RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: Trp3a-1
Target: L-tryptophan
Type of nucleic acid: ssDNA
Sequence: 5'AGCACGTTGGTTAGGTCAGGTTTGGGTTTCGTGC3'
Sequence length: 34
GC content: 0.5294117647058824
Affinity: Kd: 1.757±0.174 uM
Pool type: 5'-ACTGGAGCTCTCACACACGA-N45-GTCCAGTCCAGTGTCCAGCA-3'
Pool random region: 45
Binding buffer/conditions: 137 mM NaCl, 0.5 mM MgCl2, 2.7 mM KCl, 2 mM KH2PO4, 10 mM Na2HPO4, pH 7.4
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated (there is a g–t wobble base pair in the stem of trp3a, and thus we truncated trp3a from this base pair to obtain trp3a-1.)
Application as quoted in the referenced paper: Diagnostic and Detection: "This aptamer has also been proved to be an effective ligand for the chiral separation of D/L-tryptophan. L-tryptophan and its derivatives are known to play important biological roles; this aptamer ligand could be used as a tool for the analysis of tryptophan and other related studies."
Reference (2010, Analyst ): Yang, X., Bing, T., Mei, H., Fang, C., Cao, Z., & Shangguan, D. (2011). Characterization and application of a DNA aptamer binding to L-tryptophan. The Analyst, 136(3), 577–585. https://doi.org/10.1039/c0an00550a
Aptamer: IBA 2
Target: (R)-ibuprofen
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTACAGTAGTGAGGGGTCCGTCGTGGGGTAGTTGGGTCGTGGAGATAGTAAGTGCAATCT3′
Sequence length: 76
GC content: 0.4736842105263157
Affinity: Kd: 3.0 uM
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection and Therapeutic: "Single stranded DNA aptamers that can bind to ibuprofen, a widely used anti-inflammation drug, were selected from random DNA library of 1015 nucleotides by FluMag-SELEX process. The affinity of five ssDNA aptamers isolated was in a range of 1.5–5.2 μM. In addition, all of these five aptamers did not show any affinity to analogues of ibuprofen in its profen’s group (fenoprofen, flubiprofen, and naproxen) and the antibiotics of oxytetracycline, another control."
Reference (2010, Bioorg Med Chem ): Kim, Y. S., Hyun, C. J., Kim, I. A., & Gu, M. B. (2010). Isolation and characterization of enantioselective DNA aptamers for ibuprofen. Bioorganic & medicinal chemistry, 18(10), 3467–3473. https://doi.org/10.1016/j.bmc.2010.03.074
Aptamer: IBA 12
Target: (R)-ibuprofen
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGGATCGGCGACGTGGGTGTCGTGATTCGGGGTGAGATAGTAAGTGCAATCT3′
Sequence length: 69
GC content: 0.4782608695652174
Affinity: Kd: 3.2 uM
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection and Therapeutic: "Single stranded DNA aptamers that can bind to ibuprofen, a widely used anti-inflammation drug, were selected from random DNA library of 1015 nucleotides by FluMag-SELEX process. The affinity of five ssDNA aptamers isolated was in a range of 1.5–5.2 μM. In addition, all of these five aptamers did not show any affinity to analogues of ibuprofen in its profen’s group (fenoprofen, flubiprofen, and naproxen) and the antibiotics of oxytetracycline, another control."
Reference (2010, Bioorg Med Chem ): Kim, Y. S., Hyun, C. J., Kim, I. A., & Gu, M. B. (2010). Isolation and characterization of enantioselective DNA aptamers for ibuprofen. Bioorganic & medicinal chemistry, 18(10), 3467–3473. https://doi.org/10.1016/j.bmc.2010.03.074
Aptamer: IBA 4
Target: (S)-ibuprofen
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTCCACAGACCCTTAGCTTTCCTATTATTCTGCGCGACGCTGAGATAGTAAGTGCAATCT3′
Sequence length: 76
GC content: 0.4210526315789473
Affinity: Kd: 1.5 uM
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection and Therapeutic: "Single stranded DNA aptamers that can bind to ibuprofen, a widely used anti-inflammation drug, were selected from random DNA library of 1015 nucleotides by FluMag-SELEX process. The affinity of five ssDNA aptamers isolated was in a range of 1.5–5.2 μM. In addition, all of these five aptamers did not show any affinity to analogues of ibuprofen in its profen’s group (fenoprofen, flubiprofen, and naproxen) and the antibiotics of oxytetracycline, another control."
Reference (2010, Bioorg Med Chem ): Kim, Y. S., Hyun, C. J., Kim, I. A., & Gu, M. B. (2010). Isolation and characterization of enantioselective DNA aptamers for ibuprofen. Bioorganic & medicinal chemistry, 18(10), 3467–3473. https://doi.org/10.1016/j.bmc.2010.03.074
Aptamer: IBA 17
Target: (S)-ibuprofen
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTACAGCGTGGGCGGTGTCGGATTTTCGTATGGATGGGGATGAGATAGTAAGTGCAATCT3′
Sequence length: 76
GC content: 0.4473684210526316
Affinity: Kd: 3.8 uM
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection and Therapeutic: "Single stranded DNA aptamers that can bind to ibuprofen, a widely used anti-inflammation drug, were selected from random DNA library of 1015 nucleotides by FluMag-SELEX process. The affinity of five ssDNA aptamers isolated was in a range of 1.5–5.2 μM. In addition, all of these five aptamers did not show any affinity to analogues of ibuprofen in its profen’s group (fenoprofen, flubiprofen, and naproxen) and the antibiotics of oxytetracycline, another control."
Reference (2010, Bioorg Med Chem ): Kim, Y. S., Hyun, C. J., Kim, I. A., & Gu, M. B. (2010). Isolation and characterization of enantioselective DNA aptamers for ibuprofen. Bioorganic & medicinal chemistry, 18(10), 3467–3473. https://doi.org/10.1016/j.bmc.2010.03.074
Aptamer: Apt 1
Target: Egg white lysozyme
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGATGGCAGCTAAGCAGGCGGCTCACAAAACCATTCGCATGCGGCCCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.575
Affinity: Kd: 2.8 ± 0.3 nM
Pool type: 5'-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3'
Pool random region: 40
Binding buffer/conditions: 10 mM trizma base, 50 mM NaCl, and 1 mM EDTA pH = 7.5
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "We have selected aptamers binding to lysozyme from a DNA library using capillary electrophoresis-systematic evolution of ligands by exponential enrichment. The aptamers were successfully challenged for specificity against other egg white proteins. The high affinity aptamers open up possibilities for the development of aptamer based food and medical diagnostics."
Reference (2010, Molecules ): Tran DT, Janssen KPF, Pollet J, Lammertyn E, Anné J, Van Schepdael A, Lammertyn J. Selection and Characterization of DNA Aptamers for Egg White Lysozyme. Molecules. 2010; 15(3):1127-1140. https://doi.org/10.3390/molecules15031127
Aptamer: Apt 3
Target: Egg white lysozyme
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGATGGCGGGTCGGTTGCTCGCTTCGCCCGATCGGTCTAAGGGTGCCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.6125
Affinity: Kd: 47.1 ± 16.3 nM
Pool type: 5'-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3'
Pool random region: 40
Binding buffer/conditions: 10 mM trizma base, 50 mM NaCl, and 1 mM EDTA pH = 7.5
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "We have selected aptamers binding to lysozyme from a DNA library using capillary electrophoresis-systematic evolution of ligands by exponential enrichment. The aptamers were successfully challenged for specificity against other egg white proteins. The high affinity aptamers open up possibilities for the development of aptamer based food and medical diagnostics."
Reference (2010, Molecules ): Tran DT, Janssen KPF, Pollet J, Lammertyn E, Anné J, Van Schepdael A, Lammertyn J. Selection and Characterization of DNA Aptamers for Egg White Lysozyme. Molecules. 2010; 15(3):1127-1140. https://doi.org/10.3390/molecules15031127
Aptamer: Apt 8
Target: Egg white lysozyme
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGATGGCACCTTGATGACATGATAGTCGTTGTGTATGCAGTTGGCCCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.5125
Affinity: Kd: 52.1 ± 12.7 nM
Pool type: 5'-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3'
Pool random region: 40
Binding buffer/conditions: 10 mM trizma base, 50 mM NaCl, and 1 mM EDTA pH = 7.5
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "We have selected aptamers binding to lysozyme from a DNA library using capillary electrophoresis-systematic evolution of ligands by exponential enrichment. The aptamers were successfully challenged for specificity against other egg white proteins. The high affinity aptamers open up possibilities for the development of aptamer based food and medical diagnostics."
Reference (2010, Molecules ): Tran DT, Janssen KPF, Pollet J, Lammertyn E, Anné J, Van Schepdael A, Lammertyn J. Selection and Characterization of DNA Aptamers for Egg White Lysozyme. Molecules. 2010; 15(3):1127-1140. https://doi.org/10.3390/molecules15031127
Aptamer: Aptamer 7
Target: Chloramphenicol (Cam)
Type of nucleic acid: ssDNA
Sequence: 5′AGCAGCACAGAGGTCAGATGACTTCAGTGAGTTGTCCCACGGTCGGCGAGTCGGTGGTAGCCTATGCGTGCTACCGTGAA3′
Sequence length: 80
GC content: 0.575
Affinity: Kd: 0.766 μM
Pool type: 5′-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02 Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "Chloramphenicol (Cam), although an effective antibiotic, has lost favour due to some fatal side effects. Thus there is an urgent need for rapid and sensitive methods to detect residues in food, feed and environment. These aptamers open up possibilities to allow easy detection of Cam via aptamer-based biosensors."
Reference (2011, J Biotechnol ): Mehta, J., Van Dorst, B., Rouah-Martin, E., Herrebout, W., Scippo, M. L., Blust, R., & Robbens, J. (2011). In vitro selection and characterization of DNA aptamers recognizing chloramphenicol. Journal of biotechnology, 155(4), 361–369. https://doi.org/10.1016/j.jbiotec.2011.06.043
Aptamer: Aptamer 9
Target: Chloramphenicol (Cam)
Type of nucleic acid: ssDNA
Sequence: 5′AGCAGCACAGAGGTCAGATGCACCAAGCGCAGGGAATTACATTGAAGTGTGGGATTGGCTCCTATGCGTGCTACCGTGAA3′
Sequence length: 80
GC content: 0.525
Affinity: Kd: 20.03 μM
Pool type: 5′-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02 Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "Chloramphenicol (Cam), although an effective antibiotic, has lost favour due to some fatal side effects. Thus there is an urgent need for rapid and sensitive methods to detect residues in food, feed and environment. These aptamers open up possibilities to allow easy detection of Cam via aptamer-based biosensors."
Reference (2011, J Biotechnol ): Mehta, J., Van Dorst, B., Rouah-Martin, E., Herrebout, W., Scippo, M. L., Blust, R., & Robbens, J. (2011). In vitro selection and characterization of DNA aptamers recognizing chloramphenicol. Journal of biotechnology, 155(4), 361–369. https://doi.org/10.1016/j.jbiotec.2011.06.043
Aptamer: Aptamer 12
Target: Chloramphenicol (Cam)
Type of nucleic acid: ssDNA
Sequence: 5′AGCAGCACAGAGGTCAGATGGGCGGGGAACGGTTATGAACCATACAAAATGATCATTATTCCTATGCGTGCTACCGTGAA3′
Sequence length: 80
GC content: 0.475
Affinity: Kd: ~1.87e + 014 μM
Pool type: 5′-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02 Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "Chloramphenicol (Cam), although an effective antibiotic, has lost favour due to some fatal side effects. Thus there is an urgent need for rapid and sensitive methods to detect residues in food, feed and environment. These aptamers open up possibilities to allow easy detection of Cam via aptamer-based biosensors."
Reference (2011, J Biotechnol ): Mehta, J., Van Dorst, B., Rouah-Martin, E., Herrebout, W., Scippo, M. L., Blust, R., & Robbens, J. (2011). In vitro selection and characterization of DNA aptamers recognizing chloramphenicol. Journal of biotechnology, 155(4), 361–369. https://doi.org/10.1016/j.jbiotec.2011.06.043
Aptamer: Aptamer 16
Target: Chloramphenicol (Cam)
Type of nucleic acid: ssDNA
Sequence: 5′AGCAGCACAGAGGTCAGATGACTGAGGGCACGGACAGGAGGGGGAGAGATGGCGTGAGGTCCTATGCGTGCTACCGTGAA3′
Sequence length: 80
GC content: 0.6
Affinity: Kd: 1.16 μM
Pool type: 5′-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02 Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "Chloramphenicol (Cam), although an effective antibiotic, has lost favour due to some fatal side effects. Thus there is an urgent need for rapid and sensitive methods to detect residues in food, feed and environment. These aptamers open up possibilities to allow easy detection of Cam via aptamer-based biosensors."
Reference (2011, J Biotechnol ): Mehta, J., Van Dorst, B., Rouah-Martin, E., Herrebout, W., Scippo, M. L., Blust, R., & Robbens, J. (2011). In vitro selection and characterization of DNA aptamers recognizing chloramphenicol. Journal of biotechnology, 155(4), 361–369. https://doi.org/10.1016/j.jbiotec.2011.06.043
Aptamer: Aptamer 20
Target: Chloramphenicol (Cam)
Type of nucleic acid: ssDNA
Sequence: 5′AGCAGCACAGAGGTCAGATGATGCGGGTATATGGTGCGAGAAAACAAGGGGCATACTGGACCTATGCGTGCTACCGTGAA3′
Sequence length: 80
GC content: 0.525
Affinity: Kd: 2.2 μM
Pool type: 5′-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02 Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "Chloramphenicol (Cam), although an effective antibiotic, has lost favour due to some fatal side effects. Thus there is an urgent need for rapid and sensitive methods to detect residues in food, feed and environment. These aptamers open up possibilities to allow easy detection of Cam via aptamer-based biosensors."
Reference (2011, J Biotechnol ): Mehta, J., Van Dorst, B., Rouah-Martin, E., Herrebout, W., Scippo, M. L., Blust, R., & Robbens, J. (2011). In vitro selection and characterization of DNA aptamers recognizing chloramphenicol. Journal of biotechnology, 155(4), 361–369. https://doi.org/10.1016/j.jbiotec.2011.06.043
Aptamer: Apt21‐2
Target: Interleukin-17A (IL‐17A)
Type of nucleic acid: ssRNA
Sequence: 5′UAAUACGACUCACUAUAGGGAGCAGGAGAGAGGUCAGAUGGGUCUAGCCGGAGGAGUCAGUAAUCGGUAGACCCAUCUGACCUCUCUCCUGCUCCC3′
Sequence length: 96
GC content: 0.5416666666666666
Affinity: Kd: 48.5 pM
Pool type: 5′‐TAATACGACTCACTATAGGGAGCAGGAGAGAGGTCAGATG‐N30‐CATCTGACCTCTCTCCTGCTCCC‐3′
Pool random region: 30
Binding buffer/conditions: 50 mM Tris HCl, pH 8.0, 50 mM NaCl, 10% glycerol, 10 mM β‐mercaptoethanol, 20 mM imidazole, 0.5% Nonidet P40, 1 mM phenylmethylsulfonyl fluoride, and 0.5 mg/ml of lysozyme
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: " This study was undertaken to investigate the effect of a high-affinity RNA molecule, called an aptamer, against human IL-17A on IL-17A-induced signal transduction in vitro and its anti-autoimmune efficacy in vivo in 2 mouse models of inflammation. Our findings indicate that the chemically processed anti-IL-17A aptamer PEG21-2idT inhibits the actions of IL-17A as well as the development of autoimmunity in 2 mouse models of inflammation. These results offer for the first time an aptamer-based therapeutic approach to the treatment of Th17 cell-mediated autoimmune disorders."
Reference (2011, Arthritis Rheum ): Ishiguro, A., Akiyama, T., Adachi, H., Inoue, J., & Nakamura, Y. (2011). Therapeutic potential of anti-interleukin-17A aptamer: suppression of interleukin-17A signaling and attenuation of autoimmunity in two mouse models. Arthritis and rheumatism, 63(2), 455–466. https://doi.org/10.1002/art.30108
Aptamer: CLN0003
Target: C-Met receptor
Type of nucleic acid: ssDNA
Sequence: 5′GGAGGGAAAAGTTATCAGGCTGGATGGTAGCTCGGTCGGGGTGGGTGGGTTGGCAAGTCTGATTAGTTTTGGAGTACTCGCTCC3′
Sequence length: 84
GC content: 0.5476190476190477
Affinity: Kd: 0.09 ± 0.04 nM
Pool type: 5′-GGAGGGAAAAGTTATCAGGC-N40-GATTAGTTTTGGAGTACTCGCTCC-3′
Pool random region: 40
Binding buffer/conditions: 200 μl of 0.05% BSA in DPBS
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Antibody-dependent cellular cytotoxicity plays a pivotal role in antibody-based tumor therapies and is based on the recruitment of natural killer cells to antibody-bound tumor cells via binding of the Fcγ receptor III (CD16). Here we describe the generation of chimeric DNA aptamers that simultaneously bind to CD16α and c-Met, a receptor that is overexpressed in many tumors. These results represent the first gain of a tumor-effective function of two distinct oligonucleotides by linkage into a bi-specific aptamer mediating cellular cytotoxicity."
Additional information: referenced as CLN3 is https://doi.org/10.1371/journal.pone.0142412
Reference (2011, J Biol Chem ): Boltz, A., Piater, B., Toleikis, L., Guenther, R., Kolmar, H., & Hock, B. (2011). Bi-specific aptamers mediating tumor cell lysis. The Journal of biological chemistry, 286(24), 21896–21905. https://doi.org/10.1074/jbc.M111.238261
Aptamer: G5α3N.4
Target: Human papillomavirus type 16 (HPV-16) E7 oncoprotein
Type of nucleic acid: ssRNA
Sequence: 5′UAAUACGACUCACUAUAGGGAGACCCAAGCCGAUUUAUUUUGUGCAGCUUUUGUUCCCUUUAGUGAGGGUUAAUU3′
Sequence length: 75
GC content: 0.4
Affinity: Kd: 1.9 µM
Pool type: 5′-UAAUACGACUCACUAUAGGGAGACCCAAGC-N15-AGCUUUUGUUCCCUUUAGUGAGGGUUAAUU-3′
Pool random region: 15
Binding buffer/conditions: EMSA binding buffer: 4% glycerol, 1 mM MgCl2, 0.5 mM EDTA, 10 mM Tris HCl, 0.5 mM DTT, 50 mM NaCl and 25 mM spermidine
Divalent salt: MgCl
Buffer type: Tris Buffers
Molecular weight of target: 17 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Detection: "Cervical cancer is a common neoplastic disease affecting women worldwide. Expression of human papillomavirus type 16 (HPV-16) E6/E7 genes is frequently associated with cervical cancer, representing ideal targets for diagnostic and therapeutic strategies. The affinity and specificity of G5α3N.4 binding domains for the HPV-16 E7 protein may be used for the detection of papillomavirus infection and cervical cancer."
Additional information: *The paper notes this is an RNA aptamer with RNA library, but provided a DNA format of pool and sequence
Reference (2011, Arch Med Res ): Toscano-Garibay, J. D., Benítez-Hess, M. L., & Alvarez-Salas, L. M. (2011). Isolation and characterization of an RNA aptamer for the HPV-16 E7 oncoprotein. Archives of medical research, 42(2), 88–96. https://doi.org/10.1016/j.arcmed.2011.02.005
Aptamer: aptamer 1
Target: SARS CoV N protein
Type of nucleic acid: ssDNA
Sequence: 5′GCAATGGTACGGTACTTCCGGATGCGGAAACTGGCTAATTGGTGAGGCTGGGGCGGTCGTGCAGCAAAAGTGCACGCTACTTTGCTAA3′
Sequence length: 88
GC content: 0.5454545454545454
Affinity: Kd: 4.93 ± 0.30 nM
Pool type: 5′-GCAATGGTACGGTACTTCC-N45-CAAAAGTGCACGCTACTTTGCTAA-3′
Pool random region: 45
Binding buffer/conditions: 50 mM Tris/Cl, pH 8.0, 150 mM NaCl, 1.5 mM MgCl2, 2 mM dithiothreitol (DTT) and 1% (w/v) BSA
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 46 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " The outbreak of severe acute respiratory syndrome (SARS) in 2002 affected thousands of people and an efficient diagnostic system is needed for accurate detection of SARS coronavirus (SARS CoV) to prevent or limit future outbreaks. This ssDNA aptamer could be used to efficiently detect the SARS CoV nucleocapsid protein when compared with a nucleocapsid antibody. Therefore, we believe that the selected ssDNA aptamer may be a good alternative detection probe for the rapid and sensitive detection of SARS."
Reference (2011, J Biosci Bioeng ): Cho, S. J., Woo, H. M., Kim, K. S., Oh, J. W., & Jeong, Y. J. (2011). Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer. Journal of bioscience and bioengineering, 112(6), 535–540. https://doi.org/10.1016/j.jbiosc.2011.08.014