RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: 87
Target: Rev protein of HIV-1 (minimal Rev-binding element (RBE) found within the Rev Responsive Element (RRE))
Type of nucleic acid: ssRNA
Sequence: 5'AUUCUGUUUUUGAGGUACGCAAGUACGCGGCUCGACAG3'
Sequence length: 38
GC content: 0.5
Affinity: Kd: 2.3*
Pool type: 5'-AUUCUGU-N6.9-GUACGCAAGUAC-N6.9-ACAG-3'
Pool random region: 15
Binding buffer/conditions: 50 mM KCl, 50 mM Tris-Cl, pH 8.0
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " A population of improved Rev-binding aptamers can be used to inhibit viral
replication, as opposed to a single RNA species. In contrast to other pharmaceuticals, this approach will make it extremely difficult for HIV-1 to accumulate mutations that can simultaneously evade a multitude of different RRE decays."
Additional information: *Activity values are described as "representing relative Kd's" with no units

6.9 means Both random sequence tracts were systematically varied from 6 to 9 nts in length.

Sequences at the defined 5' and 3' ends of the 79.9
pool are, respectively, 5'-GGTAATACGACTCACTATAGGG_x0002_AACTCG4TG4AGCGAATT-3' and 5'-GCCTATCTATCGGAT_x0002_CCACG-3'.
Reference (1993, Nucleic Acids Res ): Giver, L., Bartel, D., Zapp, M., Pawul, A., Green, M., & Ellington, A. D. (1993). Selective optimization of the Rev-binding element of HIV-1. Nucleic acids research, 21(23), 5509–5516. https://doi.org/10.1093/nar/21.23.5509
Aptamer: Clone 5
Target: Thrombin, Human
Type of nucleic acid: 5-uracil-modified-DNA
Sequence: 5'TAGAATACTCAAGCTTCGACGGXAXAXAGXAXAGXAXXGGCAGTTTGGATCCCCGGGTAC3'
Sequence length: 52
GC content: 0.5
Affinity: Kd: 400 nM
Pool type: 5'-TAGAATACTCAAGCTTCGACG-N20-AGTTTGGATCCCCGGGTAC-3'
Pool random region: 20
Binding buffer/conditions: 20 mM Tris—acetate pH 7.4, 140 mM NaCl, 5 mM KC1, 1 mM MgCl2, 1 mM CaCl2
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " We demonstrate that the incorporation of this hydrophobic group into the random oligonucleotide library signficantly alters the outcome of the selection process against human thrombin. The isolated aptamers display enrichment for molecules containing extensive substitution with this modified nucleotide. Binding and anticoagulant activity of the isolated aptamers are discussed."
Additional information: X denotes pentynyl dU as determined via sequencing. 5-(1-pentynyl)-2'-deoxyuridine used instead of thymidine ("X" in sequences) it is also called 5-pentynyl-dU
Reference (1994, Nucleic Acids Res ): Latham, J. A., Johnson, R., & Toole, J. J. (1994). The application of a modified nucleotide in aptamer selection: novel thrombin aptamers containing 5-(1-pentynyl)-2'-deoxyuridine. Nucleic acids research, 22(14), 2817–2822. https://doi.org/10.1093/nar/22.14.2817
Aptamer: Clone 7
Target: Thrombin, Human
Type of nucleic acid: 5-uracil-modified-DNA
Sequence: 5'TAGAATACTCAAGCTTCGACGGACXAAACGCAXXGXGCCCCAGTTTGGATCCCCGGGTAC3'
Sequence length: 56
GC content: 0.5535714285714286
Affinity: Kd: 1000 nM
Pool type: 5'-TAGAATACTCAAGCTTCGACG-N20-AGTTTGGATCCCCGGGTAC-3'
Pool random region: 20
Binding buffer/conditions: 20 mM Tris—acetate pH 7.4, 140 mM NaCl, 5 mM KC1, 1 mM MgCl2, 1 mM CaCl2
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " We demonstrate that the incorporation of this hydrophobic group into the random oligonucleotide library signficantly alters the outcome of the selection process against human thrombin. The isolated aptamers display enrichment for molecules containing extensive substitution with this modified nucleotide. Binding and anticoagulant activity of the isolated aptamers are discussed."
Additional information: X denotes pentynyl dU as determined via sequencing. 5-(1-pentynyl)-2'-deoxyuridine used instead of thymidine ("X" in sequences) it is also called 5-pentynyl-dU
Reference (1994, Nucleic Acids Res ): Latham, J. A., Johnson, R., & Toole, J. J. (1994). The application of a modified nucleotide in aptamer selection: novel thrombin aptamers containing 5-(1-pentynyl)-2'-deoxyuridine. Nucleic acids research, 22(14), 2817–2822. https://doi.org/10.1093/nar/22.14.2817
Aptamer: 20t
Target: Platelet-derived growth factor (PDGF)-AB
Type of nucleic acid: ssDNA
Sequence: 5'CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACTTGGGAGGGCGCGTTCTTCGTGGTTACTTTTAGTCCCG3'
Sequence length: 87
GC content: 0.5057471264367817
Affinity: Kd: 0.147 ± 0.011 nM
Pool type: 5‘-CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACT-N40-ACTTGAGCAAAATCACCTGCAGGGG-3‘
Pool random region: 40
Binding buffer/conditions: PBSM (10.1 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl and 2.7 mM KCl, 1 mM MgCl2, pH 7.4) containing 0.01% human serum albumin (HSA)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated versions of ligand 20
Application as quoted in the referenced paper: Therapeutic: " Many tumor cell lines have since been shown to produce and secrete PDGF, some of which also express the cognate PDGF receptors; paracrine effect on the tumor stroma and, in some tumor cell lines, autocrine growth stimulation by PDGF are therefore possible; These DNA ligands therefore represent lead compounds for a novel class of high-affinity, specific antagonists of PDGF-AB and PDGF-BB."
Additional information: [3′T] represents a 3′-3′-linked thymidine nucleotide added to reduce 3′-exonuclease-mediated degradation
Reference (1996, Biochemistry ): Green, L. S., Jellinek, D., Jenison, R., Ostman, A., Heldin, C. H., & Janjic, N. (1996). Inhibitory DNA ligands to platelet-derived growth factor B-chain. Biochemistry, 35(45), 14413–14424. https://doi.org/10.1021/bi961544+
Aptamer: 20t
Target: Platelet-derived growth factor (PDGF)-AA
Type of nucleic acid: ssDNA
Sequence: 5'CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACTTGGGAGGGCGCGTTCTTCGTGGTTACTTTTAGTCCCG3'
Sequence length: 87
GC content: 0.5057471264367817
Affinity: Kd: 47 ± 4 nM
Pool type: 5‘-CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACT-N40-ACTTGAGCAAAATCACCTGCAGGGG-3‘
Pool random region: 40
Binding buffer/conditions: PBSM (10.1 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl and 2.7 mM KCl, 1 mM MgCl2, pH 7.4) containing 0.01% human serum albumin (HSA)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated versions of ligand 20
Application as quoted in the referenced paper: Therapeutic: " Many tumor cell lines have since been shown to produce and secrete PDGF, some of which also express the cognate PDGF receptors; paracrine effect on the tumor stroma and, in some tumor cell lines, autocrine growth stimulation by PDGF are therefore possible; These DNA ligands therefore represent lead compounds for a novel class of high-affinity, specific antagonists of PDGF-AB and PDGF-BB."
Additional information: [3′T] represents a 3′-3′-linked thymidine nucleotide added to reduce 3′-exonuclease-mediated degradation
Reference (1996, Biochemistry ): Green, L. S., Jellinek, D., Jenison, R., Ostman, A., Heldin, C. H., & Janjic, N. (1996). Inhibitory DNA ligands to platelet-derived growth factor B-chain. Biochemistry, 35(45), 14413–14424. https://doi.org/10.1021/bi961544+
Aptamer: 20t
Target: Platelet-derived growth factor (PDGF)-BB
Type of nucleic acid: ssDNA
Sequence: 5'CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACTTGGGAGGGCGCGTTCTTCGTGGTTACTTTTAGTCCCG3'
Sequence length: 87
GC content: 0.5057471264367817
Affinity: Kd: 0.127 ± 0.031 nM
Pool type: 5‘-CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACT-N40-ACTTGAGCAAAATCACCTGCAGGGG-3‘
Pool random region: 40
Binding buffer/conditions: PBSM (10.1 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl and 2.7 mM KCl, 1 mM MgCl2, pH 7.4) containing 0.01% human serum albumin (HSA)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated versions of ligand 20
Application as quoted in the referenced paper: Therapeutic: " Many tumor cell lines have since been shown to produce and secrete PDGF, some of which also express the cognate PDGF receptors; paracrine effect on the tumor stroma and, in some tumor cell lines, autocrine growth stimulation by PDGF are therefore possible; These DNA ligands therefore represent lead compounds for a novel class of high-affinity, specific antagonists of PDGF-AB and PDGF-BB."
Additional information: [3′T] represents a 3′-3′-linked thymidine nucleotide added to reduce 3′-exonuclease-mediated degradation
Reference (1996, Biochemistry ): Green, L. S., Jellinek, D., Jenison, R., Ostman, A., Heldin, C. H., & Janjic, N. (1996). Inhibitory DNA ligands to platelet-derived growth factor B-chain. Biochemistry, 35(45), 14413–14424. https://doi.org/10.1021/bi961544+
Aptamer: TQ21
Target: Thermus aquaticus DNA polymerase (Taq pol)
Type of nucleic acid: ssDNA
Sequence: 5'TTCTCGGTTGGTCTCTGGCGGAGCGATCATCTCAGAGCATTCTTAGCGTTTTGTTCTTGTGTATGATTCGCTTTTCCC3'
Sequence length: 78
GC content: 0.4743589743589743
Affinity: Kd: 36 ± 4 pM
Pool type: 5'-TTCTCGGTTGGTCTCTGGCGGAGC-N30-TCTTGTGTATGATTCGCTTTTCCC-3'
Pool random region: 30
Binding buffer/conditions: 50 mMKCl, 2.5 mM MgCl2,10 mM Tris-HCl (pH 8.3 at 22°C)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8.3
Molecular weight of target: 94 kDa
Application as quoted in the referenced paper: Detection: " We show that the addition of oligonucleotide inhibitors eliminated the need for ‘‘hot start’’ conditions and improved the efficiency of detection of a low copy number target in PCR. The ability to detect very low copy number nucleic acid sequences, down to the single copy level has permitted the use of PCR in a vast number of applications including clinical diagnosis of infectious agents, cancer, genetic susceptibility to diseases, forensics and blood banking"
Reference (1996, J Mol Biol ): Dang, C., & Jayasena, S. D. (1996). Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR. Journal of molecular biology, 264(2), 268–278. https://doi.org/10.1006/jmbi.1996.0640
Aptamer: TQ21
Target: DNA polymerase (Taq pol), Thermus acquaticus
Type of nucleic acid: ssDNA
Sequence: 5'TTCTCGGTTGGTCTCTGGCGGAGCGATCATCTCAGAGCATTCTTAGCGTTTTGTTCTTGTGTATGATTCGCTTTTCCC3'
Sequence length: 78
GC content: 0.4743589743589743
Affinity: Not reported
Pool type: 5'-TTCTCGGTTGGTCTCTGGCGGAGC-N30-TCTTGTGTATGATTCGCTTTTCCC-3'
Pool random region: 30
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: 94 kDa
Application as quoted in the referenced paper: Research- " These aptamers have been shown to effciently inhibit the polymerase activity of Taq pol and are useful in enhancing the amplifcation effciency of low copy number targets by the polymerase chain reaction (PCR). TQ21 aptamer inhibited both Taq and Tth polymerases. Flanking regions are required for inhibiton. TQ21 does not inhibit the Stoffel fragment."
Reference (1997, J Mol Biol ): Lin, Y., & Jayasena, S. D. (1997). Inhibition of multiple thermostable DNA polymerases by a heterodimeric aptamer. Journal of molecular biology, 271(1), 100–111. https://doi.org/10.1006/jmbi.1997.1165
Aptamer: LD196t1
Target: L-selectin–IgG fusion protein (LS-Rg)
Type of nucleic acid: ssDNA
Sequence: 5'AGCTGGCGGTACGGGCCGTGCACCCACTTACCTGGGAAGTGAGCTTA3'
Sequence length: 47
GC content: 0.6170212765957447
Affinity: Not reported
Pool type: 5'-CTACCTACGATCTGACTAGC-N40-GCTTACTCTCATGTAGTTCC-3'
Pool random region: 40
Binding buffer/conditions: 20 mM Hepes, pH 7.5, 125 mM NaCl, 1 mM MgCl2, 1 mM CaCl2, 5 mM KCl) plus 0.01% (wt/vol) human serum albumin (Sigma Chemical Co., St. Louis, MO)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Therapeutic: " Aptamers that bind with nanomolar affinity to L-selectin's lectin domain, prevent L-selectin from binding to SLex, and function in vivo to prevent the homing of human lymphocytes to lymph nodes in severe combined immunodeficiency (SCID) mice"
Reference (1996, J Clin Invest ): Hicke, B. J., Watson, S. R., Koenig, A., Lynott, C. K., Bargatze, R. F., Chang, Y. F., Ringquist, S., Moon-McDermott, L., Jennings, S., Fitzwater, T., Han, H. L., Varki, N., Albinana, I., Willis, M. C., Varki, A., & Parma, D. (1996). DNA aptamers block L-selectin function in vivo. Inhibition of human lymphocyte trafficking in SCID mice. The Journal of clinical investigation, 98(12), 2688–2692. https://doi.org/10.1172/JCI119092
Aptamer: Tuda-1
Target: Tubulin purified, Calf brain
Type of nucleic acid: ssDNA
Sequence: 5′TAGGGAATTCGTCGTCGTCGACGGATCCATGCTCGCGCCTGCTGTGTTGTTGCTTGGTTTGGTCTTTTTTTGGTTTGTTTTGGGTTCTGCAGGTCGACGCATGCGCCG3′
Sequence length: 108
GC content: 0.5370370370370371
Affinity: Kd: 4.50×10−5 M
Pool type: 5′-TAGGGAATTCGTCGTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3′
Pool random region: 59
Binding buffer/conditions: 100 mM PIPES pH 6.9, 1 mM EGTA, 5 mM MgSO4, 100 mM NaCl
Buffer type: Other Buffers
pH: 6.9
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Acquisition of DNA aptamers that bind to tubulin using SELEX. Tubulin is the main component of microtubules, which are involvedin a variety of biological events such as intracellular transport, cellular motility, and construction of cytoskeletons.5 These cytoskeletal elements also act pivotal roles in mitotic spindle assembly and cell division. Numerous ligands that bind to tubulin and affect its assembly have been employedas anticancer drug candidates. Tubulin ligands have been also believed as useful probes for studying the structures of tubulin molecules."
Reference (2001, Bioorg Med Chem Lett ): Fukusaki, E., Hasunuma, T., Kajiyama, S., Okazawa, A., Itoh, T. J., & Kobayashi, A. (2001). SELEX for tubulin affords specific T-rich DNA aptamers. Systematic evolution of ligands by exponeential enrichment. Bioorganic & medicinal chemistry letters, 11(22), 2927–2930. https://doi.org/10.1016/s0960-894x(01)00584-4
Aptamer: 4C8
Target: Proteinase K-resistant isoform (PrPSc)
Type of nucleic acid: ssDNA
Sequence: 5'GGTATTGAGGGTCGCATCTTTCTGTCTTGTGTTACTTGTTTGTCCGGTTTCTTTTCTCCCCCCGATGGCTCTAACTCTCCTCT3'
Sequence length: 83
GC content: 0.4819277108433735
Affinity: Kd: 56 nM
Pool type: 5'-GGTATTGAGGGTCGCATC-N45-GATGGCTCTAACTCTCCTCT-3'
Pool random region: 45
Binding buffer/conditions: Selection Buffer: 50 mM NaH2PO4, pH 8.0, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.005% (v/v) Tween-23
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "Aptamers such as those described in the present study offer potentially more sensitive assay formats including rolling circle amplification (Yang et al., 2007), molecular beacon FRET-based signalling (Tombelli et al., 2005) and proximity-dependent DNA ligation, a method capable of detecting zeptomolar concentrations of proteins (Fredriksson et al., 2002). Aptamers may in future also have potential therapeutic application in TSE diseases by inhibiting conversion of PrPC to the pathological PrPSc isoform."
Reference (2008, J Virol Methods ): Bibby, D. F., Gill, A. C., Kirby, L., Farquhar, C. F., Bruce, M. E., & Garson, J. A. (2008). Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. Journal of virological methods, 151(1), 107–115. https://doi.org/10.1016/j.jviromet.2008.03.013
Aptamer: 4C10
Target: Proteinase K-resistant isoform (PrPSc)
Type of nucleic acid: ssDNA
Sequence: 5'GGTATTGAGGGTCGCATCTTTCTGTCTTGTGTTACTTGTTTGTCCGGTTTCTTTTCTCCCCCTGATGGCTCTAACTCTCCTCT3'
Sequence length: 83
GC content: 0.4698795180722891
Affinity: Kd: 33 nM
Pool type: 5'-GGTATTGAGGGTCGCATC-N45-GATGGCTCTAACTCTCCTCT-3'
Pool random region: 45
Binding buffer/conditions: Selection Buffer: 50 mM NaH2PO4, pH 8.0, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.005% (v/v) Tween-24
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "Aptamers such as those described in the present study offer potentially more sensitive assay formats including rolling circle amplification (Yang et al., 2007), molecular beacon FRET-based signalling (Tombelli et al., 2005) and proximity-dependent DNA ligation, a method capable of detecting zeptomolar concentrations of proteins (Fredriksson et al., 2002). Aptamers may in future also have potential therapeutic application in TSE diseases by inhibiting conversion of PrPC to the pathological PrPSc isoform."
Reference (2008, J Virol Methods ): Bibby, D. F., Gill, A. C., Kirby, L., Farquhar, C. F., Bruce, M. E., & Garson, J. A. (2008). Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. Journal of virological methods, 151(1), 107–115. https://doi.org/10.1016/j.jviromet.2008.03.013
Aptamer: 4C26
Target: Proteinase K-resistant isoform (PrPSc)
Type of nucleic acid: ssDNA
Sequence: 5'GGTATTGAGGGTCGCATCTCCTTTTGTTGTTTATTCTCTGTTCTCTGTTCCTGTACTCTTTATCCGATGGCTCTAACTCTCCTCT3'
Sequence length: 85
GC content: 0.4352941176470588
Affinity: Kd: 18 nM
Pool type: 5'-GGTATTGAGGGTCGCATC-N45-GATGGCTCTAACTCTCCTCT-3'
Pool random region: 45
Binding buffer/conditions: Selection Buffer: 50 mM NaH2PO4, pH 8.0, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.005% (v/v) Tween-27
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "Aptamers such as those described in the present study offer potentially more sensitive assay formats including rolling circle amplification (Yang et al., 2007), molecular beacon FRET-based signalling (Tombelli et al., 2005) and proximity-dependent DNA ligation, a method capable of detecting zeptomolar concentrations of proteins (Fredriksson et al., 2002). Aptamers may in future also have potential therapeutic application in TSE diseases by inhibiting conversion of PrPC to the pathological PrPSc isoform."
Reference (2008, J Virol Methods ): Bibby, D. F., Gill, A. C., Kirby, L., Farquhar, C. F., Bruce, M. E., & Garson, J. A. (2008). Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. Journal of virological methods, 151(1), 107–115. https://doi.org/10.1016/j.jviromet.2008.03.013
Aptamer: TLS9a
Target: Liver cancer cell line BNL 1ME A.7R.1 (MEAR) (T-cell acute lymphoblastic leukemia cell line, CCRF-CEM)
Type of nucleic acid: ssDNA
Sequence: 5'AGTCCATTTTATTCCTGAATATTTGTTAACCTCATGGAC3'
Sequence length: 39
GC content: 0.3333333333333333
Affinity: Kd: 7.38 ± 0.28 nM
Pool type: 5'-ACGCTCGGATGCCACTACAG-N45-CTCATGGACGTGCTGGTGAC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline with calcium chloride and magnesium chloride (Sigma); yeast tRNA (0.1 mg/mL; Sigma) and BSA (1 mg/mL; Fisher)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Optimized truncated version of tls9 aptamer (sequence not. Provided)
Application as quoted in the referenced paper: Diagnostic and Detection: "The cell-SELEX shows that the newly generated aptamers could be effective molecular probes for liver cancer analysis. The close relationship between MEAR cells and BNL cells indicated that cell-SELEX can be used to identify minor molecular-level differences among cells. It further indicates that the target molecules would be specific biomarkers for this kind of liver cancer and would provide useful information for explaining the mechanism of oncogenesis."
Reference (2008, Anal Chem ): Shangguan, D., Meng, L., Cao, Z. C., Xiao, Z., Fang, X., Li, Y., Cardona, D., Witek, R. P., Liu, C., & Tan, W. (2008). Identification of liver cancer-specific aptamers using whole live cells. Analytical chemistry, 80(3), 721–728. https://doi.org/10.1021/ac701962v
Aptamer: HA7
Target: Recombinant HA protein from swine IAV H3 cluster IV
Type of nucleic acid: ssDNA
Sequence: 5'GTGCAGTCAAAGACGTCCCACTCCGTCACTTTAGTGGATCTTTATAAAACCGATGCTGGGCAATCGCACTTCATGGTC3'
Sequence length: 78
GC content: 0.4871794871794871
Affinity: Kd: 22.3 nM
Pool type: 5'-GTGCAGTCAAAGACGTCC-N40-GGCAATCGCACTTCATGGTC-'3
Pool random region: 40
Binding buffer/conditions: 500 μl of 50 mM NaH2PO4, 300 mM NaCl, and 20 mM imidazole (pH 8.0)
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Triple reassortant influenza A viruses (IAVs) of swine, particularly the North American H3N2 subtype, circulate in swine herds and may reassort and result in the emergence of novel zoonotic strains. Aptamer HA68 was also able to bind and detect H3N2v isolated from recent human cases. We provide subtype-specific aptamers against H3N2 IAVs of swine that can now be used in rapid detection and typing protocols for field applications."
Additional information: Selected aptamer sequences were synthesized and labeled with biotin (5′), while amplicons containing enriched aptamer pool were amplified by pcr with 5′-biotin-labeled forward primer (bio-wp18: biotingtgcagtcaaagacgtcc)
Reference (2012, J Clin Microbiol ): Wongphatcharachai, M., Wang, P., Enomoto, S., Webby, R. J., Gramer, M. R., Amonsin, A., & Sreevatsan, S. (2013). Neutralizing DNA aptamers against swine influenza H3N2 viruses. Journal of clinical microbiology, 51(1), 46–54. https://doi.org/10.1128/JCM.02118-12
Aptamer: HA2a
Target: Recombinant HA protein from swine IAV H3 cluster IV
Type of nucleic acid: ssDNA
Sequence: 5'GTGCAGTCAAAGACGTCCGCCACTCCGTCACTTTAGTGGTTTTTTTTATAAATGCTTCGGCAATCGCACTTCATGGTC3'
Sequence length: 78
GC content: 0.4615384615384615
Affinity: Kd: 16 nM
Pool type: 5'GTGCAGTCAAAGACGTCC-N40-GGCAATCGCACTTCATGGTC'5
Pool random region: 40
Binding buffer/conditions: 500 μl of 50 mM NaH2PO4, 300 mM NaCl, and 20 mM imidazole (pH 8.0)
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Triple reassortant influenza A viruses (IAVs) of swine, particularly the North American H3N2 subtype, circulate in swine herds and may reassort and result in the emergence of novel zoonotic strains. Aptamer HA68 was also able to bind and detect H3N2v isolated from recent human cases. We provide subtype-specific aptamers against H3N2 IAVs of swine that can now be used in rapid detection and typing protocols for field applications."
Additional information: Selected aptamer sequences were synthesized and labeled with biotin (5′), while amplicons containing enriched aptamer pool were amplified by pcr with 5′-biotin-labeled forward primer (bio-wp18: biotingtgcagtcaaagacgtcc)
Reference (2012, J Clin Microbiol ): Wongphatcharachai, M., Wang, P., Enomoto, S., Webby, R. J., Gramer, M. R., Amonsin, A., & Sreevatsan, S. (2013). Neutralizing DNA aptamers against swine influenza H3N2 viruses. Journal of clinical microbiology, 51(1), 46–54. https://doi.org/10.1128/JCM.02118-12