RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: GL56
Target: Glioblastoma cell line U87MG
Type of nucleic acid: ssRNA
Sequence: 5′GGAGACAAGAAUAAACGCUCAAUGAUUUUGCAGCACUUCUUGUUAUCUUAACGAACUGUUGAUGAUUCGACAGGAGGCUCACAACAGGC3′
Sequence length: 89
GC content: 0.4269662921348314
Affinity: Kd: 6 nM
Pool type: 5′GGAGACAAGAAUAAACGCUCAA-N43-UUCGACAGGAGGCUCACAACAGGC-3′
Pool random region: 43
Binding buffer/conditions: 50 mmol/l Tris-HCl pH 8.0 buffer containing 150 mmol/l NaCl, 1% Nonidet P-40, 2 µg/ml aprotinin, 1 µg/ml pepstatin, 2 µg/ml leupeptin, 1 mmol/l Na3VO4
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 95 kDa
Post-SELEX modifications: Gl56 aptamer contains 2′-f-py modifications that are expected to increase endonuclease resistance.
Application as quoted in the referenced paper: Therapeutic and Drug Delivery: " Nucleic acid-based aptamers are emerging as therapeutic antagonists of disease-associated proteins such as receptor tyrosine kinases. Here, we describe a nuclease resistant RNA aptamer, named GL56, which specifically recognizes the insulin receptor (IR). Given the growing interest in the insulin receptor as target for cancer treatment, GL56 reveals a novel molecule with great translational potential as inhibitor and delivery tool for IR-dependent cancers."
Reference (2016, Mol Ther Nucleic Acids ): Iaboni, M., Fontanella, R., Rienzo, A., Capuozzo, M., Nuzzo, S., Santamaria, G., Catuogno, S., Condorelli, G., de Franciscis, V., & Esposito, C. L. (2016). Targeting Insulin Receptor with a Novel Internalizing Aptamer. Molecular therapy. Nucleic acids, 5(9), e365. https://doi.org/10.1038/mtna.2016.73
Aptamer: #5
Target: Chloramphenicol (CAP)
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGATGCAATAAGCGATGCGCCCTCGCCTGGGGGCCTAGTCCTCTCCTATGCGTGCTACCGTGAA3'
Sequence length: 79
GC content: 0.5949367088607594
Affinity: Kd: 32.24 ± 8.19 nM
Pool type: 5′-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 100 mM of NaCl, 20 mM of Tris–HCl, 2 mM of MgCl2, 5 mM of KCl, 1 mM of CaCl2, and 0.02 % aqueous solution of Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: 3 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor: " Chloramphenicol (CAP) has been widely used to treat bacterial infections in livestock and aquatic animals. In this study, magnetic bead-based systematic evolution of ligands by exponential enrichment (Mag-SELEX) strategy was performed to select and identify CAP-specific single-stranded DNA (ssDNA) aptamers from a random oligonucleotide library. These results indicated that the potential aptamer No. 5 with highest specificity and affinity for CAP would be an ideal aptamer for future detection of residual CAP in animal-sourced food."
Reference (2016, Appl Biochem Biotechnol ): Duan, Y., Gao, Z., Wang, L., Wang, H., Zhang, H., & Li, H. (2016). Selection and Identification of Chloramphenicol-Specific DNA Aptamers by Mag-SELEX. Applied biochemistry and biotechnology, 180(8), 1644–1656. https://doi.org/10.1007/s12010-016-2193-6
Aptamer: #4
Target: Chloramphenicol (CAP)
Type of nucleic acid: ssDNA
Sequence: 5′AGCAGCACAGAGGTCAGATGGCAGGGCACGCGGGTCGTCCACTGGAGATTACTGCTGCGCCCTATGCGTGCTACCGTGAA3′
Sequence length: 80
GC content: 0.6125
Affinity: Kd: 101.62 ± 11.1 nM
Pool type: 5′-AGCAGCACAGAGGTCAGATG-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 101 mM of NaCl, 20 mM of Tris–HCl, 2 mM of MgCl2, 5 mM of KCl, 1 mM of CaCl2, and 0.02 % aqueous solution of Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: 3 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor: " Chloramphenicol (CAP) has been widely used to treat bacterial infections in livestock and aquatic animals. In this study, magnetic bead-based systematic evolution of ligands by exponential enrichment (Mag-SELEX) strategy was performed to select and identify CAP-specific single-stranded DNA (ssDNA) aptamers from a random oligonucleotide library. These results indicated that the potential aptamer No. 5 with highest specificity and affinity for CAP would be an ideal aptamer for future detection of residual CAP in animal-sourced food."
Reference (2016, Appl Biochem Biotechnol ): Duan, Y., Gao, Z., Wang, L., Wang, H., Zhang, H., & Li, H. (2016). Selection and Identification of Chloramphenicol-Specific DNA Aptamers by Mag-SELEX. Applied biochemistry and biotechnology, 180(8), 1644–1656. https://doi.org/10.1007/s12010-016-2193-6
Aptamer: BDE-A-8
Target: Tetra-BDE congener (BDE47)
Type of nucleic acid: ssDNA
Sequence: 5'GCAATGGTACGGTACTTCCGACAGCCGGGGCATCAGAGCAGCCGATTGTCTGTTGTGCCCAAAAGTGCACGCTACTTTGCTAA3'
Sequence length: 83
GC content: 0.5421686746987951
Affinity: Kd: 0.20 nM
Pool type: 5′-GCAATGGTACGGTACTTCC-N40-CAAAAGTGCACGCTACTTTGCTAA-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris-HCl, 2 mM MgCl2, 5 mM KCl, and 1 mM CaCl2 at pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Polybrominated diphenyl ethers (PBDEs) are group of chemicals which are representative persistent organic pollutants (POPs) and used as brominated flame retardants for many consumer products. Here, we report ssDNA aptamers which bind to BDE47, one of the PBDE congeners commonly found in various environmental matrices, and show affinity to other major tri-to hepta- BDE congeners. These aptamers are expected to provide a tool for preliminary screening or quick separation of PBDEs in environmental samples prior to trace quantitative analysis."
Additional information: ssDNAs that were bound to OH-BDE47-immobilized magnetic beads
Reference (2016, Anal Chim Acta ): Kim, U. J., & Kim, B. C. (2016). DNA aptamers for selective identification and separation of flame retardant chemicals. Analytica chimica acta, 936, 208–215. https://doi.org/10.1016/j.aca.2016.06.040
Aptamer: BDE-A-12
Target: Tetra-BDE congener (BDE47)
Type of nucleic acid: ssDNA
Sequence: 5'GCAATGGTACGGTACTTCCATTGCACGTCTCCGCCGCTTGGGTGGAGAGGCTATTCGGCCAAAAGTGCACGCTACTTTGCTAA3'
Sequence length: 83
GC content: 0.5421686746987951
Affinity: Kd: 1.52 nM
Pool type: 5′-GCAATGGTACGGTACTTCC-N40-CAAAAGTGCACGCTACTTTGCTAA-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris-HCl, 2 mM MgCl2, 5 mM KCl, and 1 mM CaCl2 at pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Polybrominated diphenyl ethers (PBDEs) are group of chemicals which are representative persistent organic pollutants (POPs) and used as brominated flame retardants for many consumer products. Here, we report ssDNA aptamers which bind to BDE47, one of the PBDE congeners commonly found in various environmental matrices, and show affinity to other major tri-to hepta- BDE congeners. These aptamers are expected to provide a tool for preliminary screening or quick separation of PBDEs in environmental samples prior to trace quantitative analysis."
Additional information: ssDNAs that were bound to OH-BDE47-immobilized magnetic beads
Reference (2016, Anal Chim Acta ): Kim, U. J., & Kim, B. C. (2016). DNA aptamers for selective identification and separation of flame retardant chemicals. Analytica chimica acta, 936, 208–215. https://doi.org/10.1016/j.aca.2016.06.040
Aptamer: PA1T4PPZZ
Target: Prostate specific membrane antigen (PSMA) positive LNCaP cells
Type of nucleic acid: ssDNA
Sequence: 5'CATCCATGGGAATTCGTCGACGAGATCTTTTTGAATATTCCTCAATGACCCAAAATTCCTGCCTAGGTTCGAGCTCG3'
Sequence length: 77
GC content: 0.4545454545454545
Affinity: Kd: 0.03378 ± 0.00377 nM
Pool type: 5'-CATCCATGGGATTCGTCGAC-N40-CTGCCT AGGCTCGAG-3'
Pool random region: 40
Binding buffer/conditions: 4.5 g of glucose and 5 ml of 1 M MgCl2 in 1 L of Dulbecco's Phosphate-Buffered Saline (DPBS) with yeast tRNA and BSA
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 Drug Delivery: " Prostate Specific Membrane Antigen (PSMA), over expressed in prostate cancer, is a highly specific marker and therefore can be used for diagnosis of the prostate cancer cells. The aim of the present study was to select single-stranded DNA aptamers against LNCap cells highly expressing PSMA, using cell-SELEX method which can be used as a diagnostic tool for the detection of prostate cancer cells. Our results indicated that selected aptamers may turn out to be ideal candidates for the development of a detection tool and also can be used in targeted drug delivery for future smart drugs."
Reference (2016, Avicenna J Med Biotechnol ): Almasi, F., Mousavi Gargari, S. L., Bitaraf, F., & Rasoulinejad, S. (2016). Development of a Single Stranded DNA Aptamer as a Molecular Probe for LNCap Cells Using Cell-SELEX. Avicenna journal of medical biotechnology, 8(3), 104–111.
Aptamer: B1
Target: Prostate specific membrane antigen (PSMA) positive LNCaP cells
Type of nucleic acid: ssDNA
Sequence: 5'CATCCATGGGATTCGTCGACCCTGCAGGCATGCAAGCTTTCCCTATAGTGAGTCGTATTACTGCCT AGGCTCGAG3'
Sequence length: 75
GC content: 0.5333333333333333
Affinity: Kd: 0.05749 ± 0.002214 nM
Pool type: 5'-CATCCATGGGATTCGTCGAC-N40-CTGCCT AGGCTCGAG-3'
Pool random region: 40
Binding buffer/conditions: 4.5 g of glucose and 5 ml of 1 M MgCl2 in 1 L of Dulbecco's Phosphate-Buffered Saline (DPBS) with yeast tRNA and BSA
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 Drug Delivery: " Prostate Specific Membrane Antigen (PSMA), over expressed in prostate cancer, is a highly specific marker and therefore can be used for diagnosis of the prostate cancer cells. The aim of the present study was to select single-stranded DNA aptamers against LNCap cells highly expressing PSMA, using cell-SELEX method which can be used as a diagnostic tool for the detection of prostate cancer cells. Our results indicated that selected aptamers may turn out to be ideal candidates for the development of a detection tool and also can be used in targeted drug delivery for future smart drugs."
Reference (2016, Avicenna J Med Biotechnol ): Almasi, F., Mousavi Gargari, S. L., Bitaraf, F., & Rasoulinejad, S. (2016). Development of a Single Stranded DNA Aptamer as a Molecular Probe for LNCap Cells Using Cell-SELEX. Avicenna journal of medical biotechnology, 8(3), 104–111.
Aptamer: BM2
Target: Mannose-capped lipoarabinomannan (ManLAM) of Bacillus Calmette–Guérin (BCG)
Type of nucleic acid: ssDNA
Sequence: 5'GCGGAATTCTAATACGACTCACTATAGGGAACAGTCCGAGCCCCCCATGAACTAGGCTCCACAATGAGTTTGGGGGTCAATGCGTCATA3'
Sequence length: 89
GC content: 0.5056179775280899
Affinity: Kd: 8.59 ± 1.23 nM
Pool type: 5'-GCGGAATTCTAATACGACTCACTATAGGGAACAGTCCGAGCC-N31-GGGTCAATGCGTCATA-3'
Pool random region: 31
Binding buffer/conditions: 20 mM Tris-HCl, 0.15 M NaCl, 10 mM CaCl2, 6 mM MnCl2, pH 7.2 at 37 ˚C
Divalent salt: CaCl
Buffer type: Tris Buffers
pH: 7.2
Molecular weight of target: 72–95 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Theruputic: " Because Mycobacterium bovis, termed bacillus Calmette-Guérin (BCG), the only available used tuberculosis (TB) vaccine, retains immunomodulatory properties that limit its protective immunogenicity, there are continuous efforts to identify the immunosuppression mechanism as well as new strategies for improving the immunogenicity of BCG. Here, an ssDNA aptamer "antibody" BM2 specifically bound to the mannose-capped lipoarabinomannan (ManLAM) of BCG was selected. We report a new mechanism of the interaction between ManLAM and CD44 on macrophages and CD4(+) T cells and reveal that ManLAM-binding membrane molecule CD44 is a novel target for the enhancement of BCG immunogenicity, and BM2 has strong potential as an immune enhancer for BCG."
Reference (2016, J Am Chem Soc ): Sun, X., Pan, Q., Yuan, C., Wang, Q., Tang, X. L., Ding, K., Zhou, X., & Zhang, X. L. (2016). A Single ssDNA Aptamer Binding to Mannose-Capped Lipoarabinomannan of Bacillus Calmette-Guérin Enhances Immunoprotective Effect against Tuberculosis. Journal of the American Chemical Society, 138(36), 11680–11689. https://doi.org/10.1021/jacs.6b05357
Aptamer: VDBA14
Target: 25-HydroxyvitaminD3
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCATGGGGGGTGTGACTTTGGTGTGCCTATGCGTGCTACGGAA3'
Sequence length: 56
GC content: 0.5714285714285714
Affinity: Kd: 11 nM
Pool type: 5′-AGCAGCACAGAGGTCATG-20N-CCTATGCGTGCTACGGAA-3'
Pool random region: 20
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris-HCl, 2 mM MgCl2, 5 mM KCl, 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: Not applicable
Application as quoted in the referenced paper: Diagnostic: " For the prevention of 25-HydroxyvitaminD3 deficiency, in this study, aptamers which can bind to 25-HydroxyvitaminD3 with high specificity and affinity, were successfully developed by GO-SELEX. The results clearly indicated that the structure of VDBA14 aptamer was changed upon the binding of the target, 25-HydroxyvitaminD3, and so the indicator sequences (partially complementary to the aptamer sequence) tagged with an enzyme as a signaling molecule could be de-hybridized from the aptamer. All these results were taken together, the aptamer which was developed could play an exquisite role in the fields of early medical diagnosis of vitamin D deficiency with accurate, rapid and simple analytical method."
Reference (2016, Biosens Bioelectron ): Lee, B. H., Nguyen, V. T., & Gu, M. B. (2017). Highly sensitive detection of 25-HydroxyvitaminD3 by using a target-induced displacement of aptamer. Biosensors & bioelectronics, 88, 174–180. https://doi.org/10.1016/j.bios.2016.08.011
Aptamer: P12-17
Target: Escherichia coli (E. coli) ATCC 25922
Type of nucleic acid: ssDNA
Sequence: 5'CATACGATTTAGGTGACACTATAGGACGGTGGCAGGGAAAGGGGTCGGGCATATGGCGGAGGGGATTTCTCCTACTGGGATAGGTGGA3'
Sequence length: 88
GC content: 0.5454545454545454
Affinity: Kd: 56.33 ± 15.87 nM
Pool type: 5'-CATACGATTTAGGTGACACTATAG-N40-ATTTCTCCTACTGGGATAGGTGGA-3'
Pool random region: 40
Binding buffer/conditions: PBS containing 1.4 mM MgCl2
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: " Escherichia coli is a bacterial species found ubiquitously in the intestinal flora of animals, although pathogenic variants cause major public health problems. We used cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) to isolate four single stranded DNA (ssDNA) aptamers that bind strongly to E. coli cells (ATCC generic strain 25922), with Kd values in the nanomolar range. This aptamer binds to Meningitis/sepsis associated E. coli (MNEC) clinical isolates, and is the first aptamer described with potential for use in the diagnosis of MNEC-borne pathologies."
Reference (2016, PLoS One ): Marton, S., Cleto, F., Krieger, M. A., & Cardoso, J. (2016). Isolation of an Aptamer that Binds Specifically to E. coli. PloS one, 11(4), e0153637. https://doi.org/10.1371/journal.pone.0153637
Aptamer: P12-31
Target: Escherichia coli (E. coli) ATCC 25922
Type of nucleic acid: ssDNA
Sequence: 5'CATACGATTTAGGTGACACTATAGTCATCGGGATACCTGGTAAGGATAATTTCTCCTACTGGGATAGGTGGA3'
Sequence length: 72
GC content: 0.4305555555555556
Affinity: Kd: 87.03 ± 17.32 nM
Pool type: 5'-CATACGATTTAGGTGACACTATAG-N40-ATTTCTCCTACTGGGATAGGTGGA-3'
Pool random region: 40
Binding buffer/conditions: PBS containing 1.4 mM MgCl2
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: " Escherichia coli is a bacterial species found ubiquitously in the intestinal flora of animals, although pathogenic variants cause major public health problems. We used cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) to isolate four single stranded DNA (ssDNA) aptamers that bind strongly to E. coli cells (ATCC generic strain 25922), with Kd values in the nanomolar range. This aptamer binds to Meningitis/sepsis associated E. coli (MNEC) clinical isolates, and is the first aptamer described with potential for use in the diagnosis of MNEC-borne pathologies."
Reference (2016, PLoS One ): Marton, S., Cleto, F., Krieger, M. A., & Cardoso, J. (2016). Isolation of an Aptamer that Binds Specifically to E. coli. PloS one, 11(4), e0153637. https://doi.org/10.1371/journal.pone.0153637
Aptamer: P12-52
Target: Escherichia coli (E. coli) ATCC 25922
Type of nucleic acid: ssDNA
Sequence: 5'CATACGATTTAGGTGACACTATAGCCGCCCAGCGGGGGTAGGGCCGGACGTAGGAGGAGCTGCGATTTCTCCTACTGGGATAGGTGGA3'
Sequence length: 88
GC content: 0.5795454545454546
Affinity: Kd:11.97 ± 2.94 nM
Pool type: 5'-CATACGATTTAGGTGACACTATAG-N40-ATTTCTCCTACTGGGATAGGTGGA-3'
Pool random region: 40
Binding buffer/conditions: PBS containing 1.4 mM MgCl2
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: " Escherichia coli is a bacterial species found ubiquitously in the intestinal flora of animals, although pathogenic variants cause major public health problems. We used cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) to isolate four single stranded DNA (ssDNA) aptamers that bind strongly to E. coli cells (ATCC generic strain 25922), with Kd values in the nanomolar range. This aptamer binds to Meningitis/sepsis associated E. coli (MNEC) clinical isolates, and is the first aptamer described with potential for use in the diagnosis of MNEC-borne pathologies."
Reference (2016, PLoS One ): Marton, S., Cleto, F., Krieger, M. A., & Cardoso, J. (2016). Isolation of an Aptamer that Binds Specifically to E. coli. PloS one, 11(4), e0153637. https://doi.org/10.1371/journal.pone.0153637
Aptamer: P12-55
Target: Escherichia coli (E. coli) ATCC 25922
Type of nucleic acid: ssDNA
Sequence: 5'CATACGATTTAGGTGACACTATAGCCGGAGGTGGGTGAGGTCTGCGGCAGGCTGTGTGGGTGGACCGGAGGGGGGTGAGGTCTGCGGCAGGCTGTGTGGGTGGAATTTCTCCTACTGGGATAGGTGGA3'
Sequence length: 128
GC content: 0.6015625
Affinity: Kd: 161.0 ± 34.74 nM
Pool type: 5'-CATACGATTTAGGTGACACTATAG-N40-ATTTCTCCTACTGGGATAGGTGGA-3'
Pool random region: 40
Binding buffer/conditions: PBS containing 1.4 mM MgCl2
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: " Escherichia coli is a bacterial species found ubiquitously in the intestinal flora of animals, although pathogenic variants cause major public health problems. We used cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) to isolate four single stranded DNA (ssDNA) aptamers that bind strongly to E. coli cells (ATCC generic strain 25922), with Kd values in the nanomolar range. This aptamer binds to Meningitis/sepsis associated E. coli (MNEC) clinical isolates, and is the first aptamer described with potential for use in the diagnosis of MNEC-borne pathologies."
Reference (2016, PLoS One ): Marton, S., Cleto, F., Krieger, M. A., & Cardoso, J. (2016). Isolation of an Aptamer that Binds Specifically to E. coli. PloS one, 11(4), e0153637. https://doi.org/10.1371/journal.pone.0153637
Aptamer: aptamer 2
Target: Zika non-structural 1 (NS1) protein
Type of nucleic acid: ssDNA
Sequence: 5′GATAGAATTCGAGCTCGGGCACTAGGTTGCAGGGGACTGCTCGGGATTGCGGATCAACCTAGTTGCTTCTCTCGTATGATGCGGGTCGACAAGCTTTAAT3'
Sequence length: 100
GC content: 0.52
Affinity: Kd: 24 pM
Pool type: 5′-GATAGAATTCGAGCTCGGGC-N60-GCGGGTCGACAAGCTTTAAT-3'
Pool random region: 60
Binding buffer/conditions: 20 mM Tris at pH 7.5 with 150 mM NaCl, 1 mM MgCl2, 2.7 mM KCl and 0.005% NP-40
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: Diagnostic: " We report here a few Zika NS1-binding ssDNA aptamers selected using the conventional SELEX protocol, and their application in an ELISA assay for sensitive diagnosis of Zika NS1 protein. Among the aptamers identified, aptamers 2 and 10 could recognize different binding epitopes of Zika NS1 protein. These results suggest that the selected aptamers would be useful for medical diagnosis of Zika virus infection in various aptamer-based diagnostic devices including ELISA assay."
Reference (2017, Anal Chem ): Lee, K. H., & Zeng, H. (2017). Aptamer-Based ELISA Assay for Highly Specific and Sensitive Detection of Zika NS1 Protein. Analytical chemistry, 89(23), 12743–12748. https://doi.org/10.1021/acs.analchem.7b02862
Aptamer: aptamer 10
Target: Zika non-structural 1 (NS1) protein
Type of nucleic acid: ssDNA
Sequence: 5′GATAGAATTCGAGCTCGGGCGGCTGTTGTTGTTACCTATTGCGTGGCGATCGGACTTTCGATTCCGATTAACGCCGGAGGGCGGGTCGACAAGCTTTAAT3'
Sequence length: 100
GC content: 0.53
Affinity: Kd: 134 nM
Pool type: 5′-GATAGAATTCGAGCTCGGGC-N60-GCGGGTCGACAAGCTTTAAT-3'
Pool random region: 60
Binding buffer/conditions: 20 mM Tris at pH 7.5 with 150 mM NaCl, 1 mM MgCl2, 2.7 mM KCl and 0.005% NP-40
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: Diagnostic: " We report here a few Zika NS1-binding ssDNA aptamers selected using the conventional SELEX protocol, and their application in an ELISA assay for sensitive diagnosis of Zika NS1 protein. Among the aptamers identified, aptamers 2 and 10 could recognize different binding epitopes of Zika NS1 protein. These results suggest that the selected aptamers would be useful for medical diagnosis of Zika virus infection in various aptamer-based diagnostic devices including ELISA assay."
Reference (2017, Anal Chem ): Lee, K. H., & Zeng, H. (2017). Aptamer-Based ELISA Assay for Highly Specific and Sensitive Detection of Zika NS1 Protein. Analytical chemistry, 89(23), 12743–12748. https://doi.org/10.1021/acs.analchem.7b02862
Aptamer: aptCTLA-4
Target: Cytotoxic T lymphocyte antigen-4 (CTLA-4)
Type of nucleic acid: ssDNA
Sequence: 5'TCCCTACGGCGCTAACGATGGTGAAAATGGGCCTAGGGTGGACGGTGCCACCGTGCTACAAC3'
Sequence length: 62
GC content: 0.5967741935483871
Affinity: Kd: 11.84 nM
Pool type: 5'-TCCCTACGGCGCTAAC-N30-GCCACCGTGCTACAAC3'
Pool random region: 30
Binding buffer/conditions: 20 mM Tris-HCl, pH 7.5, 100 mM NaCl, and 5 mM MgCl2
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: Therapeutic: " The successful translation of cytotoxic T lymphocyte antigen-4 (CTLA-4) blockade has revolutionized the concept of cancer immunotherapy. Here, we report a novel high-affinity CTLA-4-antagonizing DNA aptamer (dissociation constant, 11.84 nM), aptCTLA-4, which was identified by cell-based SELEX and high-throughput sequencing. aptCTLA-4 is relatively stable in serum, promotes lymphocyte proliferation, and inhibits tumor growth in cell and animal models. Our study demonstrates the developmental pipeline of a functional CTLA-4-targeting aptamer and suggests a translational potential for aptCTLA-4."
Reference (2017, Mol Ther Nucleic Acids ): Huang, B. T., Lai, W. Y., Chang, Y. C., Wang, J. W., Yeh, S. D., Lin, E. P., & Yang, P. C. (2017). A CTLA-4 Antagonizing DNA Aptamer with Antitumor Effect. Molecular therapy. Nucleic acids, 8, 520–528. https://doi.org/10.1016/j.omtn.2017.08.006