Oligonucleotide and nucleotide amine analogs, methods of synthesis and use

A compound having the structure:

• 17
• wherein B is a purine or pyrimidine heterocyclic base, R8 and R9 are independently H, PO2−, a nucleotide, an oligonucleotide or an amine-containing species, and at least one of R8 and R9 is a purine containing oligonucleotide;
• and at least one of R8, R9 and A is a species comprising the formula L1-L2-polyamine wherein L1 is an amino linker and L2 is a heterobifunctional linker;
• wherein if R8 is not a purine containing oligonucleotide or polyamine species, then R8 is a nucleotide or PO2—;
• if R9 is not a purine containing oligonucleotide or polyamine species, then R9 is H or a nucleotide;
• and if A is not a polyamine species then A is H or OH.

A method of preparing a composition having the structure:

• 18
• wherein R1 and R2 are independently H, a nucleotide, an oligonucleotide, or an amine-containing species and at least one of R1 and R2 is a purine containing oligonucleotide, R3 is a linear or cyclic non-aromatic amine-containing species, and X is H, O—R11, S—R11, F, Cl, Br, CN, CF3, OCF3, OCN, SOCH3, SO2CH3, ONO2, N3, HN2, heterocylcoalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, a reporter molecule, an RNA cleaving group, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide wherein R11 is H, C1 to C10 straight or branched chain lower alkyl or substituted lower alkyl, C2 to C10 straight or branched chain lower alkenyl or substituted lower alkenyl, C3 to C10 straight or branched chain lower alkynyl or substituted lower alkynyl, a 14C containing lower alkyl, lower alkenyl or lower alkynyl, C7 to C14 substituted or unsubstituted alkyaryl or aralkyl, a 14C containing C7 to C14 alkaryl or aralkyl, alicyclic, heterocyclic, a reporter molecule, a RNA cleaving group, a group for improving the pharmacokinetic properties of an oligonucleotide or a group for improving the pharmacodynamic properties of an oligonucleotide comprising the steps of:
• providing a synthon having the structure:
• 19
• wherein R1 and R2 are independently H, a nucleotide, an oligonucleotide, or an amine-containing species and at least one of R1 and R2 is a purine containing oligonucleotide, and X is H, O—R11, S—R11, F, Cl, Br, CN, CF3, OCF3, OCN, SOCH3, SO2CH3, ONO2, N3, HN2, heterocylcoalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, a reporter molecule, an RNA cleaving group, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide wherein R11 is H, C1 to C10 straight or branched chain lower alkyl or substituted lower alkyl, C2 to C10 straight or branched chain lower alkenyl or substituted lower alkenyl, C3 to C10 straight or branched chain lower alkynyl or substituted lower alkynyl, a 14C containing lower alkyl, lower alkenyl or lower alkynyl, C7 to C14 substituted or unsubstituted alkyaryl or aralkyl, a 14C containing C7 to C14 alkaryl or aralkyl, alicyclic, heterocyclic, a reporter molecule, a RNA cleaving group, a group for improving the pharmacokinetic properties of an oligonucleotide or a group for improving the pharmacodynamic properties of an oligonucleotide;
• and reacting said synthon with —NH(R3), wherein R3 is a linear or cyclic non-aromatic amine-containing species, under reducing conditions to yield said compound.

A method of preparing a compound having the structure:

• 20
• wherein R4 is an oligonucleotide and M is a pendent group having an amine-containing species attached thereto comprising the steps of:
• providing a compound having the structure:
• 21
• wherein R4 is an oligonucleotide, R12 is an oligonucleotide and B is urea or a heterocyclic base having a corresponding glycosylase;
• reacting the compound with an endonuclease to generate a conjugated α,β-unsaturated system in the sugar residue of the 3′ terminal nucleotide;
• reacting the compound with a pendent group containing a nucleophilic functionality thereon;
• reacting the compound with a reducing agent to stabilize the compound;
• and
• reacting the compound with an amine-containing species to add a pendent amine-containing species to said pendent group.

A method of preparing a compound having the structure:

• 22
• wherein R4 is an oligonucleotide, R5 is a linear or cyclic amine-containing species containing only non-amide nitrogen atoms, and R6 is H, a purine heterocycle or a pyrimidine heterocycle comprising the steps of:
• reacting an oligonucleotide having a, 3′ ribofuranosyl sugar with an oxidizing agent to produce an activated dialdehyde-terminated oligonucleotide;
• and
• reacting said activated oligonucleotide with a linear or cyclic amine-containing species under reducing conditions to yield said compound.

A method of treating an animal having a disease characterized by undesired production of protein comprising:

• contacting an animal with a compound having the structure:
• 24
• wherein R1 and R2 are independently H, a nucleotide, an oligonucleotide or an amine-containing species, and at least one of R1 and R2 is a purine containing oligonucleotide, R3 is a linear or cyclic amine-containing species, and X is H, O—R11, S—R11, F, Cl, Br, CN, CF3, OCF3, OCN, SOCH3, SO2CH3, ONO2, N3, HN2, heterocylcoalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, a reporter molecule, an RNA cleaving group, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide wherein R11 is H, C1 to C10 straight or branched chain lower alkyl or substituted lower alkyl, C2 to C10 straight or branched chain lower alkenyl or substituted lower alkenyl, C3 to C10 straight or branched chain lower alkynyl or substituted lower alkynyl, a 14C containing lower alkyl, lower alkenyl or lower alkynyl, C7 to C14 substituted or unsubstituted alkyaryl or aralkyl, a 14C containing C7 to C14 alkaryl or aralkyl, alicyclic, heterocyclic, a reporter molecule, a RNA cleaving group, a group for improving the pharmacokinetic properties of an oligonucleotide or a group for improving the pharmacodynamic properties of an oligonucleotide.

A method for detecting the presence or absence of an RNA in a biological sample suspected of containing said RNA comprising:

• contacting a sample with a compound having the structure:
• 25
• wherein R1 and R2 are independently H, a nucleotide, an oligonucleotide or an amine-containing species, and at least one of R1 and R2 is a purine containing oligonucleotide, R3 is a linear or cyclic amine-containing species, and X is H, O—R11, S—R11, F, Cl, Br, CN, CF3, OCF3, OCN, SOCH3, SO2CH3, ONO2, N3, HN2, heterocylcoalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, a reporter molecule, an RNA cleaving group, a group for improving the pharmacokinetic properties of an oligonucleotide, or a groups for improving the pharmacodynamic properties of an oligonucleotide wherein R11 is H, C1 to C10 straight or branched chain lower alkyl or substituted lower alkyl, C2 to C10 straight or branched chain lower alkenyl or substituted lower alkenyl, C3 to C10 straight or branched chain lower alkynyl or substituted lower alkynyl, a 14C containing lower alkyl, lower alkenyl or lower alkynyl, C7 to C14 substituted or unsubstituted alkyaryl or aralkyl, a 14C containing C7 to C14 alkaryl or aralkyl, alicyclic, heterocyclic, a reporter molecule, a RNA cleaving group, a group for improving the pharmacokinetic properties of an oligonucleotide or a group for improving the pharmacodynamic properties of an oligonucleotide;
• said compound being specifically hybridizable with said RNA;
• and
• detecting the presence or absence of hybridization of the compound to the sample wherein hybridization is indicative of the presence of RNA in the sample.

A method for detecting the presence or absence of an RNA in a biological sample suspected of containing said RNA comprising:

• contacting a sample with a compound having the structure:
• 28
• wherein R4 is an oligonucleotide and M is a pendent group having an amine-containing species attached thereto;
• said compound being specifically hybridizable with said RNA;
• and
• detecting the presence or absence of hybridization of the compound to the sample wherein hybridization is indicative of the presence of RNA in the sample.

A method for detecting the presence or absence of an RNA in a biological sample suspected of containing said RNA comprising:

• contacting the sample with a compound having the structure:
• 31
• wherein R4 is an oligonucleotide, R5 is a linear or cyclic amine-containing species containing only non-amide nitrogen atoms, and R6 is H, a purine heterocycle or a pyrimidine heterocycle;
• said compound being specifically hybridizable with RNA;
• and
• detecting hybridization of the compound to the sample where the presence or absence of hybridization is indicative of the presence of said RNA in the sample.

A method for modulating the production of a protein by an organism comprising:

• contacting an organism with a compound having the structure:
• 32
• wherein B is a purine or pyrimidine heterocycle, R8 and R9 are independently H, PO2−, a nucleotide, an oligonucleotide or an amine-containing species, and at least one of R8 and R9 is a purine containing oligonucleotide, and at least one of R8, R9 and A is a species comprising the formula L1-L2-polyamine wherein L1 is an amino linker and L2 is a heterobifunctional linker;
• wherein if R8 is not a purine containing oligonucleotide or polyamine species, then R8 is a nucleotide or PO2−;
• if R9 is not a purine containing oligonucleotide or polyamine species, then R9 is H or a nucleotide;
• and if A is not a polyamine species then A is H or OH.

A method of treating an animal having a disease characterized by undesired production of protein comprising:

• contacting an animal with a compound having the structure:
• 33
• wherein B is a purine or pyrimidine heterocycle, R8 and R9 are independently H, PO2−, a nucleotide, an oligonucleotide or an amine-containing species, and at least one of R8 and R9 is a purine containing oligonucleotide, and at least one of R8, R9 and A is a species comprising the formula L1-L2-polyamine wherein L1 is an amino linker and L2 is a heterobifunctional linker, in a pharmaceutically acceptable carrier;
• and
• wherein if R8 is not a purine containing oligonucleotide or polyamine species, then R8 is a nucleotide or PO2−;
• if R9 is not a purine containing oligonucleotide or polyamine species, then R9 is H or a nucleotide;
• and if A is not a polyamine species then A is H or OH.

A method for detecting the presence or absence of an RNA in a biological sample suspected of containing said RNA comprising:

• contacting a sample with a compound having the structure:
• 34
• wherein B is a purine or pyrimidine heterocycle, R8 and R9 are independently H, PO2−, a nucleotide, an oligonucleotide or an amine-containing species, and at least one of R8 and R9 is a purine containing oligonucleotide, and at least one of R8, R9 and A is a species comprising the formula L1-L2-polyamine wherein L1 is an amino linker and L2 is a heterobifunctional linker;
• and
• wherein if R8 is not a purine containing oligonucleotide or polyamine species, then R8 is a nucleotide or PO2−;
• if R9 is not a purine containing oligonucleotide or polyamine species, then R9 is H or a nucleotide;
• and if A is not a polyamine species then A is H or OH;
• said compound being specifically hybridizable with said RNA;
• and
• detecting the presence or absence of hybridization of the compound to the sample wherein hybridization is indicative of the presence of RNA in the sample.