RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: LDH7r-9
Target: Lactate dehydrogenase (LDH), Human
Type of nucleic acid: ssDNA
Sequence: 5'ATAGGAGTCACGACGACCAGAAAGAGTGCTACAGCATGATGGTTTGGGCACCGTACCGAACGTATGTGCGTCTACCTCTTGACTAAT3'
Sequence length: 87
GC content: 0.4942528735632184
Affinity: Kd: 12.0 ± 4.4 nM
Pool type: 5'-ATAGGAGTCACGACGACCAGAA-N40-TATGTGCGTCTACCTCTTGACTAAT-3'
Pool random region: 40
Binding buffer/conditions: 50 mM Tris-HCl, 5 mM KCl, 100 mM NaCl, 1 mM MgCl2, pH 7.4
Divalent salt: MgCl
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: " This study provides new ideas for rapid detection of LDH protein content and enzyme activity, thus contributing to the development of rapid medical detection and also provided new ideas for the rapid detection of other serum markers. This aptamer sequence has the potential use for LDH content and enzyme activity detections, which could further combine with the microfluidic chip and surface-enhanced Raman spectroscopy to construct a high-efficiency and low-cost method for rapid disease diagnosis."
Reference (2021, Anal Bioanal Chem ): Guo, L., Song, Y., Yuan, Y. et al. Identification of nucleic acid aptamers against lactate dehydrogenase via SELEX and high-throughput sequencing. Anal Bioanal Chem 413, 4427–4439 (2021). https://doi.org/10.1007/s00216-021-03397-2
Aptamer: LDH8r-2
Target: Lactate dehydrogenase (LDH), Human
Type of nucleic acid: ssDNA
Sequence: 5'ATAGGAGTCACGACGACCAGAAAGACTTCCGATAGGTTAGGGTTATAGAAAATGCAGGGGAGTAAAAAGAGCTATGTGCGTCTACCTCTTGACTAAT3'
Sequence length: 97
GC content: 0.4329896907216495
Affinity: Kd: 10.2 ± 4.7 nM
Pool type: 5'-ATAGGAGTCACGACGACCAGAA-N50-TATGTGCGTCTACCTCTTGACTAAT-3'
Pool random region: 50
Binding buffer/conditions: 50 mM Tris-HCl, 5 mM KCl, 100 mM NaCl, 1 mM MgCl2, pH 7.4
Divalent salt: MgCl
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: " This study provides new ideas for rapid detection of LDH protein content and enzyme activity, thus contributing to the development of rapid medical detection and also provided new ideas for the rapid detection of other serum markers. This aptamer sequence has the potential use for LDH content and enzyme activity detections, which could further combine with the microfluidic chip and surface-enhanced Raman spectroscopy to construct a high-efficiency and low-cost method for rapid disease diagnosis."
Reference (2021, Anal Bioanal Chem ): Guo, L., Song, Y., Yuan, Y. et al. Identification of nucleic acid aptamers against lactate dehydrogenase via SELEX and high-throughput sequencing. Anal Bioanal Chem 413, 4427–4439 (2021). https://doi.org/10.1007/s00216-021-03397-2
Aptamer: LDH9r-1
Target: Lactate dehydrogenase (LDH), Human
Type of nucleic acid: ssDNA
Sequence: 5'ATAGGAGTCACGACGACCAGAAGCATGTGAGGAGAGAACAAATGAAGTGGCCTATGTGCGTCTACCTCTTGACTAAT3'
Sequence length: 77
GC content: 0.4675324675324675
Affinity: Kd: 19.3 ± 6.2 nM
Pool type: 5'-ATAGGAGTCACGACGACCAGAA-N30-TATGTGCGTCTACCTCTTGACTAAT-3'
Pool random region: 30
Binding buffer/conditions: 50 mM Tris-HCl, 5 mM KCl, 100 mM NaCl, 1 mM MgCl2, pH 7.4
Divalent salt: MgCl
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: " This study provides new ideas for rapid detection of LDH protein content and enzyme activity, thus contributing to the development of rapid medical detection and also provided new ideas for the rapid detection of other serum markers. This aptamer sequence has the potential use for LDH content and enzyme activity detections, which could further combine with the microfluidic chip and surface-enhanced Raman spectroscopy to construct a high-efficiency and low-cost method for rapid disease diagnosis."
Reference (2021, Anal Bioanal Chem ): Guo, L., Song, Y., Yuan, Y. et al. Identification of nucleic acid aptamers against lactate dehydrogenase via SELEX and high-throughput sequencing. Anal Bioanal Chem 413, 4427–4439 (2021). https://doi.org/10.1007/s00216-021-03397-2
Aptamer: Aptamer-1
Target: Receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein (S/RBD)
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCATCGAGTGGCTTGTTTGTAATGTAGGGTTCCGGTCGTGGGTTGGACACGGTGGCTTAGT3'
Sequence length: 76
GC content: 0.5394736842105263
Affinity: Kd: 6.05 ± 2.05 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N40-TGGACACGGTGGCTTAGT-3'
Pool random region: 40
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Because of its critical function in host cell entry and virus dissemination, S/RBD is an ideal target for the development of vaccines, neutralizing antibodies, and blocking inhibitors. To enhance the degree of effective virus neutralization, aptamer cocktails that allow targeting of multiple S/RBD epitopes may show promise. The development of neutralizing aptamers provides a new promising therapeutic approach to treat COVID‐19, in addition to neutralization antibodies and molecular blockers."
Additional information: Labeled with a Cy3 fluorescent reporter at 5′ end for functional assessment.
Reference (2021, Angew Chem Int Ed Engl ): Liu, X., Wang, Y. L., Wu, J., Qi, J., Zeng, Z., Wan, Q., Chen, Z., Manandhar, P., Cavener, V. S., Boyle, N. R., Fu, X., Salazar, E., Kuchipudi, S. V., Kapur, V., Zhang, X., Umetani, M., Sen, M., Willson, R. C., Chen, S. H., & Zu, Y. (2021). Neutralizing Aptamers Block S/RBD-ACE2 Interactions and Prevent Host Cell Infection. Angewandte Chemie (International ed. in English), 60(18), 10273–10278. https://doi.org/10.1002/anie.202100345
Aptamer: Aptamer-2
Target: Receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein (S/RBD)
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCAATTACCGATGGCTTGTTTGTAATGTAGGGTTCCGTCGGATTGGACACGGTGGCTTAGT3'
Sequence length: 76
GC content: 0.5
Affinity: Kd: 6.95 ± 1.10 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N40-TGGACACGGTGGCTTAGT-3'
Pool random region: 40
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Because of its critical function in host cell entry and virus dissemination, S/RBD is an ideal target for the development of vaccines, neutralizing antibodies, and blocking inhibitors. To enhance the degree of effective virus neutralization, aptamer cocktails that allow targeting of multiple S/RBD epitopes may show promise. The development of neutralizing aptamers provides a new promising therapeutic approach to treat COVID‐19, in addition to neutralization antibodies and molecular blockers."
Additional information: Labeled with a Cy3 fluorescent reporter at 5′ end for functional assessment.
Reference (2021, Angew Chem Int Ed Engl ): Liu, X., Wang, Y. L., Wu, J., Qi, J., Zeng, Z., Wan, Q., Chen, Z., Manandhar, P., Cavener, V. S., Boyle, N. R., Fu, X., Salazar, E., Kuchipudi, S. V., Kapur, V., Zhang, X., Umetani, M., Sen, M., Willson, R. C., Chen, S. H., & Zu, Y. (2021). Neutralizing Aptamers Block S/RBD-ACE2 Interactions and Prevent Host Cell Infection. Angewandte Chemie (International ed. in English), 60(18), 10273–10278. https://doi.org/10.1002/anie.202100345
Aptamer: Aptamer-6
Target: Receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein (S/RBD)
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCAGGGCTTGGGTTGGGAATAAGGATGTGGGAGGCGGCGAACATGGACACGGTGGCTTAGT3'
Sequence length: 76
GC content: 0.5789473684210527
Affinity: Kd: 7.52 ± 3.20 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N40-TGGACACGGTGGCTTAGT-3'
Pool random region: 40
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Because of its critical function in host cell entry and virus dissemination, S/RBD is an ideal target for the development of vaccines, neutralizing antibodies, and blocking inhibitors. To enhance the degree of effective virus neutralization, aptamer cocktails that allow targeting of multiple S/RBD epitopes may show promise. The development of neutralizing aptamers provides a new promising therapeutic approach to treat COVID‐19, in addition to neutralization antibodies and molecular blockers."
Additional information: Labeled with a Cy3 fluorescent reporter at 5′ end for functional assessment.
Reference (2021, Angew Chem Int Ed Engl ): Liu, X., Wang, Y. L., Wu, J., Qi, J., Zeng, Z., Wan, Q., Chen, Z., Manandhar, P., Cavener, V. S., Boyle, N. R., Fu, X., Salazar, E., Kuchipudi, S. V., Kapur, V., Zhang, X., Umetani, M., Sen, M., Willson, R. C., Chen, S. H., & Zu, Y. (2021). Neutralizing Aptamers Block S/RBD-ACE2 Interactions and Prevent Host Cell Infection. Angewandte Chemie (International ed. in English), 60(18), 10273–10278. https://doi.org/10.1002/anie.202100345
Aptamer: SKBR3-R1
Target: SKBR3 spheroid breast cancer cells, Human
Type of nucleic acid: ssDNA
Sequence: 5′ATCCAGAGTGACGCAGCATCGTTGCTAATAGTGCCGACGCCGGCGAAATTAATAGGTCGGTCACTTCTCCTGTAGGCACCATCAATC3′
Sequence length: 87
GC content: 0.5172413793103449
Affinity: Not reported
Pool type: 5′-ATCCAGAGTGACGCAGCA-N51-CTGTAGGCACCATCAATC-3′
Pool random region: 51
Binding buffer/conditions: DPBS, 5 mM MgCl2, 22.5 mM d-glucose, 1 mg/mL BSA, and 100 μg/mL tRNA (Baker's Yeast)
Divalent salt: MgCl
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: " We identified DNA aptamers that bind with high affinity and specificity to SKBR3 spheroid breast cancer cells. Using a modular polymeric approach, we constructed multivalent aptamer polymers with DNA boxes carrying doxorubicin payloads that are effective and specific in killing target breast cancer cells. The innovative modular DNA aptamer platform based on 3D Cell SELEX and polymer multivalency holds great promise for diagnostics and treatment of breast cancer."
Reference (2021, Pharmaceuticals (Basel) ): Nelissen, F., Peeters, W., Roelofs, T. P., Nagelkerke, A., Span, P. N., & Heus, H. A. (2021). Improving Breast Cancer Treatment Specificity Using Aptamers Obtained by 3D Cell-SELEX. Pharmaceuticals (Basel, Switzerland), 14(4), 349. https://doi.org/10.3390/ph14040349
Aptamer: T18.3
Target: Factors V and Va (FV and FVa)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGACUUGGAUAACCUCACCGCAAUGGCGGCUUGUCAGACGACUCGCUGAGGAUCCGAG3'
Sequence length: 58
GC content: 0.5862068965517241
Affinity: Kd: 11.4 ± 3.0 nM (FV); Kd: 4.73 ± 0.69 nM (FVa)
Pool type: 5'-GGGAGGACGAUGCGG-N40-CAGACGACUCGCUGAGGAUCCGAGA-3'
Pool random region: 40
Binding buffer/conditions: 20 mM Hepes pH 7.4, 150 mM NaCl, 2 mM CaCl2
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: " Our success in generating an anticoagulant aptamer targeting FV/Va demonstrates the feasibility of using cofactor-binding aptamers as therapeutic protein inhibitors and reveals an unconventional working mechanism of an aptamer by interrupting protein-membrane interactions."
Additional information: all C and U were 2'F modified
Reference (2022, Cell Chem Biol ): Soule, E. E., Yu, H., Olson, L., Naqvi, I., Kumar, S., Krishnaswamy, S., & Sullenger, B. A. (2022). Generation of an anticoagulant aptamer that targets factor V/Va and disrupts the FVa-membrane interaction in normal and COVID-19 patient samples. Cell chemical biology, 29(2), 215–225.e5. https://doi.org/10.1016/j.chembiol.2022.01.009
Aptamer: CD44E-Apt01
Target: Hepatocellular carcinoma (HCC) CD44E
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCATCGCAACGATTAGTATGCACCCACCGTATAGGTTGGTCTCTGGACACGGTGGCTTAGT3'
Sequence length: 76
GC content: 0.5263157894736842
Affinity: Kd: 1.22 ± 0.31 nM
Pool type: 5'ATCCAGAGTGACGCAGCA-N40-TGGACACGGTGGCTTAGT3'
Pool random region: 40
Binding buffer/conditions: 1 L of DPBS with 4.5 g of glucose, 100 mg yeast tRNA, 1g BSA, and 5 ml of MgCl2 1M
Divalent salt: MgCl
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: Drug Delivery: " The high cell-penetrating capability and drug guiding ability of CD44-Apt1 could serve as a useful tool to efficiently arrest CD44E/s-positive HCC tumors through guiding therapies. Our findings both in vitro and in vivo concurred in highlighting the great potential of CD44E/s aptamers as a drug guiding probe. Other than by oligo synthesis-based conjugation method, as shown in linking aptamers with 5-FU in our study, CD44E/s aptamers could also be loaded with other therapeutic drugs, for instance sorafenib which is the first-line FDA approved drug for HCC, by methods such as liposome-based nanocarriers. It could also be linked with siRNA/miRNA for targeted gene therapy."
Reference (2022, Nanotheranostics ): Lo, C. W., Chan, C., Yu, J., He, M., Choi, C., Lau, J., & Wong, N. (2022). Development of CD44E/s dual-targeting DNA aptamer as nanoprobe to deliver treatment in hepatocellular carcinoma. Nanotheranostics, 6(2), 161–174. https://doi.org/10.7150/ntno.62639
Aptamer: CD44E-Apt01
Target: Hepatocellular carcinoma (HCC) CD44s
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCATCGCAACGATTAGTATGCACCCACCGTATAGGTTGGTCTCTGGACACGGTGGCTTAGT3'
Sequence length: 76
GC content: 0.5263157894736842
Affinity: Kd: 2.09 ± 0.29 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N40-TGGACACGGTGGCTTAGT-3'
Pool random region: 40
Binding buffer/conditions: 1 L of DPBS with 4.5 g of glucose, 100 mg yeast tRNA, 1g BSA, and 5 ml of MgCl2 1M
Divalent salt: MgCl
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: Drug Delivery: " The high cell-penetrating capability and drug guiding ability of CD44-Apt1 could serve as a useful tool to efficiently arrest CD44E/s-positive HCC tumors through guiding therapies. Our findings both in vitro and in vivo concurred in highlighting the great potential of CD44E/s aptamers as a drug guiding probe. Other than by oligo synthesis-based conjugation method, as shown in linking aptamers with 5-FU in our study, CD44E/s aptamers could also be loaded with other therapeutic drugs, for instance sorafenib which is the first-line FDA approved drug for HCC, by methods such as liposome-based nanocarriers. It could also be linked with siRNA/miRNA for targeted gene therapy."
Reference (2022, Nanotheranostics ): Lo, C. W., Chan, C., Yu, J., He, M., Choi, C., Lau, J., & Wong, N. (2022). Development of CD44E/s dual-targeting DNA aptamer as nanoprobe to deliver treatment in hepatocellular carcinoma. Nanotheranostics, 6(2), 161–174. https://doi.org/10.7150/ntno.62639
Aptamer: glu1d04
Target: Glutamate/Glutamic Acid
Type of nucleic acid: ssDNA
Sequence: 5'GCATCAGTCCACTCGTGAGGTCGACTGATGAGGCTCGATCAGGAGCGCCGCTCGATCGCACTTTCACAGGATAGTAGTTGGTAGCGACCTCTGCTAGA3'
Sequence length: 98
GC content: 0.5612244897959183
Affinity: Kd:12 ± 6 µM
Pool type: 5-GCATCAGTCCACTCGTGA-N10-TGAGGCTCGAT-N42-AGCGACCTCTGCTAGA-3'
Pool random region: 52
Binding buffer/conditions: Selection buffer (SB buffer) [100 mM NaCl, 20 mM Tris–HCl, 5 mM KCl, 2 mM MgCl2, 1 mM CaCl2, pH 7.6]
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Diagnostic: " Given this physiological importance, glutamic acid and the dynamics of its level in nervous tissue are important subjects of study. Therefore, noninvasive, easy-to-use specific and high-affinity detection methods are highly relevant for monitoring glutamic acid levels for both scientific and clinical purposes. It is well suited for point-of-care applications. Furthermore, future advancements in aptamer/transducer implementation, for instance, in microelectrode arrays, can be envisioned for this novel receptor, which will benefit monitoring of the release of the neurotransmitter glutamate in vitro and in vivo. Furthermore, the distinct on-signal response suggests a considerable analyte-induced conformation change, which can be utilized to realize molecular beacon-based sensors."
Reference (2022, Anal Bioanal Chem ): Wu, C., Barkova, D., Komarova, N., Offenhäusser, A., Andrianova, M., Hu, Z., Kuznetsov, A., & Mayer, D. (2022). Highly selective and sensitive detection of glutamate by an electrochemical aptasensor. Analytical and bioanalytical chemistry, 414(4), 1609–1622. https://doi.org/10.1007/s00216-021-03783-w
Aptamer: glu1
Target: Glutamate/Glutamic Acid
Type of nucleic acid: ssDNA
Sequence: 5'GCATCAGTCCACTCGTGAGGTCGACTGATGAGGCTCGAT3'
Sequence length: 39
GC content: 0.5641025641025641
Affinity: Not reported
Pool type: 5-GCATCAGTCCACTCGTGA-N10-TGAGGCTCGAT-N42-AGCGACCTCTGCTAGA-3'
Pool random region: 52
Binding buffer/conditions: Selection buffer (SB buffer) [100 mM NaCl, 20 mM Tris–HCl, 5 mM KCl, 2 mM MgCl2, 1 mM CaCl2, pH 7.6]
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated sequnce
Application as quoted in the referenced paper: Biosensors: " A truncation permitted implementation of the aptamer in an electrochemical sensor. Therefore, this short aptamer sequence was modified with a thiol binding group and ferrocene redox probes to facilitate amperometric glutamate detection. The proposed aptasensor exhibited a wide concentration detection range from 0.01 pM to 1 nM with a low detection limit at the fM level for a very light molecule. This performance is sensitive enough to detect physiological concentrations of glutamate in various in vitro and in vivo samples."
Additional information: glu1 was labelled with a ferrocene redox tag at the 3′-end and immobilized on a gold electrode surface via Au-thiol bonds. Using 6-mercapto-1-hexanol as the backfill, the sensor performance was characterized by alternating current voltammetry. The glu1 aptasensor showed a limit of detection of 0.0013 pM, a wide detection range between 0.01 pM and 1 nM, and good selectivity for glutamate in tenfold diluted human serum
Reference (2022, Anal Bioanal Chem ): Wu, C., Barkova, D., Komarova, N., Offenhäusser, A., Andrianova, M., Hu, Z., Kuznetsov, A., & Mayer, D. (2022). Highly selective and sensitive detection of glutamate by an electrochemical aptasensor. Analytical and bioanalytical chemistry, 414(4), 1609–1622. https://doi.org/10.1007/s00216-021-03783-w
Aptamer: C7
Target: SARS-CoV-2 Spike glycoprotein
Type of nucleic acid: ssDNA
Sequence: 5'CACGACGACAGAGACCACAGCACGTGGCCCACGTTAATCCGTTATAAGTCAAGCTCGATCCAGCAGCCAGAGACGAACA3'
Sequence length: 79
GC content: 0.5443037974683544
Affinity: Kd: 89.41 ± 18 nM
Pool type: 5'-CACGACGACAGAGACCACAG-N40-CCAGCAGCCAGAGACGAACA-3'
Pool random region: 40
Binding buffer/conditions: 50 mM Tris-HCl pH 7.0, 110 mM NaCl, 1 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor: " The rapid spread of SARS-CoV-2 infection throughout the world led to a global public health and economic crisis triggering an urgent need for the development of low-cost vaccines, therapies and high-throughput detection assays. In this work, we used a combination of Ideal-Filter Capillary Electrophoresis SELEX (IFCE-SELEX), Next Generation Sequencing (NGS) and binding assays to isolate and validate single-stranded DNA aptamers that can specifically recognize the SARS-CoV-2 Spike glycoprotein. Two selected non-competing DNA aptamers, C7 and C9 were successfully used as sensitive and specific biological recognition elements for the development of electrochemical and fluorescent aptasensors for the SARS-CoV-2 Spike glycoprotein"
Reference (2022, Anal Biochem ): Martínez-Roque, M. A., Franco-Urquijo, P. A., García-Velásquez, V. M., Choukeife, M., Mayer, G., Molina-Ramírez, S. R., Figueroa-Miranda, G., Mayer, D., & Alvarez-Salas, L. M. (2022). DNA aptamer selection for SARS-CoV-2 spike glycoprotein detection. Analytical biochemistry, 645, 114633. https://doi.org/10.1016/j.ab.2022.114633
Aptamer: AptOle1#6
Target: Olive (Olea europaea L.) pollen 1 (Ole e 1)
Type of nucleic acid: ssDNA
Sequence: 5'GCGGATGAAGACTGGTGTAGAGGCATCGTTGCCTGGTTTTATTTCCTGCCCCATTGCTGCCCTAAATACGAGCAAC3'
Sequence length: 76
GC content: 0.5131578947368421
Affinity: Not reported
Pool type: 5'-GCGGATGAAGACTGGTCT-N40-GTTGCTCGTATTTAGGGC-3'
Pool random region: 40
Binding buffer/conditions: 20 mM Tris-HCl pH 7.4, 1 mM MgCl2, 150 mM NaCl, 5 mM KCl
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: 20 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic, Therapeutic: " Our results indicate that aptamer AptOle1#6 provided the highest binding for this allergenic protein. Besides, the aptamer affinity monolith with the selected oligonucleotide sequence was successfully applied to recognize Ole e 1 in allergy skin test. All these results demonstrate that the aptamers and aptamer-based methodologies (e.g. affinity monolithic columns) can potentially serve as powerful analytical tools in separation, enrichment and diagnostic of allergenic proteins in therapeutic and clinical fields."
Reference (2022, Anal Chim Acta ): Vergara-Barberán, M., Lerma-García, M. J., Simó-Alfonso, E. F., García-Hernández, M., Martín, M. E., García-Sacristán, A., González, V. M., & Herrero-Martínez, J. M. (2022). Selection and characterization of DNA aptamers for highly selective recognition of the major allergen of olive pollen Ole e 1. Analytica chimica acta, 1192, 339334. https://doi.org/10.1016/j.aca.2021.339334
Aptamer: AP-9R
Target: Cancer stem cells (CSCs) A549 shEcad cells
Type of nucleic acid: ssDNA
Sequence: 5'ACAGCACCACAGACCAGTGCTTTATTATTCCTATTTTGATTCGACGCCAGTTACGGTGTTTGTCTTCCTGCC3'
Sequence length: 72
GC content: 0.4583333333333333
Affinity: Kd: 54.29 ± 9.55 nM
Pool type: 5′-GGCAGGAAGACAAACA-N40-GGTCTGTGGTGCTGT-3′
Pool random region: 40
Binding buffer/conditions: 1 L of DPBS, 4.5 g of glucose, 100 mg of tRNA, 1 g of bovine serum albumin (BSA), and 5 mL of 1 M MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 38 kDa
Application as quoted in the referenced paper: Biomaker, Therapeutic, Diagnostic: " The expression of Annexin A2 was associated with signatures of stemness and metastasis, as well as poor clinical outcomes, in lung cancer in silico. Moreover, AP-9R decreased Annexin A2 expression and suppressed CSC properties in CSCs in vitro and in vivo. The present findings suggest that Annexin A2 is a CSC marker and regulator, and the CSC-specific aptamer AP-9R has potential theranostic applications for lung cancer."
Additional information: Secondary strucutre sequence does not match with the given pool sequnce. They both have 72 sequence.
Reference (2022, Mol Ther Nucleic Acids ): Wu, Y. Y., Hsieh, I. S., Tung, C. H., Weng, C. H., Wu, J. E., Yu, J. S., Hong, T. M., & Chen, Y. L. (2022). A novel DNA aptamer targeting lung cancer stem cells exerts a therapeutic effect by binding and neutralizing Annexin A2. Molecular therapy. Nucleic acids, 27, 956–968. https://doi.org/10.1016/j.omtn.2022.01.012