Modified oligonucleotides and applications thereof
AssigneeApplera Corporation
InventorsZhaochun Ma, Khairuzzaman Bashar Mullah
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Abstract
Disclosed, among other things, are primers containing certain modified nucleobases in the 3′ terminal region of the primers that provide reduced formation of primer-dimers during amplification reactions, and various methods of use thereof.
Claims17
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is C1-C6 alkyl.
A polynueleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is C1-C6 substituted alkyl.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is C3-C10 aryl.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nueleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is C3-C10 substituted aryl.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is CF3.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is amino.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is substituted amino.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is C3-C6 cyclic alkyl.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is C3-C6 substituted cyclic alkyl.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is phenyl.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is substituted phenyl.
A polynueleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is C5-C10 heteroaryl.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is selected from —H, —F, —Cl, C1-C6 alkyl, C1-C6 substituted alkyl, C3-C10 aryl, C3-C10 substituted aryl, C3-C10 aryl ether, C3-C10 substituted aryl ether, —CF3, —NR1R1, C3-C6 cyclic alkyl, C3-C6 substituted cyclic alkyl, phenyl, substituted phenyl and C5-C10 heteroaryl, wherein R1 is selected from —H, —F, —Cl, C1-C6 alkyl, C1-C6 substituted alkyl, C3-C10 aryl, C3-C10 substituted aryl:
- and wherein at least one modified nucleotide is the 3′ terminal nucleotide of the polynucleotide.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is selected from —H, —F, —Cl, C1-C6 alkyl, C1-C6 substituted alkyl, C3-C10 aryl, C3-C10 substituted aryl, C3-C10 aryl ether, C3-C10 substituted aryl ether, —CF3, —NR1R1, C3-C6 cyclic alkyl, C3-C6 substituted cyclic alkyl, phenyl, substituted phenyl and C5-C10 heteroaryl, wherein R1 is C1-C6 alkyl, C1-C6 substituted alkyl, C3-C10 aryl, C3-C10 substituted aryl;
- and wherein the polynucleotide further comprises at least one of a detectable label, a quencher, a minor groove binder or any combination thereof.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is selected from —H, —F, —Cl, C1-C6 alkyl, C1-C6 substituted alkyl, C3-C10 aryl, C3-C10 substituted aryl, C3-C10 aryl ether, C3-C10 substituted aryl ether, —CF3, —NR1R1, C3-C6 cyclic alkyl, C3-C6 substituted cyclic alkyl, phenyl, substituted phenyl and C5-C10 heteroaryl, wherein R1 is C1-C6 alkyl, C1-C6 substituted alkyl, C3-C10 aryl, C3-C10 substituted aryl;
- and wherein the polynucleotide further comprises at least one of a detectable label, a quencher, a minor groove binder or any combination thereof, and wherein the polynucleotide is a probe that is not extendable at its 3′ terminus.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is —F.
A polynucleotide primer comprising at least one modified pyrimidine nucleobase no more than 4 nucleotides from the 3′ terminus of the primer, wherein the modified pyrimidine nucleobase comprises the structure
- wherein R is —Cl.
Dependencies are inferred from the claim text.