RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: LS-5
Target: Amyloid-like fibrils formed in vitro from monomeric beta-2-microglobulin (β2m)
Type of nucleic acid: ssRNA
Sequence: 5'GGGCCAAGCUUGCAUGCCUGCAGGCAAACGGGGGCGUUUCGGCGGAGGAGUGGGAAGAAAAACGAGAGAAGAGUUGGAACGGGUACCGAGCUCAGGUUCCC3'
Sequence length: 101
GC content: 0.6039603960396039
Affinity: Kd: 2.21E-08 M
Pool type: 5'-GGGCCAAGCTTGCATGCCTGCAG-N60-GGTACCGAGCTCAGGTTCCC-3'
Pool random region: 60
Binding buffer/conditions: 25 mm sodium acetate, 25 mm sodium phosphate buffer (Buffer A), pH 3.6, without NaCl, at pH 2.5
Buffer type: PBS/phosphate buffers
pH: 3.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Whereas the full potential of aptamers as therapeutics or diagnostics has yet to be realized, our results demonstrate the power of RNA aptamers for detection and identification of amyloid and, possibly, other protein misfolding diseases. They also pave the way for future experiments to derive aptamers able to bind tightly and specifically to different amyloid precursors (monomers, oligomers, or other protofibrillar forms), or amyloid fibrils with distinct structural properties that give rise to different disease phenotypes."
Reference (2007, J Biol Chem ): Bunka, D. H., Mantle, B. J., Morten, I. J., Tennent, G. A., Radford, S. E., & Stockley, P. G. (2007). Production and characterization of RNA aptamers specific for amyloid fibril epitopes. The Journal of biological chemistry, 282(47), 34500–34509. https://doi.org/10.1074/jbc.M703679200
Aptamer: Apt A
Target: Bifunctional ribulose 5-phosphate reductase (Bcs1)
Type of nucleic acid: ssDNA
Sequence: 5'CAGGTCCATCGAGTGGTAGGAGTAGTTATTGGAGGGGTGGGCGGGAAGCGACGATTGTGGGTCGCACTGCTCCTGAACGTAC3'
Sequence length: 82
GC content: 0.5853658536585366
Affinity: Kd: 39 nM
Pool type: 5'-CAGGTCCATCGAGTGGTAGGA-N40-TCGCACTGCTCCTGAACGTAC-3'
Pool random region: 40
Binding buffer/conditions: Tris‐HCl (50 mM, pH 7.5), NaCl (150 mM), MgCl2 (10 mM), Tween‐20 (0.02 %), NADH (50 mM), and CTP (50 mM)
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: Detection and Therapeutic: "The isolated DNA aptamers also acted as inhibitors for a metabolic enzyme, and provide new molecular tools for the examination of enzyme functions. It is conceivable that the DNA aptamers isolated in this study could be utilized in similar efforts to search for chemical probes that inhibit the function of Bcs1, and might eventually lead to the discovery of molecules with antimicrobial properties."
Reference (2007, Chembiochem ): Allali-Hassani, A., Pereira, M. P., Navani, N. K., Brown, E. D., & Li, Y. (2007). Isolation of DNA aptamers for CDP-ribitol synthase, and characterization of their inhibitory and structural properties. Chembiochem : a European journal of chemical biology, 8(17), 2052–2057. https://doi.org/10.1002/cbic.200700257
Aptamer: Apt B
Target: Bifunctional ribulose 5-phosphate reductase (Bcs1)
Type of nucleic acid: ssDNA
Sequence: 5'CAGGTCCATCGAGTGGTAGGAGGTGCGAAATTGGGGGGGTGGGGTAGCGGTGTTGAGCACATCGCACTGCTCCTGAACGTAC3'
Sequence length: 82
GC content: 0.5975609756097561
Affinity: Kd: 29 nM
Pool type: 5'-CAGGTCCATCGAGTGGTAGGA-N40-TCGCACTGCTCCTGAACGTAC-3'
Pool random region: 40
Binding buffer/conditions: Tris‐HCl (50 mM, pH 7.5), NaCl (150 mM), MgCl2 (10 mM), Tween‐20 (0.02 %), NADH (50 mM), and CTP (50 mM)
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: Detection and Therapeutic: "The isolated DNA aptamers also acted as inhibitors for a metabolic enzyme, and provide new molecular tools for the examination of enzyme functions. It is conceivable that the DNA aptamers isolated in this study could be utilized in similar efforts to search for chemical probes that inhibit the function of Bcs1, and might eventually lead to the discovery of molecules with antimicrobial properties."
Reference (2007, Chembiochem ): Allali-Hassani, A., Pereira, M. P., Navani, N. K., Brown, E. D., & Li, Y. (2007). Isolation of DNA aptamers for CDP-ribitol synthase, and characterization of their inhibitory and structural properties. Chembiochem : a European journal of chemical biology, 8(17), 2052–2057. https://doi.org/10.1002/cbic.200700257
Aptamer: 9-15
Target: Hepatitis C virus (HCV)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGCCGUUCGAACACGAGCAUGGAUCGAGGAUGGGAACACCCAGUAGGAGGAUGGGCAUGGCCGGACCCAAAAUUAGCAGUGGGACAGUACUCAGGUCAUCCUAGG3'
Sequence length: 106
GC content: 0.5754716981132075
Affinity: Kd: 224 nM via format protein chip assay (Biacore)
Pool type: 5'-GGGCCGTTCGAACACGAGCATG-N60-GGACAGTACTCAGGTCATCCTAGG-3'
Pool random region: 60
Binding buffer/conditions: Binding Buffer for Binding Assay: 0.01 M Hepes, pH 7.4, 0.15 M NaCl, 3 mM EDTA, and 0.005% (v/v) surfactant P20
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Using the same sol–gel materials as those used for the protein chips [22], we immobilized the 2′-F modified (for protection of aptamers against RNases) aptamers (2′F-9-14 , 2′F-9-15, and 2′F-9-19) along with the core and NS5 proteins as diagnostic controls
Application as quoted in the referenced paper: Diagnostic: " The selected aptamers specifically bound to the core antigen, but not to another HCV antigen, NS5, in a protein chip-based assay. Using these aptamers, we developed an aptamer-based biosensor for HCV diagnosis and detected the core antigen from HCV infected patients’ sera with good specificity. This novel aptamer-based antigen detection sensor could be applied to the early diagnosis of HCV infection."
Additional information: Protein info: A fusion protein including the N-terminal amino acids 2–114 of the core antigen with the C-terminal His tag was bacterially expressed, and the resulting core(2-114)-His6 proteins were purified using Ni-NTA affinity chromatography
Reference (2007, Biochem Biophys Res Commun ): Lee, S., Kim, Y. S., Jo, M., Jin, M., Lee, D. K., & Kim, S. (2007). Chip-based detection of hepatitis C virus using RNA aptamers that specifically bind to HCV core antigen. Biochemical and biophysical research communications, 358(1), 47–52. https://doi.org/10.1016/j.bbrc.2007.04.057
Aptamer: TD05
Target: Ramos (CRL-1596, B lymphocyte, human Burkitt's lymphoma) cells
Type of nucleic acid: ssDNA
Sequence: 5'AACACCGTGGAGGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCCGGTG3'
Sequence length: 48
GC content: 0.6041666666666666
Affinity: Kd: 74.7 ± 8.7 nM
Pool type: 5‘-AAGGAGCAGCGTGGAGGATA-N45-TTAGGGTGTGTCGTCGTGGT-3‘
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's PBS (Sigma), yeast tRNA (0.1 mg/mL) (Sigma) and BSA (1 mg/mL)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this paper, we describe a new way to generate molecular probes for specific recognition of cancer cells. The strategies used here will be highly useful for aptamer selection against complex target samples in order to generate a large number of aptamers in a variety of biomedical and biotechnological applications, paving the way for molecular diagnosis, therapy, and biomarker discovery."
Additional information: *target binding: specific responses to Ramos cells and no binding to CCRF-CEM or Toledo cells. Aptamer sequence was larger than random region
Reference (2007, Anal Chem ): Tang, Z., Shangguan, D., Wang, K., Shi, H., Sefah, K., Mallikratchy, P., Chen, H. W., Li, Y., & Tan, W. (2007). Selection of aptamers for molecular recognition and characterization of cancer cells. Analytical chemistry, 79(13), 4900–4907. https://doi.org/10.1021/ac070189y
Aptamer: TD08
Target: Ramos (CRL-1596, B lymphocyte, human Burkitt's lymphoma) cells
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATACTCTAATTGCCGTATAAGGTCAGGGGGTTGGTTGGTTCCTAGTGCTTAGGGTGTGTCGTCGTGGT3'
Sequence length: 85
GC content: 0.5294117647058824
Affinity: Kd: 3.26 ± 0.13 nM
Pool type: 5‘-AAGGAGCAGCGTGGAGGATA-N45-TTAGGGTGTGTCGTCGTGGT-3‘
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's PBS (Sigma), yeast tRNA (0.1 mg/mL) (Sigma) and BSA (1 mg/mL)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this paper, we describe a new way to generate molecular probes for specific recognition of cancer cells. The strategies used here will be highly useful for aptamer selection against complex target samples in order to generate a large number of aptamers in a variety of biomedical and biotechnological applications, paving the way for molecular diagnosis, therapy, and biomarker discovery."
Additional information: *target binding: strong response to Ramos cells and a weak response to CCRF-CEM and/or Toledo cells
Reference (2007, Anal Chem ): Tang, Z., Shangguan, D., Wang, K., Shi, H., Sefah, K., Mallikratchy, P., Chen, H. W., Li, Y., & Tan, W. (2007). Selection of aptamers for molecular recognition and characterization of cancer cells. Analytical chemistry, 79(13), 4900–4907. https://doi.org/10.1021/ac070189y
Aptamer: TD09
Target: Ramos (CRL-1596, B lymphocyte, human Burkitt's lymphoma) cells
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATAGCTGTCATCGGCTTATGTGCTTTCCAGGGTCCGTGCTGTCCGTTGTTAGGGTGTGTCGTCGTGGT3'
Sequence length: 85
GC content: 0.5647058823529412
Affinity: Kd: 5.15 ± 0.96 nM
Pool type: 5‘-AAGGAGCAGCGTGGAGGATA-N45-TTAGGGTGTGTCGTCGTGGT-3‘
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's PBS (Sigma), yeast tRNA (0.1 mg/mL) (Sigma) and BSA (1 mg/mL)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this paper, we describe a new way to generate molecular probes for specific recognition of cancer cells. The strategies used here will be highly useful for aptamer selection against complex target samples in order to generate a large number of aptamers in a variety of biomedical and biotechnological applications, paving the way for molecular diagnosis, therapy, and biomarker discovery."
Additional information: *target binding: showed equal response to Ramos & Toledo cell lines
Reference (2007, Anal Chem ): Tang, Z., Shangguan, D., Wang, K., Shi, H., Sefah, K., Mallikratchy, P., Chen, H. W., Li, Y., & Tan, W. (2007). Selection of aptamers for molecular recognition and characterization of cancer cells. Analytical chemistry, 79(13), 4900–4907. https://doi.org/10.1021/ac070189y
Aptamer: TE02
Target: Ramos (CRL-1596, B lymphocyte, human Burkitt's lymphoma) cells
Type of nucleic acid: ssDNA
Sequence: 5‘AAGGAGCAGCGTGGAGGATATAGGCAGTGGTTTGACGTCCGCATGTTGGGAATAGCCACGCCTTTAGGGTGTGTCGTCGTGGT3‘
Sequence length: 83
GC content: 0.5542168674698795
Affinity: Kd: 0.76 ± 0.13 nM
Pool type: 5‘-AAGGAGCAGCGTGGAGGATA-N45-TTAGGGTGTGTCGTCGTGGT-3‘
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's PBS (Sigma), yeast tRNA (0.1 mg/mL) (Sigma) and BSA (1 mg/mL)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this paper, we describe a new way to generate molecular probes for specific recognition of cancer cells. The strategies used here will be highly useful for aptamer selection against complex target samples in order to generate a large number of aptamers in a variety of biomedical and biotechnological applications, paving the way for molecular diagnosis, therapy, and biomarker discovery."
Additional information: *target binding: strong response to Ramos cells and a weak response to CCRF-CEM and/or Toledo cells
Reference (2007, Anal Chem ): Tang, Z., Shangguan, D., Wang, K., Shi, H., Sefah, K., Mallikratchy, P., Chen, H. W., Li, Y., & Tan, W. (2007). Selection of aptamers for molecular recognition and characterization of cancer cells. Analytical chemistry, 79(13), 4900–4907. https://doi.org/10.1021/ac070189y
Aptamer: TE04
Target: Ramos (CRL-1596, B lymphocyte, human Burkitt's lymphoma) cells
Type of nucleic acid: ssDNA
Sequence: 5‘AAGGAGCAGCGTGGAGGATATCCTCGATGCACCAGTTCACCTTATTTGCTTCTTCTCTCTGTTCTGACTGGGTGCTGAGGATTAGGGTGTGTCGTCGTGGT3‘
Sequence length: 101
GC content: 0.5148514851485149
Affinity: Kd: 207 ± 41 nM
Pool type: 5‘-AAGGAGCAGCGTGGAGGATA-N45-TTAGGGTGTGTCGTCGTGGT-3‘
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's PBS (Sigma), yeast tRNA (0.1 mg/mL) (Sigma) and BSA (1 mg/mL)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this paper, we describe a new way to generate molecular probes for specific recognition of cancer cells. The strategies used here will be highly useful for aptamer selection against complex target samples in order to generate a large number of aptamers in a variety of biomedical and biotechnological applications, paving the way for molecular diagnosis, therapy, and biomarker discovery."
Additional information: *target binding: strong response to Ramos cells and a weak response to CCRF-CEM and/or Toledo cells. Aptamer sequence was larger than random region
Reference (2007, Anal Chem ): Tang, Z., Shangguan, D., Wang, K., Shi, H., Sefah, K., Mallikratchy, P., Chen, H. W., Li, Y., & Tan, W. (2007). Selection of aptamers for molecular recognition and characterization of cancer cells. Analytical chemistry, 79(13), 4900–4907. https://doi.org/10.1021/ac070189y
Aptamer: TE13
Target: Ramos (CRL-1596, B lymphocyte, human Burkitt's lymphoma) cells
Type of nucleic acid: ssDNA
Sequence: 5‘AAGGAGCAGCGTGGAGGATAAGGCCCCCAGGCTCGGTGGATGCAAACACATGACTATGGGCCCGTTTAGGGTGTGTCGTCGTGGT3‘
Sequence length: 85
GC content: 0.5882352941176471
Affinity: Kd: 202 ± 52 nM
Pool type: 5‘-AAGGAGCAGCGTGGAGGATA-N45-TTAGGGTGTGTCGTCGTGGT-3‘
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's PBS (Sigma), yeast tRNA (0.1 mg/mL) (Sigma) and BSA (1 mg/mL)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this paper, we describe a new way to generate molecular probes for specific recognition of cancer cells. The strategies used here will be highly useful for aptamer selection against complex target samples in order to generate a large number of aptamers in a variety of biomedical and biotechnological applications, paving the way for molecular diagnosis, therapy, and biomarker discovery."
Additional information: *target binding: showed equal response to all three cell lines [Ramos, CCRF-CEM, Toledo]
Reference (2007, Anal Chem ): Tang, Z., Shangguan, D., Wang, K., Shi, H., Sefah, K., Mallikratchy, P., Chen, H. W., Li, Y., & Tan, W. (2007). Selection of aptamers for molecular recognition and characterization of cancer cells. Analytical chemistry, 79(13), 4900–4907. https://doi.org/10.1021/ac070189y
Aptamer: 1.12.2
Target: Ochratoxin A (OTA)
Type of nucleic acid: ssDNA
Sequence: 5'GATCGGGTGTGGGTGGCGTAAAGGGAGCATCGGACA3'
Sequence length: 36
GC content: 0.6111111111111112
Affinity: Kd: 0.2
Pool type: 5'TGGTGGCTGTAGGTCA-N30-CGTTGTCCGATGCTC
Pool random region: 30
Binding buffer/conditions: Selection buffer (SB), composed of 10 mM HEPES, pH 7.0, 120 mM NaCl, 5 mM KCl, and 5 mM MgCl2; binding buffer (BB): (10 mM TRIS, pH 8.5,120 mM NaCl, 5 mM KCl, and 20 mM CaCl2)
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Removing the forward primer in 1.12 and a section of the 5′-nonconsensus sequence. Further removal of three bases from the 3′-end, (aptamers 1.12.2 and 1.12.8) resulted in a significant increase in binding affinity
Application as quoted in the referenced paper: Research and Detection: "This work describes the identification of an aptamer that binds with high affinity and specificity to ochratoxin A (OTA), a mycotoxin that occurs in wheat and other foodstuffs, and a quantitative detection method for OTA based on the use of this aptamer. Further work is ongoing to broaden the application demonstrated here with the development of sensors, affinity columns, and other analytical systems for field and laboratory determination of this toxin in food and agricultural products."
Additional information: The library was designed with 30 random nucleotides, flanked with two constant regions for primer annealing. The primers were as follows: reverse, Biotin_x0002_CGTTGTCCGATGCTC; and forward, Cy3-TGGTGGCTGTAGGTCA
Reference (2008, J Agric Food Chem ): Cruz-Aguado, J. A., & Penner, G. (2008). Determination of ochratoxin a with a DNA aptamer. Journal of agricultural and food chemistry, 56(22), 10456–10461. https://doi.org/10.1021/jf801957h
Aptamer: 1.12.8
Target: Ochratoxin A (OTA)
Type of nucleic acid: ssDNA
Sequence: 5'GATCGGGTGTGGGTGGCGTAAAGGGAGCATCGG3'
Sequence length: 33
GC content: 0.6363636363636364
Affinity: Kd: 0.2
Pool type: 5'TGGTGGCTGTAGGTCA-N30-CGTTGTCCGATGCTC
Pool random region: 30
Binding buffer/conditions: Selection buffer (SB), composed of 10 mM HEPES, pH 7.0, 120 mM NaCl, 5 mM KCl, and 5 mM MgCl2; binding buffer (BB): (10 mM TRIS, pH 8.5,120 mM NaCl, 5 mM KCl, and 20 mM CaCl2)
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Removing the forward primer in 1.12 and a section of the 5′-nonconsensus sequence. Further removal of three bases from the 3′-end, (aptamers 1.12.2 and 1.12.8) resulted in a significant increase in binding affinity
Application as quoted in the referenced paper: Research and Detection: "This work describes the identification of an aptamer that binds with high affinity and specificity to ochratoxin A (OTA), a mycotoxin that occurs in wheat and other foodstuffs, and a quantitative detection method for OTA based on the use of this aptamer. Further work is ongoing to broaden the application demonstrated here with the development of sensors, affinity columns, and other analytical systems for field and laboratory determination of this toxin in food and agricultural products."
Additional information: The library was designed with 30 random nucleotides, flanked with two constant regions for primer annealing. The primers were as follows: reverse, Biotin_x0002_CGTTGTCCGATGCTC; and forward, Cy3-TGGTGGCTGTAGGTCA
Reference (2008, J Agric Food Chem ): Cruz-Aguado, J. A., & Penner, G. (2008). Determination of ochratoxin a with a DNA aptamer. Journal of agricultural and food chemistry, 56(22), 10456–10461. https://doi.org/10.1021/jf801957h
Aptamer: 1.12.9
Target: Ochratoxin A (OTA)
Type of nucleic acid: ssDNA
Sequence: 5'GATCGGGTGTGGGTGGCGTAAAGGGAGCAT3'
Sequence length: 30
GC content: 0.6
Affinity: Kd: 1.6
Pool type: 5'TGGTGGCTGTAGGTCA-N30-CGTTGTCCGATGCTC
Pool random region: 30
Binding buffer/conditions: Selection buffer (SB), composed of 10 mM HEPES, pH 7.0, 120 mM NaCl, 5 mM KCl, and 5 mM MgCl2; binding buffer (BB): (10 mM TRIS, pH 8.5,120 mM NaCl, 5 mM KCl, and 20 mM CaCl2)
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Removing the forward primer in 1.12 and a section of the 5′ nonconsensus sequence. Removal of nucleotide from 3'-end
Application as quoted in the referenced paper: Research and Detection: "This work describes the identification of an aptamer that binds with high affinity and specificity to ochratoxin A (OTA), a mycotoxin that occurs in wheat and other foodstuffs, and a quantitative detection method for OTA based on the use of this aptamer. Further work is ongoing to broaden the application demonstrated here with the development of sensors, affinity columns, and other analytical systems for field and laboratory determination of this toxin in food and agricultural products."
Additional information: The library was designed with 30 random nucleotides, flanked with two constant regions for primer annealing. The primers were as follows: reverse, Biotin_x0002_CGTTGTCCGATGCTC; and forward, Cy3-TGGTGGCTGTAGGTCA
Reference (2008, J Agric Food Chem ): Cruz-Aguado, J. A., & Penner, G. (2008). Determination of ochratoxin a with a DNA aptamer. Journal of agricultural and food chemistry, 56(22), 10456–10461. https://doi.org/10.1021/jf801957h
Aptamer: 1.12.11
Target: Ochratoxin A (OTA)
Type of nucleic acid: ssDNA
Sequence: 5'GATCGGGTGTGGGTGGCGTAAAGGGAGCATCG3'
Sequence length: 32
GC content: 0.625
Affinity: Kd: 0.4
Pool type: 5'TGGTGGCTGTAGGTCA-N30-CGTTGTCCGATGCTC
Pool random region: 30
Binding buffer/conditions: Selection buffer (SB), composed of 10 mM HEPES, pH 7.0, 120 mM NaCl, 5 mM KCl, and 5 mM MgCl2; binding buffer (BB): (10 mM TRIS, pH 8.5,120 mM NaCl, 5 mM KCl, and 20 mM CaCl2)
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Removing the forward primer in 1.12 and a section of the 5′ nonconsensus sequence. Removal of nucleotide from 3'-end
Application as quoted in the referenced paper: Research and Detection: "This work describes the identification of an aptamer that binds with high affinity and specificity to ochratoxin A (OTA), a mycotoxin that occurs in wheat and other foodstuffs, and a quantitative detection method for OTA based on the use of this aptamer. Further work is ongoing to broaden the application demonstrated here with the development of sensors, affinity columns, and other analytical systems for field and laboratory determination of this toxin in food and agricultural products."
Additional information: The library was designed with 30 random nucleotides, flanked with two constant regions for primer annealing. The primers were as follows: reverse, Biotin_x0002_CGTTGTCCGATGCTC; and forward, Cy3-TGGTGGCTGTAGGTCA
Reference (2008, J Agric Food Chem ): Cruz-Aguado, J. A., & Penner, G. (2008). Determination of ochratoxin a with a DNA aptamer. Journal of agricultural and food chemistry, 56(22), 10456–10461. https://doi.org/10.1021/jf801957h
Aptamer: No. 4
Target: Oxytetracycline (OTC)
Type of nucleic acid: ssDNA
Sequence: 5′CGTACGGAATTCGCTAGCCGACGCGCGTTGGTGGTGGATGGTGTGTTACACGTGTTGTGGATCCGAGCTCCACGTG3′
Sequence length: 76
GC content: 0.5921052631578947
Affinity: Kd: 9.61 ± 0.3 nM
Pool type: 5′-CGTACGGAATTCGCTAGC-N40-GGATCCGAGCTCCACGTG-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: " OTC is one of the most frequently used tetracyclines for its application as growth promoter supplied with livestock feed. This study describes the in-vitro selection of ssDNA aptamers that bind to OTC with high affinity, and characterization of their specificity and selectivity. The aptamers developed can be good candidates for development of biosensors for detection of OTC, which may be present as contaminant in meat, milk, and other food products."
Reference (2008, Bioorg Med Chem ): Niazi, J. H., Lee, S. J., Kim, Y. S., & Gu, M. B. (2008). ssDNA aptamers that selectively bind oxytetracycline. Bioorganic & medicinal chemistry, 16(3), 1254–1261. https://doi.org/10.1016/j.bmc.2007.10.073