RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: No. 5
Target: Oxytetracycline (OTC)
Type of nucleic acid: ssDNA
Sequence: 5′CGTACGGAATTCGCTAGCACGTTGACGCTGGTGCCCGGTTGTGGTGCGAGTGTTGTGTGGATCCGAGCTCCACGTG3′
Sequence length: 76
GC content: 0.6052631578947368
Affinity: Kd: 12.08 ± 2.25 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
Aptamer: No. 20
Target: Oxytetracycline (OTC)
Type of nucleic acid: ssDNA
Sequence: 5′CGTACGGAATTCGCTAGCCGAGTTGAGCCGGGCGCGGTACGGGTACTGGTATGTGTGGGGATCCGAGCTCCACGTG3′
Sequence length: 76
GC content: 0.631578947368421
Affinity: Kd: 56.84 ± 3.62 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
Aptamer: MUC1-5TR-1
Target: Mucin 1 (MUC1) recombinant protein MUC1-5TR
Type of nucleic acid: ssDNA
Sequence: 5′GGGAGACAAGAATAAACGCTCAAGAAGTGAAAATGACAGAACACAACATTCGACAGGAGGCTCACAACAGGC3'
Sequence length: 72
GC content: 0.4583333333333333
Affinity: Kd: 47.3 ± 0.984 nM
Pool type: 5′-GGGAGACAAGAATAAACGCTCAA-N25-TTCGACAGGAGGCTCACAACAGGC-3'
Pool random region: 25
Binding buffer/conditions: 100 mM NaCl and 5 mM MgCl2, pH 7.4
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " MUC1 is a well-known tumour marker present in epithelial malignancies and is used in immunotherapeutic and diagnostic approaches. Our results aim towards the formation of new diagnostic assays against this tumour marker for the early diagnosis of primary or metastatic disease in breast, bladder and other epithelial tumours."
Additional information: Selection was done using affinity chromatography
Reference (2008, Anal Bioanal Chem ): Ferreira, C. S., Papamichael, K., Guilbault, G., Schwarzacher, T., Gariepy, J., & Missailidis, S. (2008). DNA aptamers against the MUC1 tumour marker: design of aptamer-antibody sandwich ELISA for the early diagnosis of epithelial tumours. Analytical and bioanalytical chemistry, 390(4), 1039–1050. https://doi.org/10.1007/s00216-007-1470-1
Aptamer: MUC1-5TR-2
Target: Mucin 1 (MUC1) recombinant protein MUC1-5TR
Type of nucleic acid: ssDNA
Sequence: 5′GGGAGACAAGAATAAACGCTCAAGGCTATAGCACATGGGTAAAACGACTTCGACAGGAGGCTCACAACAGGC3'
Sequence length: 72
GC content: 0.5
Affinity: Kd: 85.2 ± 0.986 nM
Pool type: 5′-GGGAGACAAGAATAAACGCTCAA-N25-TTCGACAGGAGGCTCACAACAGGC-3'
Pool random region: 25
Binding buffer/conditions: 100 mM NaCl and 5 mM MgCl2, pH 7.4
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " MUC1 is a well-known tumour marker present in epithelial malignancies and is used in immunotherapeutic and diagnostic approaches. Our results aim towards the formation of new diagnostic assays against this tumour marker for the early diagnosis of primary or metastatic disease in breast, bladder and other epithelial tumours."
Additional information: Selection was done using affinity chromatography
Reference (2008, Anal Bioanal Chem ): Ferreira, C. S., Papamichael, K., Guilbault, G., Schwarzacher, T., Gariepy, J., & Missailidis, S. (2008). DNA aptamers against the MUC1 tumour marker: design of aptamer-antibody sandwich ELISA for the early diagnosis of epithelial tumours. Analytical and bioanalytical chemistry, 390(4), 1039–1050. https://doi.org/10.1007/s00216-007-1470-1
Aptamer: MUC1-5TR-3
Target: Mucin 1 (MUC1) recombinant protein MUC1-5TR
Type of nucleic acid: ssDNA
Sequence: 5′GGGAGACAAGAATAAACGCTCAACAAACAATCAAACAGCAGTGGGGTGTTCGACAGGAGGCTCACAACAGGC3'
Sequence length: 72
GC content: 0.5
Affinity: Kd: 83.0 ± 0.981 nM
Pool type: 5′-GGGAGACAAGAATAAACGCTCAA-N25-TTCGACAGGAGGCTCACAACAGGC-3'
Pool random region: 25
Binding buffer/conditions: 100 mM NaCl and 5 mM MgCl2, pH 7.4
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " MUC1 is a well-known tumour marker present in epithelial malignancies and is used in immunotherapeutic and diagnostic approaches. Our results aim towards the formation of new diagnostic assays against this tumour marker for the early diagnosis of primary or metastatic disease in breast, bladder and other epithelial tumours."
Additional information: Selection was done using affinity chromatography
Reference (2008, Anal Bioanal Chem ): Ferreira, C. S., Papamichael, K., Guilbault, G., Schwarzacher, T., Gariepy, J., & Missailidis, S. (2008). DNA aptamers against the MUC1 tumour marker: design of aptamer-antibody sandwich ELISA for the early diagnosis of epithelial tumours. Analytical and bioanalytical chemistry, 390(4), 1039–1050. https://doi.org/10.1007/s00216-007-1470-1
Aptamer: MUC1-5TR-4
Target: Mucin 1 (MUC1) recombinant protein MUC1-5TR
Type of nucleic acid: ssDNA
Sequence: 5′GGGAGACAAGAATAAACGCTCAATACTGCATGCACACCACTTCAACTATTCGACAGGAGGCTCACAACAGGC3'
Sequence length: 72
GC content: 0.4861111111111111
Affinity: Kd: 69.0 ± 0.974 nM
Pool type: 5′-GGGAGACAAGAATAAACGCTCAA-N25-TTCGACAGGAGGCTCACAACAGGC-3'
Pool random region: 25
Binding buffer/conditions: 100 mM NaCl and 5 mM MgCl2, pH 7.4
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " MUC1 is a well-known tumour marker present in epithelial malignancies and is used in immunotherapeutic and diagnostic approaches. Our results aim towards the formation of new diagnostic assays against this tumour marker for the early diagnosis of primary or metastatic disease in breast, bladder and other epithelial tumours."
Additional information: Selection was done using affinity chromatography
Reference (2008, Anal Bioanal Chem ): Ferreira, C. S., Papamichael, K., Guilbault, G., Schwarzacher, T., Gariepy, J., & Missailidis, S. (2008). DNA aptamers against the MUC1 tumour marker: design of aptamer-antibody sandwich ELISA for the early diagnosis of epithelial tumours. Analytical and bioanalytical chemistry, 390(4), 1039–1050. https://doi.org/10.1007/s00216-007-1470-1
Aptamer: ANG9-4
Target: Angiopoietin-1 (Ang1)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGAGAGAGGAAGAGGGAUGGGACUCGAACAUUUCCACUAACCAACCAUACUAAAGCACCGCCAUAACCCAGAGGUCGAUAGUACUGGAUCCCCCC3′
Sequence length: 96
GC content: 0.53125
Affinity: Kd: 2.8 nM
Pool type: 5'-GGGAGAGAGGAAGAGGGAUGGG-N40-CAUAACCCAGAGGUCGAUAGUACUGGAUCCCCCC-3′
Pool random region: 40
Binding buffer/conditions: 20 mM HEPES, pH 7.4, 50 mM [round 1] - 150 mM [round 7] NaCl, 2 mM CaCl2, 0.05% CHAPS
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Tie2 is a receptor tyrosine kinase that is expressed predominantly in the endothelium and plays key roles in both physiological and pathological angiogenesis. Moreover, ANG9-4 inhibited Ang1-induced endothelial cell survival. Together, these findings demonstrate the feasibility of developing an Ang1-inhibitory aptamer. ANG9-4 and its derivatives may provide useful tools for elucidating the biology of Ang1 and for treating certain angiogenic diseases."
Additional information: in pool type N40 represents 40 random nucleotides with equimolar 2′-hydroxy ATP, 2′-hydroxy GTP, 2′-fluoro CTP, and 2′-fluoro UTP content
RNA aptamers are promising tools with which to study the angiopoietins in vitro and in vivo. The use of 2′-modified nucleotides confers resistance to nuclease degradation, and 2′-fluoro-modified RNAs have plasma half-lives of greater than 12 h [37]. The in vivo circulating half-life of these aptamers can be improved further by the addition of PEG or cholesterol moieties to their 5′ ends [38]. The full-length ANG9-4 aptamer (96 nucleotides) can be transcribed in vitro in quantities sufficient for cell culture and some small animal models. However, chemical synthesis, with or without 5′ modification, is inefficient for RNAs greater than 60 nucleotides in length. Work is ongoing to truncate and modify the full-length aptamer for large-scale synthesis and application in animal models.
Reference (2008, Angiogenesis ): White, R. R., Roy, J. A., Viles, K. D., Sullenger, B. A., & Kontos, C. D. (2008). A nuclease-resistant RNA aptamer specifically inhibits angiopoietin-1-mediated Tie2 activation and function. Angiogenesis, 11(4), 395–401. https://doi.org/10.1007/s10456-008-9122-4
Aptamer: A
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTACCAAACTGAATACTGGGAATCAATTCCCTATAGTGAGTCGTATTAGCTAGTAAGCTTGCCGT3'
Sequence length: 97
GC content: 0.4123711340206185
Affinity: Kd: 228.4 nM and 7485.3 nM *this Kd was determined with affinity test on entire n round pool
Pool type: 5'-TAATACGACTCACTATAGGGAATTCTATCCGGGTA-N25-GCTAGTAAGCTTGCCGT-3'
Pool random region: 25
Binding buffer/conditions: EMSA binding buffer: 1 pmol BSA, Streptavidin and ANEPIII (5 µL total volume each)
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Current immunoassays detecting MUC1 are sensitive for predicting relapse in breast cancer, but they are not in widespread use in the follow-up of this disease. It has therefore been proposed that aptamers may offer this additional advantage in improving the sensitivity of such immunoassays."
Reference (2008, Arch Pharm Res ): Zhu, J., Wang, J., Su, Z. C., Li, Q., Cheng, M. S., & Zhang, J. H. (2008). Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Archives of pharmacal research, 31(9), 1120–1128. https://doi.org/10.1007/s12272-001-1278-2
Aptamer: C
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTATAGGGAATTCTATCCGGGCTAGTTTCGAAGCCGTAAGACTGGAGATCTGGATCCCTGCTAGTAAGCTTGCCGT3'
Sequence length: 108
GC content: 0.4722222222222222
Affinity: Kd: 228.4 nM and 7485.3 nM *this Kd was determined with affinity test on entire n round pool
Pool type: 5'-TAATACGACTCACTATAGGGAATTCTATCCGGGTA-N25-GCTAGTAAGCTTGCCGT-3'
Pool random region: 25
Binding buffer/conditions: EMSA binding buffer: 1 pmol BSA, Streptavidin and ANEPIII (5 µL total volume each)
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Current immunoassays detecting MUC1 are sensitive for predicting relapse in breast cancer, but they are not in widespread use in the follow-up of this disease. It has therefore been proposed that aptamers may offer this additional advantage in improving the sensitivity of such immunoassays."
Reference (2008, Arch Pharm Res ): Zhu, J., Wang, J., Su, Z. C., Li, Q., Cheng, M. S., & Zhang, J. H. (2008). Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Archives of pharmacal research, 31(9), 1120–1128. https://doi.org/10.1007/s12272-001-1278-2
Aptamer: D
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTAGCTTCCAAACTGAATACTGGGATTCAATTCCCTATAGTGAGTCGTATTAGCTAGTAAGCTTGCCGT3'
Sequence length: 101
GC content: 0.4158415841584158
Affinity: Kd: 228.4 nM and 7485.3 nM *this Kd was determined with affinity test on entire n round pool
Pool type: 5'-TAATACGACTCACTATAGGGAATTCTATCCGGGTA-N25-GCTAGTAAGCTTGCCGT-3'
Pool random region: 25
Binding buffer/conditions: EMSA binding buffer: 1 pmol BSA, Streptavidin and ANEPIII (5 µL total volume each)
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Current immunoassays detecting MUC1 are sensitive for predicting relapse in breast cancer, but they are not in widespread use in the follow-up of this disease. It has therefore been proposed that aptamers may offer this additional advantage in improving the sensitivity of such immunoassays."
Reference (2008, Arch Pharm Res ): Zhu, J., Wang, J., Su, Z. C., Li, Q., Cheng, M. S., & Zhang, J. H. (2008). Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Archives of pharmacal research, 31(9), 1120–1128. https://doi.org/10.1007/s12272-001-1278-2
Aptamer: E
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTACCAAACTAGCTACTGGGAATCAATTCCCTATAGTGAGTCGTATTAGCTAGTAAGCTTGCCGT3'
Sequence length: 97
GC content: 0.422680412371134
Affinity: Kd: 228.4 nM and 7485.3 nM *this Kd was determined with affinity test on entire n round pool
Pool type: 5'-TAATACGACTCACTATAGGGAATTCTATCCGGGTA-N25-GCTAGTAAGCTTGCCGT-3'
Pool random region: 25
Binding buffer/conditions: EMSA binding buffer: 1 pmol BSA, Streptavidin and ANEPIII (5 µL total volume each)
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Current immunoassays detecting MUC1 are sensitive for predicting relapse in breast cancer, but they are not in widespread use in the follow-up of this disease. It has therefore been proposed that aptamers may offer this additional advantage in improving the sensitivity of such immunoassays."
Reference (2008, Arch Pharm Res ): Zhu, J., Wang, J., Su, Z. C., Li, Q., Cheng, M. S., & Zhang, J. H. (2008). Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Archives of pharmacal research, 31(9), 1120–1128. https://doi.org/10.1007/s12272-001-1278-2
Aptamer: F
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTACCAAACTAGCTACCGGGATACAATTCCCTATAGTGAGTCGTATTAGCTAGTAAGCTTGCCGT3'
Sequence length: 97
GC content: 0.4329896907216495
Affinity: Kd: 228.4 nM and 7485.3 nM *this Kd was determined with affinity test on entire n round pool
Pool type: 5'-TAATACGACTCACTATAGGGAATTCTATCCGGGTA-N25-GCTAGTAAGCTTGCCGT-3'
Pool random region: 25
Binding buffer/conditions: EMSA binding buffer: 1 pmol BSA, Streptavidin and ANEPIII (5 µL total volume each)
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Current immunoassays detecting MUC1 are sensitive for predicting relapse in breast cancer, but they are not in widespread use in the follow-up of this disease. It has therefore been proposed that aptamers may offer this additional advantage in improving the sensitivity of such immunoassays."
Reference (2008, Arch Pharm Res ): Zhu, J., Wang, J., Su, Z. C., Li, Q., Cheng, M. S., & Zhang, J. H. (2008). Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Archives of pharmacal research, 31(9), 1120–1128. https://doi.org/10.1007/s12272-001-1278-2
Aptamer: G
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTAACGGCTTCCAAACTAGCTACCCGGATAGAATTCCCTATAGTGAGTCGTATTAAGGCTAGTAAGCTTGCCGT3'
Sequence length: 106
GC content: 0.4433962264150943
Affinity: Kd: 228.4 nM and 7485.3 nM *this Kd was determined with affinity test on entire n round pool
Pool type: 5'-TAATACGACTCACTATAGGGAATTCTATCCGGGTA-N25-GCTAGTAAGCTTGCCGT-3'
Pool random region: 25
Binding buffer/conditions: EMSA binding buffer: 1 pmol BSA, Streptavidin and ANEPIII (5 µL total volume each)
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Current immunoassays detecting MUC1 are sensitive for predicting relapse in breast cancer, but they are not in widespread use in the follow-up of this disease. It has therefore been proposed that aptamers may offer this additional advantage in improving the sensitivity of such immunoassays."
Reference (2008, Arch Pharm Res ): Zhu, J., Wang, J., Su, Z. C., Li, Q., Cheng, M. S., & Zhang, J. H. (2008). Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Archives of pharmacal research, 31(9), 1120–1128. https://doi.org/10.1007/s12272-001-1278-2
Aptamer: H
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTACGGCTTCCAAACTAGCTACCGGGATTGAATTCCCTATAGTGAGTCGTATTAGCTAGTAAGCTTGCCGT3'
Sequence length: 103
GC content: 0.4466019417475728
Affinity: Kd: 228.4 nM and 7485.3 nM *this Kd was determined with affinity test on entire n round pool
Pool type: 5'-TAATACGACTCACTATAGGGAATTCTATCCGGGTA-N25-GCTAGTAAGCTTGCCGT-3'
Pool random region: 25
Binding buffer/conditions: EMSA binding buffer: 1 pmol BSA, Streptavidin and ANEPIII (5 µL total volume each)
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Current immunoassays detecting MUC1 are sensitive for predicting relapse in breast cancer, but they are not in widespread use in the follow-up of this disease. It has therefore been proposed that aptamers may offer this additional advantage in improving the sensitivity of such immunoassays."
Reference (2008, Arch Pharm Res ): Zhu, J., Wang, J., Su, Z. C., Li, Q., Cheng, M. S., & Zhang, J. H. (2008). Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Archives of pharmacal research, 31(9), 1120–1128. https://doi.org/10.1007/s12272-001-1278-2
Aptamer: I
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTAAAGCTGGCCACCGGAAGACTGGAGATCTGGATCCCTGCTAGTAAGCTTGCCGT3'
Sequence length: 88
GC content: 0.5
Affinity: Kd: 228.4 nM and 7485.3 nM *this Kd was determined with affinity test on entire n round pool
Pool type: 5'-TAATACGACTCACTATAGGGAATTCTATCCGGGTA-N25-GCTAGTAAGCTTGCCGT-3'
Pool random region: 25
Binding buffer/conditions: EMSA binding buffer: 1 pmol BSA, Streptavidin and ANEPIII (5 µL total volume each)
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Current immunoassays detecting MUC1 are sensitive for predicting relapse in breast cancer, but they are not in widespread use in the follow-up of this disease. It has therefore been proposed that aptamers may offer this additional advantage in improving the sensitivity of such immunoassays."
Reference (2008, Arch Pharm Res ): Zhu, J., Wang, J., Su, Z. C., Li, Q., Cheng, M. S., & Zhang, J. H. (2008). Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Archives of pharmacal research, 31(9), 1120–1128. https://doi.org/10.1007/s12272-001-1278-2
Aptamer: 10.10
Target: Anthracyclines daunomycin and doxorubicin
Type of nucleic acid: ssDNA
Sequence: 5'GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG3'
Sequence length: 80
GC content: 0.5875
Affinity: Kd: 20 nM
Pool type: 5'-GGGAATTCGAGCTCGGTACC-N40-CCAAGCTTGCATGCCTGCAG-'3
Pool random region: 40
Binding buffer/conditions: BP-T (20 mM Tris–HCl [pH 7.4], 140 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2, and 0.05% [v/v] Tween 20)
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: Detection: " We describe the characterization of a DNA aptamer that displays high affinity and specificity for the anthracyclines daunomycin and doxorubicin, both of which are frequently used in chemotherapy. This not only allows the determination of the aptamer's specificity but also allows the quantification of as little as 8.4 microg/L daunomycin and doxorubicin."
Additional information: Inconsistency in reporting aptamer sequence (reverse primer region in aptamer sequence does not match the reported pool type)
Reference (2008, Anal Biochem ): Wochner, A., Menger, M., Orgel, D., Cech, B., Rimmele, M., Erdmann, V. A., & Glökler, J. (2008). A DNA aptamer with high affinity and specificity for therapeutic anthracyclines. Analytical biochemistry, 373(1), 34–42. https://doi.org/10.1016/j.ab.2007.09.007