is NR35, then X4 is CR4 or N,
• if X5 is C and X6 is N, then X4 is NR35, and
• if X5 is C and X6 is CR34, then X4 is NR35, and
• if X5 is N, then X4 is N or CR4,
• X5 is independently from X1, X2, X3, X4 and X6 selected from the group of N and C,
• X6 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR34,
• if X5 is C and X4 is NR35, then X6 is CR34 or N,
• if X5 is C and X4 is N. then X6 is NR35,
• if X5 is C and X4 is CR4, then X6 is NR35, and
• if X5 is N, then X6 is N or CR34,
• R1, R2, R3, R4 and R34 are independently selected from the group consisting of —H, -halogen, —OR13, —SR19, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —NO2, —NR5R6, -cyano, and —C(═O)R11,
• R11 is selected from the group consisting of —OH, —(C1-C6)-alkoxy, —(C6-C22)-aryloxy, and NHR12,
• R5, R6, R12, R13, R19 and R35 are selected independently from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkinyl, —(C6-C22)-aryl, a protecting group and a reporter group,
• r and s are independently of each other an integer of from 1 to 18,
• D is the position of attachment of the group to the rest of the nucleic acid binding compound,
• said alkyl, alkenyl and alkynyl being unsubstituted or substituted by one or more moieties selected from the group consisting of -halogen, —SH, —S—(C1-C6)-alkyl, —(C1-C6)-alkoxy, —OH, —NR5R6, —COR11, —NH—CONR5R6, —NH—CSNR5R6 and —[O—(CH2)r]s—NR5R6,
• with the proviso that
• if A is O and B is a group of formula I with X4=X5=X6 =N and X1 is CR1, X2 is N and X3 is CR3, R1 and R3 are not H, OH, NH2 or protected NH2.

A precursor for the synthesis of a nucleic acid binding compound comprising a backbone, which comprises a moiety of the formula VI

• 46
• A is selected from the group consisting of O, S, CH2 and N—(C1-C6)-alkyl,
• M and M′ are independently selected from the group consisting of oxy, sulfanediyl, —NR22—, —(C1-C10)-alkyl-, or —O—(C1-C10)-alkyl-O—, and —S—(C1-C10)-alkyl-O— and —NR22—(C1-C6)-alkyl-O—,
• R22 is selected from the group of —H, —(C1-C10)-alkyl, a protecting group and a reporter group,
• R14 is selected from the group consisting of —H, —OR31, —(C1-C10)-alkoxy, O-protecting group, S-protecting group, NH2-protecting group, —(C2-C10)-alkenyloxy, —(C2-C10)-alkynyloxy, -halogen, -azido, SH, —(C1-C10)-alkylmercapto, —NH2 and -O-solid phase,
• R15 and R16 are independently selected from the group consisting of —H, —(C1-C6)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —(C2-C10)-alkyl-carbonyl, —(C3-C19)-alkenyl-carbonyl, —(C3-C19)-alkynyl-carbonyl, —(C6-C14)-aryl-(C1-C10)-alkyl, protecting group and a solid phase
• B is the link to a moiety of the formula I,
• 47
• wherein
• X1 is independently from X4, X5 and X6 selected from the group of N and
• CR1, and X1 is CR1 if each of X2 and X3 is N,
• X2 is independently from X4, X5 and X6 selected from the group of N and
• CR2, and X2 is CR2 if each of X1 and X3 is N,
• X3 is independently from X4, X5 and X6 selected from the group of N and
• CR3, and X3 is CR3 if each of X1 and X2 is N,
• X4 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR4,
• if X5 is C and X6 is NR35, then X4 is CR4 or N,
• if X5 is C and X6 is N, then X4 is NR35, and
• if X5 is C and X6 is CR34, then X4 is NR35, and
• if X5 is N, then X4 is N or CR4,
• X5 is independently from X1, X2, X3, X4 and X6 selected from the group of N and C,
• X6 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR34,
• if X5 is C and X4 is NR35, then X6 is CR34 or N,
• if X5 is C and X4 is N then X6 is NR35,
• if X5 is C and X4 is CR4, then X6 is NR35, and
• if X5 is N, then X6 is N or CR34,
• R1, R2, R3, R4 and R34 are independently selected from the group consisting of —H, -halogen, —OR13, —SR19, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —NO2, —NR5R6, -cyano, and —C(═O)R11,
• R11 is selected from the group consisting of —OH, —(C1-C6)-alkoxy, —(C6-C22)-aryloxy, and NHR12,
• R5, R6, R12, R13, R19 and R35 are selected independently from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkinyl, —(C6-C22)-aryl, a protecting group and a reporter group,
• D is the position of attachment of the group to the backbone,
• wherein any alkyl, alkenyl and alkynyl can be substituted or unsubstituted by one or more moieties selected from the group consisting of -halogen, —SH, —S—(C1-C6)-alkyl, —(C1-C6)-alkoxy, —OH, —NR5R6, —COR11, —NH—CONR5R6, —NH—CSNR5R6 and —[O—(CH2)r]s—NR5R6.
• r and s are independently of each other an integer of from 1 to 18,
• wherein one of R14, R15 or R16 is a solid phase.

A precursor or intermediate for the synthesis of a nucleic acid binding compound, comprising a backbone which comprises a moiety of the formula III

• 48
• wherein
• A is selected from the group consisting of O, S, CH2 and N—(C1-C6)-alkyl,
• M is selected from the group consisting of oxy, sulfanediyl, —NR22—, —(C1-C10)-alkyl-, or —O—(C1-C10)-alkyl-O—, and —S—(C1-C10)-alkyl-O— and —NR22—(C1-C6)-alkyl-O—,
• R22 is selected from the group of —H, —(C1-C10)-alkyl, a protecting group and a reporter group,
• R14 is selected from the group consisting of —H, —OH, —(C1-C10)-alkoxy, —(C2-C10)-alkenyloxy, —(C2-C10)-alkynyloxy, -halogen, -azido, SH, —(C1-C10)-alkylmercapto, O-reporter group, O-solid phase and —NH2,
• R15 is selected from the group consisting of —H, —(C1-C6)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —(C2-C10)-alkyl-carbonyl, —(C3-C19)-alkenyl-carbonyl, —(C3-C19)-alkynyl-carbonyl, —(C6-C14)-aryl-(C1-C10)-alkyl and a solid phase,
• B is the link to a moiety of the formula I,
• 49
• wherein
• X1 is independently from X4, X5 and X6 selected from the group of N and
• CR1, and X1 is CR1 if each of X2 and X3 is N,
• X2 is independently from X4, X5 and X6 selected from the group of N and
• CR2, and X2 is CR2 if each of X1 and X3 is N,
• X3 is independently from X4, X5 and X6 selected from the group of N and
• CR3, and X3 is CR3 if each of X1 and X2 is N,
• X4 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR4,
• if X5 is C and X6 is NR35, then X4 is CR4 or N,
• if X5 is C and X6 is N, then X4 is NR35, and
• if X5 is C and X6 is CR34, then X4 is NR35, and
• if X5 is N, then X4 is N or CR4,
• X5 is independently from X1, X2, X3, X4 and X6 selected from the group of N and C,
• X6 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR34,
• if X5 is C and X4 is NR35, then X6 is CR34 or N,
• if X5 is C and X4 is N then X6 is NR35,
• if X5 is C and X4 is CR4, then X6 is NR35, and
• if X5 is N, then X6 is N or CR34,
• R1, R2, R3, R4 and R34 are independently selected from the group consisting of —H, -halogen, —OR13, —SR19, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —NO2, —NR5R6, -cyano, and —C(═O)R11,
• R11 is selected from the group consisting of —OH, —(C1-C6)-alkoxy, —(C6-C22)-aryloxy, and NHR12,
• R5, R6, R12, R13, R19 and R35 are selected independently from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkinyl, —(C6-C22)-aryl, a protecting group and a reporter group,
• D is the position of attachment of the group to the backbone,
• wherein any alkyl, alkenyl and alkynyl can be substituted or unsubstituted by one or more moieties selected from the group consisting of -halogen, —SH, —S—(C1-C6)-alkyl, —(C1-C6)-alkoxy, —OH, —NR5R6, —COR11, —NH—CONR5R6, —NH—CSNR5R6 and —[O—(CH2)r]s—NR5R6.
• r and s are independently of each other an integer of from 1 to 18,
• wherein R14 is O-solid phase or R15 is solid phase.

A precursor or intermediate for the synthesis of a nucleic acid binding compound comprising a backbone, which comprises a heterocyclic group of the formula I

• 50
• wherein
• X1 is independently from X4, X5 and X6 selected from the group of N and
• CR1, and X1 is CR1 if each of X2 and X3 is N,
• X2 is independently from X4, X5 and X6 selected from the group of N and
• CR2, and X2 is CR2 if each of X1 and X3 is N,
• X3 is independently from X4, X5 and X6 selected from the group of N and
• CR3, and X3 is CR3 if each of X1 and X2 is N,
• X4 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR4,
• if X5 is C and X6 is NR35, then X4 is CR4 or N,
• if X5 is C and X6 is N, then X4 is NR35, and
• if X5 is C and X6 is CR34, then X4 is NR35, and
• if X5 is N, then X4 is N or CR4,
• X5 is independently from X1, X2, X3, X4 and X6 selected from the group of N and C,
• X6 is independently from X1, X2 and X3 selected from the group of N, NR35 and CR34,
• if X5 is C and X4 is NR35, then X6 is CR34 or N,
• if X5 is C and X4 is N, then X6 is NR35,
• if X5 is C and X4 is CR4, then X6 is NR35, and
• if X5 is N, then X6 is N or CR34,
• R1, R2, R3, R4 and R34 are independently selected from the group consisting of —H, -halogen, —OR13, —SR19, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkynyl, —NO2, —NR5R6, -cyano, and —C(═O)R11,
• R11 is selected from the group consisting of —OH, —(C1-C6)-alkoxy, —(C6-C22)-aryloxy, and NHR12,
• R5, R6, R12, R13, R19 and R35 are selected independently from the group consisting of —H, —(C1-C10)-alkyl, —(C2-C10)-alkenyl, —(C2-C10)-alkinyl, —(C6-C22)-aryl, a protecting group, a solid phase and a reporter group,
• r and s are independently of each other an integer of from 1 to 18,
• D is the position of attachment of the group to the backbone,
• said alkyl, alkenyl and alkynyl being unsubstituted or substituted by one or more moieties selected from the group consisting of -halogen, —SH, —S—(C1-C6)-alkyl, —(C1-C6)-alkoxy, —OH, —NR5R6, —COR11, —NH—CONR5R6, —NH—CSNR5R6 and —[O(CH2)r]s—NR5R6
• wherein either said backbone is solid phase bound or wherein at least one of R5, R6, R12, R13, R19 and R35 is solid phase.