Multiaptamer Target Detection
Described herein are compositions comprising a first aptamer, second aptamer and a target that are capable of forming a ternary complex, and wherein the first aptamer and the second aptamer comprise C-5 pyrimidine modification schemes that are different, and methods of making and using such compositions.
1 . A composition comprising a first aptamer, second aptamer, and a target,
wherein the first aptamer and the second aptamer comprise a C-5 modified pyrimidine; and
wherein the first aptamer, second aptamer and the target are capable of forming a ternary complex.
2 . The composition of claim 1 , wherein the first aptamer has binding affinity for the target and not the second aptamer.
3 . The composition of claim 1 , wherein the second aptamer has binding affinity for the target and not the first aptamer.
4 . The composition of claim 1 , wherein the second aptamer has binding affinity for a complex formed by the association of the first aptamer with the target.
5 . The composition of claim 1 , wherein the first aptamer binding region of the target and the second aptamer binding region of the target are different regions.
6 . The composition of claim 1 , wherein the first aptamer and the second aptamer, independently, comprise RNA, DNA or a combination thereof.
7 . The composition of claim 1 , wherein the C-5 modified pyrimidine is selected from the group consisting of 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU), 5-(N-benzylcarboxyamide)-2′-O-methyluridine, 5-(N-benzylcarboxyamide)-2′-fluorouridine, 5-(N-phenethylcarboxyamide)-2′-deoxyuridine (PEdU), 5-[N-(phenyl-3-propyl)carboxamide]-2′-deoxyuridine (PPdU), 5-[N-(2-thiophene-methyl)carboxamide]-2′-deoxyuridine (ThdU), 5-(N-isobutylcarboxyamide)-2′-deoxyuridine (iBudU), 5-(N-isobutylcarboxyamide)-2′-O-methyluridine, 5-(N-isobutylcarboxyamide)-2′-fluorouridine, 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-(N-tryptaminocarboxyamide)-2′-O-methyluridine, 5-(N-tryptaminocarboxyamide)-2′-fluorouridine, 5-(N-[1-(3-trimethylamonium) propyl]carboxyamide)-2′-deoxyuridine chloride, 5-[N-(1-naphthylmethyl)carboxyamide]-2′-deoxyuridine (NapdU), 5-[N-(2-naphthylmethyl)carboxyamide]-2′-deoxyuridine (2-NapdU), 5-[N-(1-naphthylethyl)carboxyamide]-2′-deoxyuridine (NEdU), 5-[N-(2-naphthylethyl)carboxyamide]-2′-deoxyuridine 2NEdU), 5-[N-(4-fluorobenzyl)carboxyamide]-2′-deoxyuridine FBndU), 5-[N-(4-hydroxyphenyl-2-ethyl)carboxamide]-2′-deoxyuridine (TyrdU), 5-(N-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-naphthylmethylcarboxyamide)-2′-fluorouridine, 5-(N-[1-(2,3-dihydroxypropyl)]carboxyamide)-2′-deoxyuridine, 5-[N-(3-benzo[b]thiophene-2-ethyl)carboxamide]-2′-deoxyuridine (BTdU), 5-[N-(3-benzo[a]furan-2-ethyl)carboxamide]-2′-deoxyuridine (BFdU), 5-[N-(3,4-methylenedioxybenzyl)carboxamide]-2′-deoxyuridine (MBndU), 5-[N#R)-2-tetrahydrofurylmethyl)carboxamide]-2′-deoxyuridine (RTHdU), 5-[N—((S)-2-tetrahydrofurylmethyl)carboxamide]-2′-deoxyuridine (STHFdU), 5-(N-2-imidazolylethylcarboxamide)-2′-deoxyuridine (ImiddU), 5-[N-(1-morpholino-2-ethyl)carboxamide]-2′-deoxyuridine (MOEdU), and a combination thereof.
8 . The composition of claim 1 , wherein the C-5 modified pyrimidine is selected from the group consisting of a 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU), a 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU) and a combination thereof.
9 . The composition of claim 1 , wherein each uracil or thymine of the first aptamer is a C-5 modified pyrimidine selected from the group consisting of 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU), 5-(N-benzylcarboxyamide)-2′-O-methyluridine, 5-(N-benzylcarboxyamide)-2′-fluorouridine, 5-(N-phenethylcarboxyamide)-2′-deoxyuridine (PEdU), 5-[N-(2-thiophene-methyl)carboxamide]-2′-deoxyuridine (ThdU), 5-(N-isobutylcarboxyamide)-2′-deoxyuridine (iBudU), 5-(N-isobutylcarboxyamide)-2′-O-methyluridine, 5-(N-isobutylcarboxyamide)-2′-fluorouridine, 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-(N-tryptaminocarboxyamide)-2′-O-methyluridine, 5-(N-tryptaminocarboxyamide)-2′-fluorouridine, 5-(N-[1-(3-trimethylamonium) propyl]carboxyamide)-2′-deoxyuridine chloride, 55-[N-(1-naphthylmethyl)carboxyamide]-2′-deoxyuridine (NapdU), 5-[N-(2-naphthylmethyl)carboxyamide]-2′-deoxyuridine (2-NapdU), 5-(N-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-naphthylmethylcarboxyamide)-2′-fluorouridine and a 5-(N-[1-(2,3-dihydroxypropyl)]carboxyamide)-2′-deoxyuridine.
10 . The composition of claim 1 , wherein each uracil or thymine of the first aptamer is a 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU).
11 . The composition of claim 1 , wherein each uracil or thymine of the second aptamer is a C-5 modified pyrimidine selected from the group consisting of 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU), 5-(N-benzylcarboxyamide)-2′-O-methyluridine, 5-(N-benzylcarboxyamide)-2′-fluorouridine, 5-(N-phenethylcarboxyamide)-2′-deoxyuridine (PEdU), 5-[N-(2-thiophene-methyl)carboxamide]-2′-deoxyuridine (ThdU), 5-(N-isobutylcarboxyamide)-2′-deoxyuridine (iBudU), 5-(N-isobutylcarboxyamide)-2′-O-methyluridine, 5-(N-isobutylcarboxyamide)-2′-fluorouridine, 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-(N-tryptaminocarboxyamide)-2′-O-methyluridine, 5-(N-tryptaminocarboxyamide)-2′-fluorouridine, 5-(N-[1-(3-trimethylamonium) propyl]carboxyamide)-2′-deoxyuridine chloride, 5-[N-(1-naphthylmethyl)carboxyamide]-2′-deoxyuridine (NapdU), 5-[N-(2-naphthylmethyl)carboxyamide]-2′-deoxyuridine (2-NapdU), 5-(N-naphthylmethylcarboxyamide)-2′-O-methyluridine, 5-(N-naphthylmethylcarboxyamide)-2′-fluorouridine and a 5-(N-[1-(2,3-dihydroxypropyl)]carboxyamide)-2′-deoxyuridine.
12 . The composition of claim 1 , wherein each uracil or thymine of the second aptamer is a 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU).
13 . The composition of claim 1 , wherein the first aptamer and the second aptamer, independently, are each from 20 to 100 nucleotides in length.
14 . The composition of claim 1 , wherein the first aptamer and/or the second aptamer further comprise a detectable moiety.
15 . The composition of claim 14 , wherein the detectable moiety is selected from the group consisting of a dye, a quantum dot, a radiolabel, an electrochemical functional group, an enzyme, an enzyme substrate, a ligand and a receptor.
16 . The composition of claim 1 , wherein the target comprises a protein or a peptide.
17 . The composition of claim 16 , wherein the target is a protein selected from the group consisting ANGPT2, TSP2, CRDL1, MATN2, GPVI, ESAM, C7, PLG, MMP-12, NPS-PLA2 and CdtA.
18 . The composition of claim 1 , wherein the dissociation constant (K d ) for the ternary complex is at least 0.02 nM, or from about 0.01 nM to about 10 nM, or from about 0.02 nM to about 6 nM, or from about 0.02 nM to about 3 nM.
19 . The composition of claim 1 , wherein the C-5 modified pyrimidine or C-5 modified pyrimidines of the first aptamer and the second aptamer are the same or different.