RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: sk6Ea
Target: Breast cancer cell line SK-BR-3, Human
Type of nucleic acid: ssDNA
Sequence: 5'TCACGCCCGATAAGGGCGATGCCGATCCCTGTGGCCGTAGGGCAGTCCCCTAG3'
Sequence length: 53
GC content: 0.660377358490566
Affinity: Kd: 49.32 ± 14.53 nM
Pool type: 5′-AGCAGAGTTCACGACCCGATAAG-N40-GAGTTACATACCAATCGTCGCAG-3′
Pool random region: 40
Binding buffer/conditions: Phosphate-buffered saline (PBS, pH 7.4), 4.5 g/L glucose, 5 mM MgCl2, 0.1 mg/mL yeast tRNA, and 1 mg/mL bovine serum albumin
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: Diagnostic and Therapeutic: " Molecular subtyping of breast cancer is of considerable interest owing to its potential for personalized therapy and prognosis. The aim of the present study is to develop a cell-specific single-stranded DNA (ssDNA) aptamer-based fluorescence probe for molecular subtyping of breast cancer. The results suggest that the aptamer-based probe is a powerful tool for fast and highly sensitive subtyping of breast cancer both in vitro and in vivo and is also very promising for the identification, diagnosis, and targeted therapy of breast cancer molecular subtypes."
Reference (2018, Theranostics ): Liu, M., Wang, Z., Tan, T., Chen, Z., Mou, X., Yu, X., Deng, Y., Lu, G., & He, N. (2018). An Aptamer-Based Probe for Molecular Subtyping of Breast Cancer. Theranostics, 8(20), 5772–5783. https://doi-org.ezproxy.lib.utexas.edu/10.7150/thno.28949
Aptamer: PB aptamer
Target: Prostate cancer bone metastasis (PB)
Type of nucleic acid: ssDNA
Sequence: 5'CGCTCGATCGATCTAGATTCGCTCTATTGATGCCTGCGTGCGTGCTTGTAGCAGTGATCTGAGCGTGATGAC3'
Sequence length: 72
GC content: 0.5277777777777778
Affinity: Not reported
Pool type: 5'-CGCTCGATCGATCTAGATTCG-N30-CAGTGATCTGAGCGTGATGAC-3'
Pool random region: 30
Binding buffer/conditions: 4.5 mg/mL glucose, 1 mg/mL BSA, 0.1 mg/mL tRNA, 5 nM MgSO4
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Drug Delivery and Therapeutic: " PB is one of the most severe complications of late stage prostate cancer and negatively impacts patient quality of life. We aimed to explore the use of aptamers as promising tools to develop a targeted drug delivery system for PBs. In vivo SELEX was applied to identify bone targeting aptamer in a mouse model with PBs. This investigation highlights the promise of in vivo SELEX for the discovery of bone targeting aptamers for use in drug delivery."
Reference (2018, Int J Nanomedicine ): Chen, L., He, W., Jiang, H., Wu, L., Xiong, W., Li, B., Zhou, Z., & Qian, Y. (2018). In vivo SELEX of bone targeting aptamer in prostate cancer bone metastasis model. International journal of nanomedicine, 14, 149–159. https://doi.org/10.2147/IJN.S188003
Aptamer: E2 aptamer
Target: 17 beta-Estradiol (17β-Estradiol) (E2）
Type of nucleic acid: ssDNA
Sequence: 5′AAGGGATGCCGTTTGGGCCCAAGTTCGGCATAGTG3′
Sequence length: 35
GC content: 0.5714285714285714
Affinity: Kd: 36 μM
Pool type: Not reported
Binding buffer/conditions: 100 mM MES pH 5
Buffer type: Other Buffers
pH: 5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Micro-pollutants such as 17β-Estradiol (E2) have been detected in different water resources and their negative effects on the environment and organisms have been observed. In this study, a previously described 35-mer E2-specific aptamer was used to analyse the binding characteristics between E2 and the aptamer with a MD simulation in an aqueous medium. The study contributes to the understanding of the behavior of ligands binding with aptamer structure in an aqueous solution. The developed workflow allows generating and examining further appealing ligand-aptamer complexes."
Additional information: *paper does not seem to discover any aptamers but instead studies an already known aptamer. The original pool is: 5'-CGAAGCGCTAGAACAT-N40-AGTACATGAGACTTAGCTGATCCTGATGG-3' (Akki, S. U., Werth, C. J., & Silverman, S. K. (2015). Selective Aptamers for Detection of Estradiol and Ethynylestradiol in Natural Waters. Environmental science & technology, 49(16), 9905–9913. https://doi.org/10.1021/acs.est.5b02401)
Reference (2018, Molecules ): Eisold, A., & Labudde, D. (2018). Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study. Molecules (Basel, Switzerland), 23(7), 1690. https://doi.org/10.3390/molecules23071690
Aptamer: CAIX aptamer
Target: Carbonic anhydrase IX (CAIX)
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGATGTGGTGCGCAGTGATGTGGTTGGTCCTATGCGTGCTACCGTCCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.5625
Affinity: Kd: 37.17±1.20 au
Pool type: Not reported
Binding buffer/conditions: PBS
Buffer type: PBS/phosphate buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Caix aptamer modified with a thiol group at the 3′ terminus and 6-carboxyfluorescein (6-fam) at the 5′ terminus.
Application as quoted in the referenced paper: Diagnositc: " Targeted nanobubbles can penetrate the tumor vasculature and achieve ultrasound molecular imaging (USMI) of tumor parenchymal cells. Targeted nanobubbles loaded with carbonic anhydrase IX (CAIX) aptamer were fabricated for USMI of various tumors, and the morphological basis of USMI with targeted nanobubbles was investigated. Targeted nanobubbles loaded with CAIX aptamer have a good imaging effect in USMI of tumor parenchymal cells, and can improve the accuracy of early diagnosis of malignant tumors from various organs."
Additional information: No primers were mentioned.
Reference (2018, Int J Nanomedicine ): Zhu, L., Wang, L., Liu, Y., Xu, D., Fang, K., & Guo, Y. (2018). CAIX aptamer-functionalized targeted nanobubbles for ultrasound molecular imaging of various tumors. International journal of nanomedicine, 13, 6481–6495. https://doi.org/10.2147/IJN.S176287
Aptamer: Apt-1
Target: Vibrio parahaemolyticus (V. parahaemolyticus)
Type of nucleic acid: ssDNA
Sequence: 5'TCAGCACGTAGCCCTATTTGTTTTCTCTTGTCTCTGTACTGCTGATGTTGGTCATTCTCTTTTCTCGGTTCCACTGAGAGATCC3'
Sequence length: 84
GC content: 0.4523809523809524
Affinity: Kd: 19.2 ± 2.8 nM
Pool type: 5'-TCAGCACGT-N60-TCCACTGAGAGATCC-3'
Pool random region: 60
Binding buffer/conditions: Binding Buffer (1X BB): 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, 4 mg/L BSA, 0.05% v/v Tween-20.
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor: " Here, we developed an advanced cell-SELEX strategy featuring functionalized graphene oxide (GO) and isothermal rolling circle amplification (RCA) to select aptamers against a prevailing foodborne pathogen, Vibrio parahaemolyticus. Simple procedure, high efficiency, and free from expensive thermal cycler (required by PCR amplification) will enable the established strategy to find its applications in aptamer selecting against fungi, stem and cancerous cells as well."
Reference (2018, Anal Chim Acta ): Song, S., Wang, X., Xu, K., Li, Q., Ning, L., & Yang, X. (2019). Selection of highly specific aptamers to Vibrio parahaemolyticus using cell-SELEX powered by functionalized graphene oxide and rolling circle amplification. Analytica chimica acta, 1052, 153–162. https://doi.org/10.1016/j.aca.2018.11.047
Aptamer: Apt-3
Target: Vibrio parahaemolyticus (V. parahaemolyticus)
Type of nucleic acid: ssDNA
Sequence: 5'TCAGCACGTTATCTAGTCAGATATCCAGACAGTCGCGGCTGGAAGCTTCTGTTAAGAATTTGAGATACTTCCACTGAGAGATCC3'
Sequence length: 84
GC content: 0.4523809523809524
Affinity: Kd: 25.2 ± 3.1 nM
Pool type: 5'-TCAGCACGT-N60-TCCACTGAGAGATCC-3'
Pool random region: 60
Binding buffer/conditions: Binding Buffer (1X BB): 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, 4 mg/L BSA, 0.05% v/v Tween-20.
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor: " Here, we developed an advanced cell-SELEX strategy featuring functionalized graphene oxide (GO) and isothermal rolling circle amplification (RCA) to select aptamers against a prevailing foodborne pathogen, Vibrio parahaemolyticus. Simple procedure, high efficiency, and free from expensive thermal cycler (required by PCR amplification) will enable the established strategy to find its applications in aptamer selecting against fungi, stem and cancerous cells as well."
Reference (2018, Anal Chim Acta ): Song, S., Wang, X., Xu, K., Li, Q., Ning, L., & Yang, X. (2019). Selection of highly specific aptamers to Vibrio parahaemolyticus using cell-SELEX powered by functionalized graphene oxide and rolling circle amplification. Analytica chimica acta, 1052, 153–162. https://doi.org/10.1016/j.aca.2018.11.047
Aptamer: Apt-4
Target: Vibrio parahaemolyticus (V. parahaemolyticus)
Type of nucleic acid: ssDNA
Sequence: 5'TCAGCACGTGCGGGCATTATTGCACTCCACGGCGAGTAGTGCTCACAGAGTCATTTACACCGGTCGTATTCCACTGAGAGATCC3'
Sequence length: 84
GC content: 0.5357142857142857
Affinity: Kd: 17.2 ± 5.1 nM
Pool type: 5'-TCAGCACGT-N60-TCCACTGAGAGATCC-3'
Pool random region: 60
Binding buffer/conditions: Binding Buffer (1X BB): 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, 4 mg/L BSA, 0.05% v/v Tween-20.
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor: " Here, we developed an advanced cell-SELEX strategy featuring functionalized graphene oxide (GO) and isothermal rolling circle amplification (RCA) to select aptamers against a prevailing foodborne pathogen, Vibrio parahaemolyticus. Simple procedure, high efficiency, and free from expensive thermal cycler (required by PCR amplification) will enable the established strategy to find its applications in aptamer selecting against fungi, stem and cancerous cells as well."
Reference (2018, Anal Chim Acta ): Song, S., Wang, X., Xu, K., Li, Q., Ning, L., & Yang, X. (2019). Selection of highly specific aptamers to Vibrio parahaemolyticus using cell-SELEX powered by functionalized graphene oxide and rolling circle amplification. Analytica chimica acta, 1052, 153–162. https://doi.org/10.1016/j.aca.2018.11.047
Aptamer: HF3
Target: Paclitaxel-resistant ovarian cancer cells (A2780T)
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATATGCTTTCCGACCGTGTTCGTTTGTTATAACGGTGTTCCGTTCCGCGTTAGGGTGTGTCGTCGTGGT3'
Sequence length: 86
GC content: 0.5348837209302325
Affinity: Kd: 0.79 ± 0.38 nM
Pool type: 5′-AAGGAGCAGCGTGGAGGATA-N45-TTAGGGTGTGTCGTCGTGGT-3′
Pool random region: 45
Binding buffer/conditions: PBS with 4.5 g L−1 glucose, 1 MMm mg mL−1 bovine serum albumin (BSA), 0.1 mg mL−1 Herring sperm DNA, without any divalent ions
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " New ligands for drug-resistant ovarian cancer cells have potential for the development of diagnosis and therapy of ovarian cancer. In present work, we reported two aptamers, HF3-58 and HA5-68 generated by cell-SELEX, against a paclitaxel-resistant ovarian cancer cell line (A2780T). Owing to the structure stability and high resistance to nuclease, these two aptamers had good performance in the detection of drug-resistant ovarian cancer cells in human serum."
Reference (2018, Talanta ): He, J., Wang, J., Zhang, N., Shen, L., Wang, L., Xiao, X., Wang, Y., Bing, T., Liu, X., Li, S., & Shangguan, D. (2019). In vitro selection of DNA aptamers recognizing drug-resistant ovarian cancer by cell-SELEX. Talanta, 194, 437–445. https://doi.org/10.1016/j.talanta.2018.10.028
Aptamer: HA5
Target: Paclitaxel-resistant ovarian cancer cells (A2780T)
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATATCGGTGTTTATGGTGTCTGTCTTCCTCCAGTTTCCTTCTGCGCCTTTAGGGTGTGTCGTCGTGGT3'
Sequence length: 85
GC content: 0.5294117647058824
Affinity: Kd: 8.0 ± 6.7 nM
Pool type: 5′-AAGGAGCAGCGTGGAGGATA-N45-TTAGGGTGTGTCGTCGTGGT-3′
Pool random region: 45
Binding buffer/conditions: PBS with 4.5 g L−1 glucose, 1 MMm mg mL−1 bovine serum albumin (BSA), 0.1 mg mL−1 Herring sperm DNA, without any divalent ions
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " New ligands for drug-resistant ovarian cancer cells have potential for the development of diagnosis and therapy of ovarian cancer. In present work, we reported two aptamers, HF3-58 and HA5-68 generated by cell-SELEX, against a paclitaxel-resistant ovarian cancer cell line (A2780T). Owing to the structure stability and high resistance to nuclease, these two aptamers had good performance in the detection of drug-resistant ovarian cancer cells in human serum."
Reference (2018, Talanta ): He, J., Wang, J., Zhang, N., Shen, L., Wang, L., Xiao, X., Wang, Y., Bing, T., Liu, X., Li, S., & Shangguan, D. (2019). In vitro selection of DNA aptamers recognizing drug-resistant ovarian cancer by cell-SELEX. Talanta, 194, 437–445. https://doi.org/10.1016/j.talanta.2018.10.028
Aptamer: HF3–58
Target: Paclitaxel-resistant ovarian cancer cells (A2780T)
Type of nucleic acid: ssDNA
Sequence: 5'TTGGAGCAGCGTGGAGGATATGCTTTCCGACCGTGTTCGTTTGTTATAACGCTGCTCC3'
Sequence length: 58
GC content: 0.5172413793103449
Affinity: Kd: 0.30 ± 0.24 nM
Pool type: 5′-AAGGAGCAGCGTGGAGGATA-N45-TTAGGGTGTGTCGTCGTGGT-3′
Pool random region: 45
Binding buffer/conditions: PBS with 4.5 g L−1 glucose, 1 MMm mg mL−1 bovine serum albumin (BSA), 0.1 mg mL−1 Herring sperm DNA, without any divalent ions
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated 27 nucleotides from 3′ end and mutating 2 nucleotides in hf3 aptamer
Application as quoted in the referenced paper: Diagnostic: " New ligands for drug-resistant ovarian cancer cells have potential for the development of diagnosis and therapy of ovarian cancer. In present work, we reported two aptamers, HF3-58 and HA5-68 generated by cell-SELEX, against a paclitaxel-resistant ovarian cancer cell line (A2780T). Owing to the structure stability and high resistance to nuclease, these two aptamers had good performance in the detection of drug-resistant ovarian cancer cells in human serum."
Additional information: Two primers were used for PCR amplification: fluorescein (FAM)-labeled forward primer (5′-FAM-AAG GAG CAG CGT GGA GGA TA-3′) and biotin-labeled reverse primer (5′-biotin-ACC ACG ACG ACA CAC CCT AA-3′).
Reference (2018, Talanta ): He, J., Wang, J., Zhang, N., Shen, L., Wang, L., Xiao, X., Wang, Y., Bing, T., Liu, X., Li, S., & Shangguan, D. (2019). In vitro selection of DNA aptamers recognizing drug-resistant ovarian cancer by cell-SELEX. Talanta, 194, 437–445. https://doi.org/10.1016/j.talanta.2018.10.028
Aptamer: Apt928
Target: Cluster of differentiation 70 (CD70) protein
Type of nucleic acid: ssDNA
Sequence: 5′GCTGTGTGACTCCTGCAAGCGGGAAGAGGGCAGGGGAGGGAGGGTGACGCGGAAGAGGCAAGCAGCTGTATCTTGTCTCC3'
Sequence length: 80
GC content: 0.625
Affinity: Kd: 66 nM
Pool type: 5′-GCTGTGTGACTCCTGCAA-N43-GCAGCTGTATCTTGTCTCC-3′
Pool random region: 43
Binding buffer/conditions: 50 mmol L−1 K2HPO4, 150 mmol L−1 NaCl, 0.05% Tween-20, BSA 1 μg mL−1, 0.1 mg mL−1 yeast tRNA, pH 7.5
Buffer type: PBS/phosphate buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Single-stranded DNA aptamers recognizing CD70 molecule overexpressed in some tumor cell lines was isolated by means of systematic evolution of ligands by exponential enrichment (SELEX). Both purified CD70 protein and CD70-expressing cells were used to isolate target-specific aptamer. Moreover, ATTO 674N-labeled Apt928 was applied as a fluorescent aptasensor for rapid and sensitive detection of SKOV-3 cells as CD70-positive cells."
Reference (2018, Talanta ): Bayat, P., Taghdisi, S. M., Rafatpanah, H., Abnous, K., & Ramezani, M. (2019). In vitro selection of CD70 binding aptamer and its application in a biosensor design for sensitive detection of SKOV-3 ovarian cells. Talanta, 194, 399–405. https://doi.org/10.1016/j.talanta.2018.10.063
Aptamer: Fur_14
Target: Furaneol
Type of nucleic acid: ssDNA
Sequence: 5'CGACCAGCTCATTCCTCACCACGAGAAAGGAGCTCGATGAACTGCGACGGATTCGACCCTATGCGAGTAGGTGGTGGATCCGAGCTCACCAGT3'
Sequence length: 93
GC content: 0.5698924731182796
Affinity: Kd: 1.1 ± 0.4 µM
Pool type: 5′-CGACCAGCTCATTCCTCA-N10-GGAGTCTCGATG-N40-GGATCCGAGCTCACCAGTC-3′
Pool random region: 50
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris-HCl [pH 7.6], 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Detection: " Furaneol is an aroma compound which occurs naturally in foods and is used as an artificial flavor. Detection of furaneol is required in food science and food processing industry. Capture- Systematic Evolution of Ligands by EXponential enrichment (SELEX) protocol was applied for the isolation of an aptamer binding to furaneol, a small volatile organic substance contributing to the flavor of various products. The reported aptamer was applied for development of the ion-sensitive field-effect transistor (ISFET)-based biosensor, for the analysis of furaneol."
Reference (2018, Molecules ): Komarova, N., Andrianova, M., Glukhov, S., & Kuznetsov, A. (2018). Selection, Characterization, and Application of ssDNA Aptamer against Furaneol. Molecules (Basel, Switzerland), 23(12), 3159. https://doi.org/10.3390/molecules23123159
Aptamer: wh6
Target: Annexin A2 (ANXA2)
Type of nucleic acid: ssDNA
Sequence: 5'ACCGACCGTGCTGGACTCAGTCCGATCTCTCCACAGAGACAAACTTAGGACCCCTAGTCCCACTATGAGCGAGCCTGGCG3'
Sequence length: 80
GC content: 0.5875
Affinity: Kd: 8.75 ± 1.26 nM
Pool type: 5′-FITC-ACCGACCGTGCTGGACTCA-N42-ACTATGAGCGAGCCTGGCG-3'
Pool random region: 42
Binding buffer/conditions: 40 mmol/L HEPES pH 7.2, 100 mmol/L NaCl, 3 mmol/L MgCl2, 2.5 mmol/L KCl, 1% BSA, 10 μg/mL tRNA
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.2
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Diagnostic and Thereaputic: " Multiple myeloma (MM) is a malignant plasma cell disease and is considered incurable. Annexin A2 (ANXA2) is closely related to the proliferation and adhesion of MM. Using protein-SELEX, we performed a screen for aptamers that bind GST-ANXA2 from a library, and GST protein was used for negative selection. The binding specificity of aptamer wh6 was confirmed in vivo in nude mouse xenografts with MM cells and with MM bone marrow aspirates. Furthermore, aptamer wh6 can block MM cell adhesion to ANXA2 and block the proliferation of MM cells induced by ANXA2. In summary, wh6 can be considered a promising candidate tool for MM diagnosis and treatment."
Reference (2018, Biochimie ): Zhou, W., Zhang, Y., Zeng, Y., Peng, M., Li, H., Sun, S., Ma, B., Wang, Y., Ye, M., & Liu, J. (2018). Screening and characterization of an Annexin A2 binding aptamer that inhibits the proliferation of myeloma cells. Biochimie, 151, 150–158. https://doi.org/10.1016/j.biochi.2018.06.003
Aptamer: R12.45 Trunc.
Target: Atrazine
Type of nucleic acid: ssDNA
Sequence: 5'ACCGTCTGAGCGATTCGTACTTTATTCGGGAAGGGTATCAGCGGGG3'
Sequence length: 46
GC content: 0.5434782608695652
Affinity: Kd: 3.7 nM
Pool type: 5′-TGTACCGTCTGAGCGATTCGTAC-N34-AGCCAGTCAGTGTTAAGGAGTGC-3′
Pool random region: 34
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris-HCl, and 5 mM MgCl2, pH 7.4
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated version of r12.45
Application as quoted in the referenced paper: Detection: " Atrazine is an herbicide that is widely used in crop production at about 70 million pounds per year in the United States. This study focuses on the identification and characterization of a single-stranded DNA (ssDNA) aptamer that binds to atrazine. SG assays and AuNPs assays showed nonconventional binding activities between the truncated R12.45 aptamer candidate and atrazine, which warrants future studies."
Reference (2018, ACS Omega ): Abraham, K. M., Roueinfar, M., Ponce, A. T., Lussier, M. E., Benson, D. B., & Hong, K. L. (2018). In Vitro Selection and Characterization of a Single-Stranded DNA Aptamer Against the Herbicide Atrazine. ACS omega, 3(10), 13576–13583. https://doi.org/10.1021/acsomega.8b01859
Aptamer: AP-1
Target: B-lymphocyte antigen (CD20)
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGGAATAAGGGGGTATTACTGTCTGGTAAACAAACGCTATGCGAGGGGATTCAAGATAGTAAGTGCAATCT3′
Sequence length: 88
GC content: 0.3977272727272727
Affinity: Kd: 96.91 ± 4.5 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N52-AGATAGTAAGTGCAATCT-3′
Pool random region: 52
Binding buffer/conditions: 4.5 g of glucose, 100 mg of yeast tRNA (Sigma-Aldrich), 1 g of bovine serum albumin, and 5 mL of 1 M MgCl2 dissolved in 1 L of Dulbecco's PBS (DPBS) (Sigma-Aldrich)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 33 to 37-kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: " The B-lymphocyte antigen (CD20) is a suitable target for single-stranded (ss) nucleic acid oligomer (aptamers). The aim of study was selection and characterization of a ssDNA aptamer against CD20 using Cell-Systematic Evolution of Ligands by Exponential Enrichment (Cell-SELEX). The AP-1, AP-2 and AP-3 could be candidate instead of antibodies for diagnostic and therapeutic applications in immune deficiency, autoimmune diseases, leukemia and lymphoma."
Reference (2018, Molecules ): Haghighi, M., Khanahmad, H., & Palizban, A. (2018). Selection and Characterization of Single-Stranded DNA Aptamers Binding Human B-Cell Surface Protein CD20 by Cell-SELEX. Molecules (Basel, Switzerland), 23(4), 715. https://doi.org/10.3390/molecules23040715
Aptamer: CA50 A01
Target: Homo sapien - CA50
Type of nucleic acid: ssRNA
Sequence: 5'AUCGUUACCUUAGAAGCUUGUGAGUUUUUCGCGGCGAAGACAAGGCUCGGGAUCCGACACGACCCUAUAGUGAGUCGUAUUA3'
Sequence length: 82
GC content: 0.4878048780487805
Affinity: Kd: 38 nM
Pool type: 5'-ATCGTTACCTTAGAAGCTT-N30-GGATCCGACACGACCCTATAGTGAGTCGTATTA-3'
Pool random region: 30
Binding buffer/conditions: BSA 1mg/ml in Dulbecco's PBS without calcium and magnesium (pH 7.3), Mg2Cl 5mM, glucose 4.5g/L, Salmon Sperm DNA 0.1 mg/ml and yeast tRNA 0.1 mg/ml
Buffer type: PBS/phosphate buffers
pH: 7.3
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therpaeutic: " these novel RNA aptamers targeting gastrointestinal cancer biomarker CEA, CA50 and CA72-4 will aid further development and standardization of clinical diagnostic method with better sensitivity and specificity, and potentially future therapeutics development of gastric cancer. It is possible that such aptamers would become applicable in clinical applications or even therapeutics in the near future with better sensitivity and specificity, and without the limitations of immunoassays."
Reference (2018, PLoS One ): Pan, Q., Law, C. O. K., Yung, M. M. H., Han, K. C., Pon, Y. L., & Lau, T. C. K. (2018). Novel RNA aptamers targeting gastrointestinal cancer biomarkers CEA, CA50 and CA72-4 with superior affinity and specificity. PloS one, 13(10), e0198980. https://doi.org/10.1371/journal.pone.0198980