RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: T13
Target: Rabies virus infected BHK-21 cells
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCACTTGTTTGCGTGTTTTTTTCGTTGTCTTGTCGGGGTCTTGTGGTTTGGACACGGTGGCTTAGT3'
Sequence length: 81
GC content: 0.4938271604938271
Affinity: Kd: 39 ± 2.4 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N45-TGGACACGGTGGCTTAGT-3'
Pool random region: 45
Binding buffer/conditions: 0.1 g/L yeast tRNA (Invitrogen, NY, USA), 4.5 g/L glucose, 1.0 g/L bovine serum albumin (Solarbio, Beijing, China), and 5 mmol/L MgCl2 in Dullbecco's PBS
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: Therapeutic: " In this study, the cell surface-systematic evolution of ligands by exponential enrichment (Cell-SELEX) strategy was used to generate DNA aptamers which targeted to the intact rabies virus-infected live cells. These data show the feasibility of generating functionally effective aptamers against rabies virus-infected cells by the Cell-SELEX iterative procedure. These aptamers may prove clinically useful as therapeutic molecules with specific antiviral potential against RABV infections."
Reference (2012,Int Immunopharmacol): Liang, H. R., Hu, G. Q., Zhang, T., Yang, Y. J., Zhao, L. L., Qi, Y. L., Wang, H. L., Gao, Y. W., Yang, S. T., & Xia, X. Z. (2012). Isolation of ssDNA aptamers that inhibit rabies virus. International immunopharmacology, 14(3), 341–347. https://doi.org/10.1016/j.intimp.2012.06.019
Aptamer: T14
Target: Rabies virus infected BHK-21 cells
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCAGGGGCCGATTGGTGGTACTGCCATCGTCGTTCTTCAGGCGTTAGTTGGACACGGTGGCTTAGT3'
Sequence length: 81
GC content: 0.5679012345679012
Affinity: Kd: 31 ± 2.1 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N45-TGGACACGGTGGCTTAGT-3'
Pool random region: 45
Binding buffer/conditions: 0.1 g/L yeast tRNA (Invitrogen, NY, USA), 4.5 g/L glucose, 1.0 g/L bovine serum albumin (Solarbio, Beijing, China), and 5 mmol/L MgCl2 in Dullbecco's PBS
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: Therapeutic: " In this study, the cell surface-systematic evolution of ligands by exponential enrichment (Cell-SELEX) strategy was used to generate DNA aptamers which targeted to the intact rabies virus-infected live cells. These data show the feasibility of generating functionally effective aptamers against rabies virus-infected cells by the Cell-SELEX iterative procedure. These aptamers may prove clinically useful as therapeutic molecules with specific antiviral potential against RABV infections."
Reference (2012,Int Immunopharmacol): Liang, H. R., Hu, G. Q., Zhang, T., Yang, Y. J., Zhao, L. L., Qi, Y. L., Wang, H. L., Gao, Y. W., Yang, S. T., & Xia, X. Z. (2012). Isolation of ssDNA aptamers that inhibit rabies virus. International immunopharmacology, 14(3), 341–347. https://doi.org/10.1016/j.intimp.2012.06.019
Aptamer: F3
Target: Rabies virus infected BHK-21 cells
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCACAGCATTCAGTCCACTACACGGTTCCTCCTTTCATCTCATAAATTTGGACACGGTGGCTTAGT3'
Sequence length: 81
GC content: 0.4814814814814814
Affinity: Kd: 28 ± 2.3 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N45-TGGACACGGTGGCTTAGT-3'
Pool random region: 45
Binding buffer/conditions: 0.1 g/L yeast tRNA (Invitrogen, NY, USA), 4.5 g/L glucose, 1.0 g/L bovine serum albumin (Solarbio, Beijing, China), and 5 mmol/L MgCl2 in Dullbecco's PBS
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: Therapeutic: " In this study, the cell surface-systematic evolution of ligands by exponential enrichment (Cell-SELEX) strategy was used to generate DNA aptamers which targeted to the intact rabies virus-infected live cells. These data show the feasibility of generating functionally effective aptamers against rabies virus-infected cells by the Cell-SELEX iterative procedure. These aptamers may prove clinically useful as therapeutic molecules with specific antiviral potential against RABV infections."
Reference (2012,Int Immunopharmacol): Liang, H. R., Hu, G. Q., Zhang, T., Yang, Y. J., Zhao, L. L., Qi, Y. L., Wang, H. L., Gao, Y. W., Yang, S. T., & Xia, X. Z. (2012). Isolation of ssDNA aptamers that inhibit rabies virus. International immunopharmacology, 14(3), 341–347. https://doi.org/10.1016/j.intimp.2012.06.019
Aptamer: F34
Target: Rabies virus infected BHK-21 cells
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCAGGGGCTGAGTTTCTTTGTCGGTCTTTTCATGGTTGGTTCTCTTTTTGGACACGGTGGCTTAGT3'
Sequence length: 81
GC content: 0.4938271604938271
Affinity: Kd: 28 ± 1.9 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N45-TGGACACGGTGGCTTAGT-3'
Pool random region: 45
Binding buffer/conditions: 0.1 g/L yeast tRNA (Invitrogen, NY, USA), 4.5 g/L glucose, 1.0 g/L bovine serum albumin (Solarbio, Beijing, China), and 5 mmol/L MgCl2 in Dullbecco's PBS
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: Therapeutic: " In this study, the cell surface-systematic evolution of ligands by exponential enrichment (Cell-SELEX) strategy was used to generate DNA aptamers which targeted to the intact rabies virus-infected live cells. These data show the feasibility of generating functionally effective aptamers against rabies virus-infected cells by the Cell-SELEX iterative procedure. These aptamers may prove clinically useful as therapeutic molecules with specific antiviral potential against RABV infections."
Reference (2012,Int Immunopharmacol): Liang, H. R., Hu, G. Q., Zhang, T., Yang, Y. J., Zhao, L. L., Qi, Y. L., Wang, H. L., Gao, Y. W., Yang, S. T., & Xia, X. Z. (2012). Isolation of ssDNA aptamers that inhibit rabies virus. International immunopharmacology, 14(3), 341–347. https://doi.org/10.1016/j.intimp.2012.06.019
Aptamer: proGRP(198)
Target: Pro-gastrin-Releasing Peptide (proGRP)
Type of nucleic acid: ssDNA
Sequence: 5'ATACCAGCTTATTCAATTTGCACCACTTATTGTTACTAATCTGAGATAGTAAGTGCAATCT3'
Sequence length: 61
GC content: 0.3278688524590163
Affinity: Kd: 1.2 μM
Pool type: 5'-ATACCAGCTTATTCAATT-N25-AGATAGTAAGTGCAATCT-3'
Pool random region: 25
Binding buffer/conditions: SELEX Buffer: 137 mM NaCl, 8.1 mM Na2HPO4, 2.68 mM KCl, 1.47 mM KH2PO4, 0.9 mM CaCl2, 5.3 mM MgCl2, and 4.5 g/L glucose, pH 7.4
Divalent salt: MgCl/CaCl
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: " Detection of tumor markers, which are molecules associated with cancer, is important for accurate diagnosis and prognosis. We attempted to select an appropriate DNA aptamer for use as a tumor marker using the SELEX technique. Here, a single-stranded DNA aptamer for proGRP(1–98) was selected using SELEX and evaluated its binding affinity using surface plasmon resonance."
Reference (2012, Appl Biochem Biotechnol ): Mie M, Kai T, Le T, Cass AE, Kobatake E. Selection of DNA aptamers with affinity for pro-gastrin-releasing peptide (proGRP), a tumor marker for small cell lung cancer. Appl Biochem Biotechnol. 2013;169(1):250-255. doi:10.1007/s12010-012-9956-5
Aptamer: hOX40 9C7 aptamer
Target: T Cell costimulatory receptor, OX40
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGAGGACGAUGCGGAAAAAAGAACACUUCCGAUUAGGGCCCACCCUAACGGCCGCAGCAGACGACUCGCCCGA3'
Sequence length: 74
GC content: 0.6081081081081081
Affinity: Kd: 50 nM
Pool type: 5'-TCGGGCGAGTCGTCTG-N40-CCGCATCGTCCTCCCTA-3'
Pool random region: 40
Binding buffer/conditions: (20 mM HEPES, pH 7.4, 150mM NaCl, 2 mM CaCl2, and 0.01% BSA
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Therapeutic: " Induction of an effective immune response that can target and eliminate malignant cells or virus-infected cells requires the stimulation of antigen-specific effector T cells. Future studies will assess the therapeutic potential of hOX40 aptamers for ex vivo stimulation of antigen specific T cells in conjunction with dendritic cell-based vaccines for adoptive cellular therapy."
Additional information: An initial 2'-fluoro (2'F) modified RNA pool was generated by transcribing the double-stranded DNA (dsDNA) templates with a mutant T7 RNA polymerase (Y639F) that allows for incorporation of the modified nucleotides
Reference (2012, Nucleic Acid Ther ): Pratico, E. D., Sullenger, B. A., & Nair, S. K. (2013). Identification and characterization of an agonistic aptamer against the T cell costimulatory receptor, OX40. Nucleic acid therapeutics, 23(1), 35–43. https://doi.org/10.1089/nat.2012.0388
Aptamer: 9C7
Target: OX40, T cell costimulatory receptor
Type of nucleic acid: ssRNA
Sequence: 5′UCGGGCGAGUCGUCUGGGGAGGACGAUGCGGAAAAAAGAACACUUCCGAUUAGGGCCCACCCUAACGGCCGCAGGGGAGGACGAUGCGGCCGCAUCGUCCUCCCUA3′
Sequence length: 106
GC content: 0.6320754716981132
Affinity: Kd: 1.7 nM
Pool type: 5′-TCGGGCGAGTCGTCTG-N40-CCGCATCGTCCTCCCTA-3′
Pool random region: 40
Binding buffer/conditions: 20 mM (4-(2-hydroxyethyl)-1-piperazine ethane sulfonic acid) (HEPES) pH 7.5, 100 mM NaCl, 2 mM CaCl2, and 0.01% bovine serum albumin (BSA)
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Induction of an effective immune response that can target and eliminate malignant cells or virus-infected cells requires the stimulation of antigen-specific effector T cells. Future studies will assess the therapeutic potential of hOX40 aptamers for ex vivo stimulation of antigen specific T cells in conjunction with dendritic cell-based vaccines for adoptive cellular therapy."
Reference (2012, Nucleic Acid Ther ): Pratico, E. D., Sullenger, B. A., & Nair, S. K. (2013). Identification and characterization of an agonistic aptamer against the T cell costimulatory receptor, OX40. Nucleic acid therapeutics, 23(1), 35–43. https://doi.org/10.1089/nat.2012.0388
Aptamer: 11F11
Target: OX40, T cell costimulatory receptor
Type of nucleic acid: ssRNA
Sequence: 5′UCGGGCGAGUCGUCUGGGGAGGACGAUGCGGAACGGGACCACCCAUGCCAGGGGACCACCUCAGGCAGCGCCAGACGACGGGAGGACGAUGCGGCCGCAUCGUCCUCCCUA3′
Sequence length: 111
GC content: 0.6936936936936937
Affinity: Kd: 10 nM
Pool type: 5′-TCGGGCGAGTCGTCTG-N40-CCGCATCGTCCTCCCTA-3′
Pool random region: 40
Binding buffer/conditions: 20 mM (4-(2-hydroxyethyl)-1-piperazine ethane sulfonic acid) (HEPES) pH 7.5, 100 mM NaCl, 2 mM CaCl2, and 0.01% bovine serum albumin (BSA)
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Induction of an effective immune response that can target and eliminate malignant cells or virus-infected cells requires the stimulation of antigen-specific effector T cells. Future studies will assess the therapeutic potential of hOX40 aptamers for ex vivo stimulation of antigen specific T cells in conjunction with dendritic cell-based vaccines for adoptive cellular therapy."
Reference (2012, Nucleic Acid Ther ): Pratico, E. D., Sullenger, B. A., & Nair, S. K. (2013). Identification and characterization of an agonistic aptamer against the T cell costimulatory receptor, OX40. Nucleic acid therapeutics, 23(1), 35–43. https://doi.org/10.1089/nat.2012.0388
Aptamer: D1
Target: Digoxin
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTAGCGAGGGCGGTGTCCAACAGCGGTTTTTTCACGAGGAGGTTGGCGGTGGAGATAGTAAGTGCAATCT3′
Sequence length: 86
GC content: 0.4883720930232558
Affinity: Kd: 0.05 nM and 17.8 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N50-AGATAGTAAGTGCAATCT-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 and 0.02% Tween 20
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 and Therapeutic: "Since aptamers have been shown to be highly specific for their targets, the aim of this study was to develop DNA aptamers for this widely used cardiac glycoside. Our finding indicated that D1 anti-digoxin aptamer can selectively bind to digoxin. Further studies might show its suitability for use in digoxin assays and as a therapeutic agent in life-threatening digoxin toxicity."
Additional information: The following forward and reverse primers were used for amplification and cloning using forward primer: 5′-ATACCAGCTTATTCAATT-3′, reverse primer: 5′-AGATTGCACTTACTATCT-3′, fluorescein-labeled forward primer: 5′-fluorescein-ATACCAGCTTATTCAATT-3′ and modified reverse primer: 5′-poly-dA20-hexaethylene glycol (HEGL)-AGATTGCACTTACTATCT-3′.
Reference (2012, Anal Chim Acta ): Kiani Z, Shafiei M, Rahimi-Moghaddam P, Karkhane AA, Ebrahimi SA. In vitro selection and characterization of deoxyribonucleic acid aptamers for digoxin. Anal Chim Acta. 2012;748:67-72. doi:10.1016/j.aca.2012.08.025
Aptamer: D2
Target: Digoxin
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGGTGGCTGTTGGTCGAGGCTTATTAGTGTAGTCAATGGAGGCAGGCGACGAGATAGTAAGTGCAATCT3′
Sequence length: 86
GC content: 0.4534883720930232
Affinity: Not reported
Pool type: 5′-ATACCAGCTTATTCAATT-N50-AGATAGTAAGTGCAATCT-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 and 0.02% Tween 20
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 and Therapeutic: "Since aptamers have been shown to be highly specific for their targets, the aim of this study was to develop DNA aptamers for this widely used cardiac glycoside. Our finding indicated that D1 anti-digoxin aptamer can selectively bind to digoxin. Further studies might show its suitability for use in digoxin assays and as a therapeutic agent in life-threatening digoxin toxicity."
Additional information: The following forward and reverse primers were used for amplification and cloning using forward primer: 5′-ATACCAGCTTATTCAATT-3′, reverse primer: 5′-AGATTGCACTTACTATCT-3′, fluorescein-labeled forward primer: 5′-fluorescein-ATACCAGCTTATTCAATT-3′ and modified reverse primer: 5′-poly-dA20-hexaethylene glycol (HEGL)-AGATTGCACTTACTATCT-3′.
Reference (2012, Anal Chim Acta ): Kiani Z, Shafiei M, Rahimi-Moghaddam P, Karkhane AA, Ebrahimi SA. In vitro selection and characterization of deoxyribonucleic acid aptamers for digoxin. Anal Chim Acta. 2012;748:67-72. doi:10.1016/j.aca.2012.08.025
Aptamer: Truncated D1
Target: Digoxin
Type of nucleic acid: ssDNA
Sequence: 5′AGCGAGGGCGGTGTCCAACAGCGGTTTTTTCACGAGGAGGTTGGCGGTGG3′
Sequence length: 50
GC content: 0.62
Affinity: Kd: 8.2 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N50-AGATAGTAAGTGCAATCT-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 and 0.02% Tween 20
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 and Therapeutic: "Since aptamers have been shown to be highly specific for their targets, the aim of this study was to develop DNA aptamers for this widely used cardiac glycoside. Our finding indicated that D1 anti-digoxin aptamer can selectively bind to digoxin. Further studies might show its suitability for use in digoxin assays and as a therapeutic agent in life-threatening digoxin toxicity."
Additional information: The following forward and reverse primers were used for amplification and cloning using forward primer: 5′-ATACCAGCTTATTCAATT-3′, reverse primer: 5′-AGATTGCACTTACTATCT-3′, fluorescein-labeled forward primer: 5′-fluorescein-ATACCAGCTTATTCAATT-3′ and modified reverse primer: 5′-poly-dA20-hexaethylene glycol (HEGL)-AGATTGCACTTACTATCT-3′.
Reference (2012, Anal Chim Acta ): Kiani Z, Shafiei M, Rahimi-Moghaddam P, Karkhane AA, Ebrahimi SA. In vitro selection and characterization of deoxyribonucleic acid aptamers for digoxin. Anal Chim Acta. 2012;748:67-72. doi:10.1016/j.aca.2012.08.025
Aptamer: AMP4
Target: Ampicillin
Type of nucleic acid: ssDNA
Sequence: 5′CACCTAATACGACTCACTATAGCGGATCCGACACGGCATGGTGGGCGTCGTGCTGGCTCGAACAAGCTTGC3′
Sequence length: 71
GC content: 0.5774647887323944
Affinity: Kd: 9.4 nM
Pool type: 5′-CACCTAATACGACTCACTATAGCGGATCCGA-N40-CTGGCTCGAACAAGCTTGC-3′
Pool random region: 40
Binding buffer/conditions: 20 mM Tris–HCl, 50 mM NaCl, 5 mM KCl, 5 mM MgCl2, pH 8.0
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " A gold nanoparticle based dual fluorescence-colorimetric method was developed as an aptasensor to detect ampicillin using its single-stranded DNA (ssDNA) aptamer, which was discovered by a magnetic bead-based SELEX technique. Because these detection limits were below the maximum residue limit of ampicillin, this aptasensor was sensitive enough to detect antibiotics in food products, such as milk and animal tissues."
Additional information: Fam conjugated to 5' end of aptamer
Reference (2012, Anal Bioanal Chem ): Song KM, Jeong E, Jeon W, Cho M, Ban C. Aptasensor for ampicillin using gold nanoparticle based dual fluorescence-colorimetric methods. Anal Bioanal Chem. 2012;402(6):2153-2161. doi:10.1007/s00216-011-5662-3
Aptamer: AMP17
Target: Ampicillin
Type of nucleic acid: ssDNA
Sequence: 5′CACCTAATACGACTCACTATAGCGGATCCGAGCGGGCGGTTGTATAGCGGCTGGCTCGAACAAGCTTGC3′
Sequence length: 69
GC content: 0.5652173913043478
Affinity: Kd: 13.4 nM
Pool type: 5′-CACCTAATACGACTCACTATAGCGGATCCGA-N40-CTGGCTCGAACAAGCTTGC-3′
Pool random region: 40
Binding buffer/conditions: 20 mM Tris–HCl, 50 mM NaCl, 5 mM KCl, 5 mM MgCl2, pH 8.0
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " A gold nanoparticle based dual fluorescence-colorimetric method was developed as an aptasensor to detect ampicillin using its single-stranded DNA (ssDNA) aptamer, which was discovered by a magnetic bead-based SELEX technique. Because these detection limits were below the maximum residue limit of ampicillin, this aptasensor was sensitive enough to detect antibiotics in food products, such as milk and animal tissues."
Additional information: Fam conjugated to 5' end of aptamer
Reference (2012, Anal Bioanal Chem ): Song KM, Jeong E, Jeon W, Cho M, Ban C. Aptasensor for ampicillin using gold nanoparticle based dual fluorescence-colorimetric methods. Anal Bioanal Chem. 2012;402(6):2153-2161. doi:10.1007/s00216-011-5662-3
Aptamer: HER2 aptamer (HB5)
Target: Epitope peptide of human epithelial growth factor receptor 2 (HER2)
Type of nucleic acid: ssDNA
Sequence: 5'AACCGCCCAAATCCCTAAGAGTCTGCACTTGTCATTTTGTATATGTATTTGGTTTTTGGCTCTCACAGACACACTACACACGCACA3'
Sequence length: 86
GC content: 0.4302325581395348
Affinity: Kd: 18.9 nM
Pool type: 5'-AACCGCCCAAATCCCTAAGAGTC-N40-CACAGACACACTACACACGCACA-3'
Pool random region: 40
Binding buffer/conditions: Hank's Buffer with 0.1 mg/mL salmon sperm DNA and 1 mg/mL of BSA
Buffer type: Other Buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " HER2 protein is an attractive target for tumor-specific drug delivery because of its overexpression in multiple malignancies, including breast, gastric, ovarian, and lung cancers. The results suggest that the selected HER2 aptamer may have application potentials in targeted therapy against HER2-positive breast cancer cells."
Reference (2012, J Transl Med ): Liu, Z., Duan, J. H., Song, Y. M., Ma, J., Wang, F. D., Lu, X., & Yang, X. D. (2012). Novel HER2 aptamer selectively delivers cytotoxic drug to HER2-positive breast cancer cells in vitro. Journal of translational medicine, 10, 148. https://doi.org/10.1186/1479-5876-10-148
Aptamer: HER2 aptamer (HB5)
Target: Extracellular domain (ECD) of human epithelial growth factor receptor 2 (HER2) protein
Type of nucleic acid: ssDNA
Sequence: 5'AACCGCCCAAATCCCTAAGAGTCTGCACTTGTCATTTTGTATATGTATTTGGTTTTTGGCTCTCACAGACACACTACACACGCACA3'
Sequence length: 86
GC content: 0.4302325581395348
Affinity: Kd: 316 nM
Pool type: 5'-AACCGCCCAAATCCCTAAGAGTC-N40-CACAGACACACTACACACGCACA-3'
Pool random region: 40
Binding buffer/conditions: Hank's Buffer with 0.1 mg/mL salmon sperm DNA and 1 mg/mL of BSA
Buffer type: Other Buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " HER2 protein is an attractive target for tumor-specific drug delivery because of its overexpression in multiple malignancies, including breast, gastric, ovarian, and lung cancers. The results suggest that the selected HER2 aptamer may have application potentials in targeted therapy against HER2-positive breast cancer cells."
Reference (2012, J Transl Med ): Liu, Z., Duan, J. H., Song, Y. M., Ma, J., Wang, F. D., Lu, X., & Yang, X. D. (2012). Novel HER2 aptamer selectively delivers cytotoxic drug to HER2-positive breast cancer cells in vitro. Journal of translational medicine, 10, 148. https://doi.org/10.1186/1479-5876-10-148
Aptamer: H2
Target: Hirame rhabdovirus (HIRRV)
Type of nucleic acid: ssRNA
Sequence: 5'GGAACGCGAGCUUAGAUUUCGGAGAACAGUUUGUAAUUGUU3'
Sequence length: 41
GC content: 0.4146341463414634
Affinity: Not reported
Pool type: 5′‐GGGCCAGGCAGCGAG-N40‐CCGACCACACGCGTCCGAGA‐3′
Pool random region: 40
Binding buffer/conditions: 2.5 mm MgCl2, 100 mm NaCl, 20 mm Tris–HCl, pH 7.5
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: " Here, we describe four Hirame rhabdovirus (HIRRV)-RNA aptamers (H1, H2, H3 and H4) that we obtained from an in vitro process called the systematic evolution of ligands by exponential enrichment (SELEX). The HIRRV-RNA aptamers specifically bind to HIRRV. Thus, the recombinant R. sulfidophilum might be a powerful tool for the prevention of HIRRV in aquaculture."
Reference (2012, J Fish Dis ): Hwang, S. D., Midorikawa, N., Punnarak, P., Kikuchi, Y., Kondo, H., Hirono, I., & Aoki, T. (2012). Inhibition of Hirame rhabdovirus growth by RNA aptamers. Journal of fish diseases, 35(12), 927–934. https://doi.org/10.1111/jfd.12000
Aptamer: H4
Target: Hirame rhabdovirus (HIRRV)
Type of nucleic acid: ssRNA
Sequence: 5'GGGUUAAGCCGGAUUGUAGACUGUAACAGGUAGAGCUGGC3'
Sequence length: 40
GC content: 0.525
Affinity: Not reported
Pool type: 5′‐GGGCCAGGCAGCGAG-N40‐CCGACCACACGCGTCCGAGA‐3′
Pool random region: 40
Binding buffer/conditions: 2.5 mm MgCl2, 100 mm NaCl, 20 mm Tris–HCl, pH 7.5
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: " Here, we describe four Hirame rhabdovirus (HIRRV)-RNA aptamers (H1, H2, H3 and H4) that we obtained from an in vitro process called the systematic evolution of ligands by exponential enrichment (SELEX). The HIRRV-RNA aptamers specifically bind to HIRRV. Thus, the recombinant R. sulfidophilum might be a powerful tool for the prevention of HIRRV in aquaculture."
Reference (2012, J Fish Dis ): Hwang, S. D., Midorikawa, N., Punnarak, P., Kikuchi, Y., Kondo, H., Hirono, I., & Aoki, T. (2012). Inhibition of Hirame rhabdovirus growth by RNA aptamers. Journal of fish diseases, 35(12), 927–934. https://doi.org/10.1111/jfd.12000