RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: Chi No 28
Target: Poly-beta-1,4-N-acetylglucosamine (Chitin) (poly-β-1,6-N-acetyl-D-glucosamine)
Type of nucleic acid: ssDNA
Sequence: 5′TAGGGAATTCGTCGACGGATCCGGCAAGATGTGCCCAGAACAGTTGCTTGTATGGTGGGGAGCGTCCATATTGGCTTAAACCTCCAGGTCGACGCATGCGCCG3'
Sequence length: 103
GC content: 0.5631067961165048
Affinity: Binding Efficiency : 6%
Pool type: 5′-TAGGGAATTCGTCGACGGATCC-N59-CTCCAGGTCGACGC-ATGCGCCG-3′
Pool random region: 59
Binding buffer/conditions: 100 mM NaCl, 100 mM KCl, 5 mM MgCl2, 50 mM Tris–acetate (pH 8.0)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Oligosaccharide antigens play essential biological roles in cellular adhesion, molecular recognition, and so on. However, little is known about the interaction concerning oligosaccharide from the viewpoints of its molecular basis. The present study demonstrated that the in vitro selection method is applicable to obtain the DNA aptamer that selectively recognizes polysaccharide, which physiologically has an important meaning."
Additional information: G-cluster motifs that were sandwiched with palindrome sequences.
Reference (2000, Bioorg Med Chem Lett ): Fukusaki, E., Kato, T., Maeda, H., Kawazoe, N., Ito, Y., Okazawa, A., Kajiyama, S., & Kobayashi, A. (2000). DNA aptamers that bind to chitin. Bioorganic & medicinal chemistry letters, 10(5), 423–425. https://doi.org/10.1016/s0960-894x(00)00013-5
Aptamer: Chi No 46
Target: Poly-beta-1,4-N-acetylglucosamine (Chitin) (poly-β-1,6-N-acetyl-D-glucosamine)
Type of nucleic acid: ssDNA
Sequence: 5′TAGGGAATTCGTCGACGGATCCCCGTAACCCTGCGGGGGGGGGAGAAGGCAATGGGGGACAACTCGCCGGTAGCCATCCATATCTCCAGGTCGACGCATGCGCCG3′
Sequence length: 105
GC content: 0.638095238095238
Affinity: Binding Efficiency : 52%
Pool type: 5′-TAGGGAATTCGTCGACGGATCC-N59-CTCCAGGTCGACGC-ATGCGCCG-3′
Pool random region: 59
Binding buffer/conditions: 100 mM NaCl, 100 mM KCl, 5 mM MgCl2, 50 mM Tris–acetate (pH 8.0)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Oligosaccharide antigens play essential biological roles in cellular adhesion, molecular recognition, and so on. However, little is known about the interaction concerning oligosaccharide from the viewpoints of its molecular basis. The present study demonstrated that the in vitro selection method is applicable to obtain the DNA aptamer that selectively recognizes polysaccharide, which physiologically has an important meaning."
Additional information: G-cluster motifs that were sandwiched with palindrome sequences.
Reference (2000, Bioorg Med Chem Lett ): Fukusaki, E., Kato, T., Maeda, H., Kawazoe, N., Ito, Y., Okazawa, A., Kajiyama, S., & Kobayashi, A. (2000). DNA aptamers that bind to chitin. Bioorganic & medicinal chemistry letters, 10(5), 423–425. https://doi.org/10.1016/s0960-894x(00)00013-5
Aptamer: Chi No 52
Target: Poly-beta-1,4-N-acetylglucosamine (Chitin) (poly-β-1,6-N-acetyl-D-glucosamine)
Type of nucleic acid: ssDNA
Sequence: 5′TAGGGAATTCGTCGACGGATCCCCTAAGGGGGGACTCAGCATTTTGTGCGGGCGGCGCTAACACAATCAGATAGAGCGGGGTTCTCCAGGTCGACGCATGCGCCG3′
Sequence length: 105
GC content: 0.6
Affinity: Binding Efficiency : 73%
Pool type: 5′-TAGGGAATTCGTCGACGGATCC-N59-CTCCAGGTCGACGC-ATGCGCCG-3′
Pool random region: 59
Binding buffer/conditions: 100 mM NaCl, 100 mM KCl, 5 mM MgCl2, 50 mM Tris–acetate (pH 8.0)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Oligosaccharide antigens play essential biological roles in cellular adhesion, molecular recognition, and so on. However, little is known about the interaction concerning oligosaccharide from the viewpoints of its molecular basis. The present study demonstrated that the in vitro selection method is applicable to obtain the DNA aptamer that selectively recognizes polysaccharide, which physiologically has an important meaning."
Additional information: G-cluster motifs that were sandwiched with palindrome sequences.
Reference (2000, Bioorg Med Chem Lett ): Fukusaki, E., Kato, T., Maeda, H., Kawazoe, N., Ito, Y., Okazawa, A., Kajiyama, S., & Kobayashi, A. (2000). DNA aptamers that bind to chitin. Bioorganic & medicinal chemistry letters, 10(5), 423–425. https://doi.org/10.1016/s0960-894x(00)00013-5
Aptamer: Tyr 1
Target: L-tyrosine
Type of nucleic acid: ssRNA
Sequence: 5'GGGAAGCUUGUACAGGGGGCAGUCAACUCGUGCGAUCGUGAAAACGGGGCAAGAUGGCCUUACAGCGGUCAAUACGGGGGUCAUCAGAUAGGGAGGCCCUCCUGGUGGUCCGUUCGGGAUCCUC3'
Sequence length: 124
GC content: 0.5967741935483871
Affinity: Kd: 35 uM
Pool type: 5'GGGAATTCCGCGTGTGC-N80-GTCCGTTCGGGATCCTC3'
Pool random region: 80
Binding buffer/conditions: 50 mM Tris-HCl, pH 7.4, 150 mM NaCl, and 5 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: N/a
Post-SELEX modifications: Mutated sequence selected from a degenerate pool derived from a previous selection
Application as quoted in the referenced paper: Research: " Tyrosie coding triplets are not involved in dopamine recognition; instead, they are selected at the level of the tyrosine binding site, where they appear to be involved in the formation of the tyrosine-binding pocket. Tyrosine aptamer will contribute to further elucidation of the role of codons in RNA–amino acid recognition"
Additional information: Pool comes from pervious selection paper https://pubmed.ncbi.nlm.nih.gov/9245404/
Reference (2000, RNA ): Mannironi, C., Scerch, C., Fruscoloni, P., & Tocchini-Valentini, G. P. (2000). Molecular recognition of amino acids by RNA aptamers: the evolution into an L-tyrosine binder of a dopamine-binding RNA motif. RNA (New York, N.Y.), 6(4), 520–527. https://doi.org/10.1017/s1355838200991763
Aptamer: G9-I
Target: Nonstructural protein 3 (NS3) protease active site in the truncated polypeptide ΔNS3, Hepatitis C virus (HCV)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAGAAUUCCGACCAGAAGCUUCGGGAUUUGAGGGUAGAAUGGGACUACCUUUCCUCUCUCCUUCCUCUUCU3'
Sequence length: 73
GC content: 0.5068493150684932
Affinity: Kd: 11.6 nM
Pool type: 5'-GGGAGAAUUCCGACCAGAAG-N30-CCUUUCCUCUCUCCUUCCUCUUCU-3'
Pool random region: 30
Binding buffer/conditions: 50 mm Tris/HCl (pH 7.8), 30 mm NaCl, 5 mm CaCl2 and 10 mm dithiothreitol
Divalent salt: CaCl
Buffer type: Tris Buffers
pH: 7.8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Nonstructural protein 3 (NS3) from hepatitis C virus (HCV) is a serine protease that provides an essential function in maturation of the virus by cleaving the nonstructural regions of the viral polyprotein. The NS3 protease activity has been identified as a potential target for anti-HCV drugs, because its activity is essential for maturation of the HCV virus particle. One source of potential highly selective NS3 inhibitors might be RNA ligands."
Reference (2000, Eur J Biochem ): Fukuda, K., Vishnuvardhan, D., Sekiya, S., Hwang, J., Kakiuchi, N., Taira, K., Shimotohno, K., Kumar, P. K., & Nishikawa, S. (2000). Isolation and characterization of RNA aptamers specific for the hepatitis C virus nonstructural protein 3 protease. European journal of biochemistry, 267(12), 3685–3694. https://doi.org/10.1046/j.1432-1327.2000.01400.x
Aptamer: G9-II
Target: Nonstructural protein 3 (NS3) protease active site in the truncated polypeptide ΔNS3, Hepatitis C virus (HCV)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAGAAUUCCGACCAGAAGUGCUCUUAGAAUGGGACUAAGACACGGGACCCUUUCCUCUCUCCUUCCUCUUCU3'
Sequence length: 74
GC content: 0.5135135135135135
Affinity: Kd: 6.3 nM
Pool type: 5'-GGGAGAAUUCCGACCAGAAG-N30-CCUUUCCUCUCUCCUUCCUCUUCU-3'
Pool random region: 30
Binding buffer/conditions: 50 mm Tris/HCl (pH 7.8), 30 mm NaCl, 5 mm CaCl2 and 10 mm dithiothreitol
Divalent salt: CaCl
Buffer type: Tris Buffers
pH: 7.8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Nonstructural protein 3 (NS3) from hepatitis C virus (HCV) is a serine protease that provides an essential function in maturation of the virus by cleaving the nonstructural regions of the viral polyprotein. The NS3 protease activity has been identified as a potential target for anti-HCV drugs, because its activity is essential for maturation of the HCV virus particle. One source of potential highly selective NS3 inhibitors might be RNA ligands."
Reference (2000, Eur J Biochem ): Fukuda, K., Vishnuvardhan, D., Sekiya, S., Hwang, J., Kakiuchi, N., Taira, K., Shimotohno, K., Kumar, P. K., & Nishikawa, S. (2000). Isolation and characterization of RNA aptamers specific for the hepatitis C virus nonstructural protein 3 protease. European journal of biochemistry, 267(12), 3685–3694. https://doi.org/10.1046/j.1432-1327.2000.01400.x
Aptamer: G9-III
Target: Nonstructural protein 3 (NS3) protease active site in the truncated polypeptide ΔNS3, Hepatitis C virus (HCV)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAGAAUUCCGACCAGAAGUACGACACGAUUGGGACGUGUCUAUGGGACCCUUUCCUCUCUCCUUCCUCUUCU3'
Sequence length: 74
GC content: 0.527027027027027
Affinity: Kd: 8.9 nM
Pool type: 5'-GGGAGAAUUCCGACCAGAAG-N30-CCUUUCCUCUCUCCUUCCUCUUCU-3'
Pool random region: 30
Binding buffer/conditions: 50 mm Tris/HCl (pH 7.8), 30 mm NaCl, 5 mm CaCl2 and 10 mm dithiothreitol
Divalent salt: CaCl
Buffer type: Tris Buffers
pH: 7.8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Nonstructural protein 3 (NS3) from hepatitis C virus (HCV) is a serine protease that provides an essential function in maturation of the virus by cleaving the nonstructural regions of the viral polyprotein. The NS3 protease activity has been identified as a potential target for anti-HCV drugs, because its activity is essential for maturation of the HCV virus particle. One source of potential highly selective NS3 inhibitors might be RNA ligands."
Reference (2000, Eur J Biochem ): Fukuda, K., Vishnuvardhan, D., Sekiya, S., Hwang, J., Kakiuchi, N., Taira, K., Shimotohno, K., Kumar, P. K., & Nishikawa, S. (2000). Isolation and characterization of RNA aptamers specific for the hepatitis C virus nonstructural protein 3 protease. European journal of biochemistry, 267(12), 3685–3694. https://doi.org/10.1046/j.1432-1327.2000.01400.x
Aptamer: clone 31
Target: Tat protein from HIV-1 in the presence of Zn2+ ion
Type of nucleic acid: ssRNA
Sequence: 5'GGGAGAAUUCCGACCAGAAGCUUUGGUUAUCAUGUUUAUGCGUACGGGCGCCCAUAUGUGCGUCUACAUGGAUCCUCA3'
Sequence length: 78
GC content: 0.5
Affinity: Kd: 0.31 uM
Pool type: 5′-GGGAGAATTCCGACCAGAAGCTT-N30-ATATGTGCGTCTACATGGATCCTCA-3′
Pool random region: 30
Binding buffer/conditions: 2.5 mM Tris–Cl (pH 7.6), 100 mM NaCl, and 2.0 mM MgCl2 or ZnCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: N/a
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Inhibition: " An in vitro selection was carried out with Zn2+ to isolate novel RNA molecules, zinc-dependent aptamers, that bind to HIV-1 Tat protein. If an aptamer is bound to a pathogenic protein, the ‘decoy’ aptamer would act as an inhibitor of the protein function. Proteins of AIDS virus (human immunodeficiency virus type 1; HIV-1) were therefore chosen as targets for in vitro selection of aptamers since the early stage of the experiments."
Reference (2000, J Inorg Biochem ): Kawakami, J., Imanaka, H., Yokota, Y., & Sugimoto, N. (2000). In vitro selection of aptamers that act with Zn2+. Journal of inorganic biochemistry, 82(1-4), 197–206. https://doi.org/10.1016/s0162-0134(00)00158-6
Aptamer: ADR58
Target: Oncostatin M (OSM), Human
Type of nucleic acid: 2'-fluoro/O-Me-RNA
Sequence: 5'GGGAGGACGAUGCGGAUCGCCCUGAACCGGCCCAGCAGACUGCUGACGGCACGAUCAGACGACUCGCCCGA3'
Sequence length: 71
GC content: 0.676056338028169
Affinity: Kd: 7 nM
Pool type: 5′-GGGAGGACGAUGCGG-N40-CCGCATCGTCCTCCC-3′
Pool random region: 40
Binding buffer/conditions: SCHMK buffer (110 mM NaCl, 1 mM MgCl2, 20 mM HEPES, pH 7.0, 1 mM CaCl2, 5 mM KCl)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7
Molecular weight of target: 28 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Oncostatin M (OSM) is a multifunctional member of the interleukin-6 cytokine family. OSM has been implicated as a powerful proinflammatory mediator and may represent a potentially important, novel therapeutic opportunity for treatment of established rheumatoid arthritis.This aptamer may be used as a tool to further investigate the role of OSM in inflammatory disorders and may also have role as a therapeutic agent."
Additional information: 2′-Fluoropyrimidine-modified RNA. pyrimidine positions are substituted with 2′ fluorine, and 14 of 18 purine positions have been substituted with 2′ O-methyl to increase stability toward nucleases
Reference (2000, J Biol Chem ): Rhodes, A., Deakin, A., Spaull, J., Coomber, B., Aitken, A., Life, P., & Rees, S. (2000). The generation and characterization of antagonist RNA aptamers to human oncostatin M. The Journal of biological chemistry, 275(37), 28555–28561. https://doi.org/10.1074/jbc.M002981200
Aptamer: truncated ADR58
Target: Oncostatin M (OSM), Human
Type of nucleic acid: 2'-fluoro/O-Me-RNA
Sequence: 5'GAACCGGCCCAGCAGACUGCUGACGGCACGAUC3'
Sequence length: 34
GC content: 0.6470588235294118
Affinity: Kd: 7 nM
Pool type: 5'-GGGAGGACGAUGCGG-N40-CCGCATCGTCCTCCC-3'
Pool random region: 40
Binding buffer/conditions: 110 mM NaCl, 1 mM MgCl2, 20 mM HEPES, pH 7.0, 1 mM CaCl2, 5mM KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7
Molecular weight of target: 28 kDa
Post-SELEX modifications: The truncated aptamer contains a 3'-3' thymidine cap at the 3' end
Application as quoted in the referenced paper: Detection: " Oncostatin M (OSM) is a multifunctional member of the interleukin-6 cytokine family. OSM has been implicated as a powerful proinflammatory mediator and may represent a potentially important, novel therapeutic opportunity for treatment of established rheumatoid arthritis.This aptamer may be used as a tool to further investigate the role of OSM in inflammatory disorders and may also have role as a therapeutic agent."
Additional information: 2′-Fluoropyrimidine-modified RNA; reported no loss in affinity from full sequence. All pyrimidine positions contain a 2' fluoro modification, and all purine positions are 2' O-methyl except the 3rd position A, 22nd position G, 23rd position A, and 31st position A, which are 2' hydroxy.
Reference (2000, J Biol Chem ): Rhodes, A., Deakin, A., Spaull, J., Coomber, B., Aitken, A., Life, P., & Rees, S. (2000). The generation and characterization of antagonist RNA aptamers to human oncostatin M. The Journal of biological chemistry, 275(37), 28555–28561. https://doi.org/10.1074/jbc.M002981200
Aptamer: F7-9D
Target: Cocaine
Type of nucleic acid: ssDNA
Sequence: 5'GACAAGGAAAATCCTTCAATGAAGTGGGTC3'
Sequence length: 30
GC content: 0.4333333333333333
Affinity: Kd ∼ 100 µM
Pool type: Not reported
Binding buffer/conditions: Selection buffer (c(TRIS) = 20 mM, pH 7.4, c(NaCl) = 140 mM, c(KCl) = 5 mM)
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Detection and Biosensor: " We engineered anti-cocaine aptamer MNS-7.9 to obtain a partially folded structure with a ligand-induced binding pocket based on terminal stem-closure. The ability of this sensor to operate in serum suggests that this design can provide a new set of analytical tools for clinical chemistry: rapid, homogeneous assays with the potential to simultaneously report the presence or absence of multiple disease-marker proteins within bodily fluids."
Additional information: All aptamers were custom-synthesized and HPLC or gel-purified by Integrated DNA Technologies, Iowa, U.S.A, and were used as received. 
Sensor F7.9D signals the presence of cocaine in solution by conformational change that approximates 5′ and 3′ ends ((F fluorescein
Reference (2001, J Am Chem Soc ): Stojanovic, M. N., de Prada, P., & Landry, D. W. (2001). Aptamer-based folding fluorescent sensor for cocaine. Journal of the American Chemical Society, 123(21), 4928–4931. https://doi.org/10.1021/ja0038171
Aptamer: MNS-4.1
Target: Cocaine
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGACAAGGAAAATCCTTCAATGAAGTGGGTCGACA3'
Sequence length: 38
GC content: 0.4736842105263157
Affinity: Kd ∼ 20 µM
Pool type: Not reported
Binding buffer/conditions: Selection buffer (c(TRIS) = 20 mM, pH 7.4, c(NaCl) = 140 mM, c(KCl) = 5 mM)
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Detection and Biosensor: " We engineered anti-cocaine aptamer MNS-7.9 to obtain a partially folded structure with a ligand-induced binding pocket based on terminal stem-closure. The ability of this sensor to operate in serum suggests that this design can provide a new set of analytical tools for clinical chemistry: rapid, homogeneous assays with the potential to simultaneously report the presence or absence of multiple disease-marker proteins within bodily fluids."
Additional information: All aptamers were custom-synthesized and HPLC or gel-purified by Integrated DNA Technologies, Iowa, U.S.A, and were used as received. 
Anti-cocaine aptamer MNS-4.1 bound to cocaine 1 (black elipsoid).
Reference (2001, J Am Chem Soc ): Stojanovic, M. N., de Prada, P., & Landry, D. W. (2001). Aptamer-based folding fluorescent sensor for cocaine. Journal of the American Chemical Society, 123(21), 4928–4931. https://doi.org/10.1021/ja0038171
Aptamer: Clone 30
Target: N-methyl mesoporphyrin IX (NMM)
Type of nucleic acid: 2'-amino-RNA
Sequence: 5'UAGGGAAUUCGUCGACGGAUCCAGUUCACUCGACCAAGGCGUCCCAAGCGGAGGAUCGCAAGGAGGUGUAGACGUCUGCAGGUCGACGCAUGCGCCG3'
Sequence length: 97
GC content: 0.6082474226804123
Affinity: Kd: 0.66 μM
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris-acetate (pH 7.4), 200 mM NaOAc, 25 mM KOAc,10 mM Mg(OAc)2, 0.5% Triton X-100, and 5% DSMO
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: 580.7
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Bisosensor: " Peroxidase activities of RNAs containing 2'-amino groups, which were selected as aptamers binding to N-methylmesoporphyrin IX, were investigated. Some clones promoted the oxidation reaction of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) with hydrogen peroxide (H(2)O(2)) in the presence of iron(III)-protoporphyrin (hemin), whereas others did not. By in vitro selection, we can produce various types of peroxidase-like non-natural RNAs."
Additional information: RNA is modified with 2' amino groups (2'-AmCTP)
Reference (2001, Biotechnol Bioeng ): Teramoto, N., Ichinari, H., Kawazoe, N., Imanishi, Y., & Ito, Y. (2001). Peroxidase activity of in vitro-selected 2'-amino RNAs. Biotechnology and bioengineering, 75(4), 463–468. https://doi.org/10.1002/bit.10078
Aptamer: RNA20
Target: WT1-ZFP & WT1[+KTS]-ZFP (two zinc finger isoforms of the WT1 DNA binding domain)
Type of nucleic acid: ssRNA
Sequence: 5'GGGGCCACCAACGACAUUGACGAAUGCGUAAAUUGCUAGGUUGAUAUAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG3'
Sequence length: 78
GC content: 0.5256410256410257
Affinity: Kd: 87.4 ± 10.4 nM (WT1-ZFP) & 69.8 ± 8.4 nM (WT1[+KTS]-ZFP)
Pool type: 5'-GGGGCCACCAACGACAUU-N20-GUUGAUAUAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG-3'
Pool random region: 20
Binding buffer/conditions: 20 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 100 mM KCl, 1 mM DTT, 5 μM ZnCl2, 5 μg/mL poly[d(I-C)], and 100 μg/mL bovine serum albumin
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research: " Wilms’ tumor is a pediatric kidney malignancy that occurs with a frequency of 1 in 10000 (1, 2). The WT1 locus on chromosome 11p13 encodes a tumor suppressor protein that is inactivated in a subtype of Wilms’ tumors. The role of RNA sequence and secondary structure in the binding of WT1-ZFP was probed by site-directed mutagenesis. Results indicate that a hairpin loop is a critical structural feature required for protein binding, and that some consensus nucleotides can be substituted provided proper base pairing of the stem of the hairpin loop is maintained."
Reference (2001, Biochemistry ): Zhai, G., Iskandar, M., Barilla, K., & Romaniuk, P. J. (2001). Characterization of RNA aptamer binding by the Wilms' tumor suppressor protein WT1. Biochemistry, 40(7), 2032–2040. https://doi.org/10.1021/bi001941r
Aptamer: RNA22
Target: WT1-ZFP & WT1[+KTS]-ZFP (two zinc finger isoforms of the WT1 DNA binding domain)
Type of nucleic acid: ssRNA
Sequence: 5'GGGGCCACCAACGACAUUGAUAUGGUGACCACCCCGGCGUUGAUAUAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG3'
Sequence length: 77
GC content: 0.5844155844155844
Affinity: Kd: 13.8 ± 1.1 nM (WT1-ZFP) & 22.8 ± 2.3 nM (WT1[+KTS]-ZFP)
Pool type: 5'-GGGGCCACCAACGACAUU-N20-GUUGAUAUAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG-3'
Pool random region: 20
Binding buffer/conditions: 20 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 100 mM KCl, 1 mM DTT, 5 μM ZnCl2, 5 μg/mL poly[d(I-C)], and 100 μg/mL bovine serum albumin
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research: " Wilms’ tumor is a pediatric kidney malignancy that occurs with a frequency of 1 in 10000 (1, 2). The WT1 locus on chromosome 11p13 encodes a tumor suppressor protein that is inactivated in a subtype of Wilms’ tumors. The role of RNA sequence and secondary structure in the binding of WT1-ZFP was probed by site-directed mutagenesis. Results indicate that a hairpin loop is a critical structural feature required for protein binding, and that some consensus nucleotides can be substituted provided proper base pairing of the stem of the hairpin loop is maintained."
Reference (2001, Biochemistry ): Zhai, G., Iskandar, M., Barilla, K., & Romaniuk, P. J. (2001). Characterization of RNA aptamer binding by the Wilms' tumor suppressor protein WT1. Biochemistry, 40(7), 2032–2040. https://doi.org/10.1021/bi001941r
Aptamer: RNA38
Target: WT1-ZFP & WT1[+KTS]-ZFP (two zinc finger isoforms of the WT1 DNA binding domain)
Type of nucleic acid: ssRNA
Sequence: 5'GGGGCCACCAACGACAUUAUCACCCACCCCGAGCUGGCGUUGAUAUAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG3'
Sequence length: 77
GC content: 0.5974025974025974
Affinity: Kd: 17.8 ± 1.4 nM (WT1-ZFP) & 33.7 ± 4.4 nM (WT1[+KTS]-ZFP) 
Pool type: 5'-GGGGCCACCAACGACAUU-N20-GUUGAUAUAAAUAGUGCCCAUGGAUCCGCGGGUGUCGGG-3'
Pool random region: 20
Binding buffer/conditions: 20 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 100 mM KCl, 1 mM DTT, 5 μM ZnCl2, 5 μg/mL poly[d(I-C)], and 100 μg/mL bovine serum albumin
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research: " Wilms’ tumor is a pediatric kidney malignancy that occurs with a frequency of 1 in 10000 (1, 2). The WT1 locus on chromosome 11p13 encodes a tumor suppressor protein that is inactivated in a subtype of Wilms’ tumors. The role of RNA sequence and secondary structure in the binding of WT1-ZFP was probed by site-directed mutagenesis. Results indicate that a hairpin loop is a critical structural feature required for protein binding, and that some consensus nucleotides can be substituted provided proper base pairing of the stem of the hairpin loop is maintained."
Reference (2001, Biochemistry ): Zhai, G., Iskandar, M., Barilla, K., & Romaniuk, P. J. (2001). Characterization of RNA aptamer binding by the Wilms' tumor suppressor protein WT1. Biochemistry, 40(7), 2032–2040. https://doi.org/10.1021/bi001941r