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

A method for the determination of a nucleic acid comprising,

• (a) providing a sample suspected to contain said nucleic acid,
• (b) providing a nucleic acid binding compound which is essentially complementary to a part or all of said nucleic acid,
• wherein said nucleic acid binding compound comprises a backbone, said backbone having attached heterocyclic groups wherein at least one of said heterocyclic groups has the formula I
• 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 X5 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 X2 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 the heterocyclic group of the general formula is 8-aza-7-deazaadenine (A*) which is attached to a 2′ deoxy β-D erythropentofuranosyl moiety the sequence of said nucleic acid binding compound is not selected from the group consisting of (A*T)6, CTGGA*TCCAG or CTGGATCCA*G,
• if the heterocyclic group of the general formula I is N6-methylated-8-aza-7-deazaadenine (A*m) which is attached to a 2′-deoxy-β-D-erythropentofuranosyl moiety the sequence of said nucleic acid binding compound is not selected from the group consisting of (A*mT)6, CTGGA*mTCCAG, CTGGATCCA*mG, ATATATA*mTATAT, ATGCAGA*mTCTGCA or CTGGATCGA*mG,
• if the heterocyclic group of the formula I is 8-aza-7-deazaadenine which is attached to a β-D-ribofuranosyl moiety the sequence of said compound contains at least one further heterocycle other than adenine and other than 8-aza-7-deazaadenine,
• if the heterocyclic group of the general formula I is 8-aza-9-deaza-9-methyl-guanin which is N8-attached with a 2′-deoxt-β-D-ribofuranosyl moiety the sequence of said compound contains at least one further heterocycle other than thymidine and other than 8-aza-9-deaza-9-methyl-guanin and
• 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,
• (c) contacting said sample with said nucleic acid binding compound under conditions for binding said nucleic acid binding compound to said nucleic acid, and
• (d) determining the binding product formed from said nucleic acid and said nucleic acid binding compound as a measure of the presence of said nucleic acid.