RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: Apt- 9.4
Target: Ethanolamine
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGCTGCGAGGTGGGTGGGTGGGAGCAATTGATCCTCGCTTAGCTTCTACGGTGGGCTATCTAGATAGTAAGTGCAATCT3′
Sequence length: 96
GC content: 0.4791666666666667
Affinity: Kd: 10 ± 2 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N60-AGATAGTAAGTGCAATCT-3′
Pool random region: 60
Binding buffer/conditions: 100 mmol L−1 NaCl/20 mmol L−1 Tris/HCl, pH 7.6/2 mmol L−1 MgCl2/5 mmol L−1 KCl/1 mmol L−1 CaCl2/0.02% 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: " The aim of the development of ethanolamine aptamers is their use for the detection of this substance in clinical and environmental analysis. Ethanolamine is associated with several diseases. Moreover, ethanolamine and its derivatives di- and tri-ethanolamine are used in chemical and cosmetic industries. The use of biosensors with ethanolamine aptamer as new molecular recognition element could be an innovative method for an easy and fast detection of ethanolamine"
Reference (2005, Biochem Biophys Res Commun ): Mann, D., Reinemann, C., Stoltenburg, R., & Strehlitz, B. (2005). In vitro selection of DNA aptamers binding ethanolamine. Biochemical and biophysical research communications, 338(4), 1928–1934. https://doi.org/10.1016/j.bbrc.2005.10.172
Aptamer: Apt- 9.1
Target: Ethanolamine
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGCTGCGAGGTGGGTGGGTGGGAGCAATTGGTCCTTGCTTAGCTTCTACGGTGGGCTATCTAGATAGTAAGTGCAATCT3′
Sequence length: 96
GC content: 0.4791666666666667
Affinity: Kd: 19 ± 7 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N60-AGATAGTAAGTGCAATCT-3′
Pool random region: 60
Binding buffer/conditions: 100 mmol L−1 NaCl/20 mmol L−1 Tris/HCl, pH 7.6/2 mmol L−1 MgCl2/5 mmol L−1 KCl/1 mmol L−1 CaCl2/0.02% 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: " The aim of the development of ethanolamine aptamers is their use for the detection of this substance in clinical and environmental analysis. Ethanolamine is associated with several diseases. Moreover, ethanolamine and its derivatives di- and tri-ethanolamine are used in chemical and cosmetic industries. The use of biosensors with ethanolamine aptamer as new molecular recognition element could be an innovative method for an easy and fast detection of ethanolamine"
Reference (2005, Biochem Biophys Res Commun ): Mann, D., Reinemann, C., Stoltenburg, R., & Strehlitz, B. (2005). In vitro selection of DNA aptamers binding ethanolamine. Biochemical and biophysical research communications, 338(4), 1928–1934. https://doi.org/10.1016/j.bbrc.2005.10.172
Aptamer: Apt- 4.20
Target: Human immunodeficiency virus reverse transcriptase (HIVRT)
Type of nucleic acid: ssDNA
Sequence: 5‘AGCAGCACAGAGGTCAGATGACATGATGTTCGGACACGTGAAGGAATAGAAAGCCCTCACTTCAGCGTAGCACGCATAGG3‘
Sequence length: 80
GC content: 0.5125
Affinity: Kd: 180 ± 70 pM
Pool type: 5‘-AGCAGCACAGAGGTCAGATG-N40-TTCAGCGTAGCACGCATAGG-3‘
Pool random region: 40
Binding buffer/conditions: 10 mM tris, 50 mM NaCl, and 1 mM EDTA pH 7.5
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: " used CE-SELEX to obtain highaffinity ssDNA aptamers for HIVRT. The number of cases of HIV worldwide continues to increase at an alarming rate. ssDNA aptamers with picomolar affinity for HIVRT would make attractive drug candidates. Alternatively, aptamers with picomolar affinity may provide the sensitivity necessary to develop an affinity-based diagnostic assay for HIV infection."
Reference (2005, Anal Chem ): Mosing, R. K., Mendonsa, S. D., & Bowser, M. T. (2005). Capillary electrophoresis-SELEX selection of aptamers with affinity for HIV-1 reverse transcriptase. Analytical chemistry, 77(19), 6107–6112. https://doi.org/10.1021/ac050836q
Aptamer: A11
Target: RPKPQQFFGLM-NH2 (peptide, Substance P )
Type of nucleic acid: ssRNA
Sequence: 5'GGAGCUUAGACAACAGCAGCGUGCAGGUGGGUAAAGGGGUGUGAUCGAGGGUCGAGAGGCACGCUCAGGUGAGUCGGUUCCAC'3
Sequence length: 83
GC content: 0.6024096385542169
Affinity: Not reported
Pool type: 5'GGAGCTTAGACAACAGCAGCGTGC-N34-GCACGCTCAGGTGAGTCGGTTCCAC3'
Pool random region: 34
Binding buffer/conditions: 20 mM Tris–HCl, pH 7.4, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2 and 0.1% Tween-20
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Therapeutic: " Identified RNA aptamers to the mirror-image configuration (d-peptide) of substance P. The peptide substance P belongs to the tachykinin family and exerts various biologically important functions, such as peripheral vasodilation, smooth muscle contraction and pain transmission."
Reference (2005, Nucleic Acids Res ): Eulberg, D., Buchner, K., Maasch, C., & Klussmann, S. (2005). Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. Nucleic acids research, 33(4), e45. https://doi.org/10.1093/nar/gni044
Aptamer: SUP-A-004
Target: RPKPQQFFGLM-NH2 (peptide, Substance P )
Type of nucleic acid: ssRNA
Sequence: 5'GGCGCAGGUGGGUAAAGGGGUGUGAUCGAGGGUCGAGAGGCGCC3'
Sequence length: 44
GC content: 0.6818181818181818
Affinity: Kd: 40 nM
Pool type: 5'GGAGCTTAGACAACAGCAGCGTGC-N34-GCACGCTCAGGTGAGTCGGTTCCAC3'
Pool random region: 34
Binding buffer/conditions: 20 mM Tris–HCl, pH 7.4, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2 and 0.1% Tween-20
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated version of a11(unmodified aptamer)
Application as quoted in the referenced paper: Therapeutic: " Identified RNA aptamers to the mirror-image configuration (d-peptide) of substance P. The peptide substance P belongs to the tachykinin family and exerts various biologically important functions, such as peripheral vasodilation, smooth muscle contraction and pain transmission."
Reference (2005, Nucleic Acids Res ): Eulberg, D., Buchner, K., Maasch, C., & Klussmann, S. (2005). Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. Nucleic acids research, 33(4), e45. https://doi.org/10.1093/nar/gni044
Aptamer: s23
Target: TFKBP*3R-2G (cell surface protein)
Type of nucleic acid: ssRNA
Sequence: 5'GGGUUCGAAUGCAAGUCUGGUGAGUGUUGGGAGGGCAGUGACUUGCUUCGUAGUGUAAACUGACGUGGCGGUGUUACUUUACUGUUACGCUAGGUUACGGG3'
Sequence length: 101
GC content: 0.5148514851485149
Affinity: Kd: 4.3 ± 0.5 nM
Pool type: 5′-CCCAAGCTTACGTTCAGACCA-N60-CAATGCGATCCAATGCCCTATAGTGAGTCGTATTAGAATTCCG-3'
Pool random region: 60
Binding buffer/conditions: 50 mM potassium phosphate (pH 7.4), 5 mM Mg(OAc)2, 150 mM KCl and 1 mM DTT
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Diagnostic: " Combined use of synthetic chemistry, protein design and RNA selection technology to produce such a cell-orthogonal RNA targeting system. The system will induce the binding of a small molecule-protein complex to RNA and serve as a useful tool for a broad range of studies on gene expression and protein function, by enabling temporal control to be exerted over the sub-cellular localization, tissue distribution, splicing and translation of RNA."
Reference (2005, Nucleic Acids Res ): Plummer, K. A., Carothers, J. M., Yoshimura, M., Szostak, J. W., & Verdine, G. L. (2005). In vitro selection of RNA aptamers against a composite small molecule-protein surface. Nucleic acids research, 33(17), 5602–5610. https://doi-org.ezproxy.lib.utexas.edu/10.1093/nar/gki867
Aptamer: T1 s23
Target: TFKBP*3R-2G (cell surface protein)
Type of nucleic acid: ssRNA
Sequence: 5'CGAAUGCAAGUCUGGUGAGUGUUGGGAGGGCAGUGACUUGCUUCG3'
Sequence length: 45
GC content: 0.5555555555555556
Affinity: Kd: 2.8 ± 0.2  nM
Pool type: 5′-CCCAAGCTTACGTTCAGACCA-N60-CAATGCGATCCAATGCCCTATAGTGAGTCGTATTAGAATTCCG-3'
Pool random region: 60
Binding buffer/conditions: 50 mM potassium phosphate (pH 7.4), 5 mM Mg(OAc)2, 150 mM KCl and 1 mM DTT
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated version of s23
Application as quoted in the referenced paper: Diagnostic: " Combined use of synthetic chemistry, protein design and RNA selection technology to produce such a cell-orthogonal RNA targeting system. The system will induce the binding of a small molecule-protein complex to RNA and serve as a useful tool for a broad range of studies on gene expression and protein function, by enabling temporal control to be exerted over the sub-cellular localization, tissue distribution, splicing and translation of RNA."
Reference (2005, Nucleic Acids Res ): Plummer, K. A., Carothers, J. M., Yoshimura, M., Szostak, J. W., & Verdine, G. L. (2005). In vitro selection of RNA aptamers against a composite small molecule-protein surface. Nucleic acids research, 33(17), 5602–5610. https://doi-org.ezproxy.lib.utexas.edu/10.1093/nar/gki867
Aptamer: T2 s23
Target: TFKBP*3R-2G (cell surface protein)
Type of nucleic acid: ssRNA
Sequence: 5'GCAAGUCUGGUGAGUGUUGGGAGGGCAGUGACUUGC3'
Sequence length: 36
GC content: 0.5833333333333334
Affinity: Kd:16.1 ± 3.6 nM
Pool type: 5′-CCCAAGCTTACGTTCAGACCA-N60-CAATGCGATCCAATGCCCTATAGTGAGTCGTATTAGAATTCCG-3'
Pool random region: 60
Binding buffer/conditions: 50 mM potassium phosphate (pH 7.4), 5 mM Mg(OAc)2, 150 mM KCl and 1 mM DTT
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated version of s23
Application as quoted in the referenced paper: Diagnostic: " Combined use of synthetic chemistry, protein design and RNA selection technology to produce such a cell-orthogonal RNA targeting system. The system will induce the binding of a small molecule-protein complex to RNA and serve as a useful tool for a broad range of studies on gene expression and protein function, by enabling temporal control to be exerted over the sub-cellular localization, tissue distribution, splicing and translation of RNA."
Reference (2005, Nucleic Acids Res ): Plummer, K. A., Carothers, J. M., Yoshimura, M., Szostak, J. W., & Verdine, G. L. (2005). In vitro selection of RNA aptamers against a composite small molecule-protein surface. Nucleic acids research, 33(17), 5602–5610. https://doi-org.ezproxy.lib.utexas.edu/10.1093/nar/gki867
Aptamer: C44
Target: IFN-gamma-inducible (IFN-γ-Inducible) mCXCL10 Chemokine (also known as IP-10 in humans and CRG-2 in mice)
Type of nucleic acid: ssRNA
Sequence: 5'UAAUACGACUCACUAUAGGGAGGACGAUGCGGCAUGCGUCUGACCUACGUGCCAAGCAUUUGUGUAACCCGUCAGACGACUCGCCCGA3'
Sequence length: 88
GC content: 0.5454545454545454
Affinity: Kd: 3.5 nM, IC50 = 40.2 nM
Pool type: 5'-GGAGGACGATGCGG-N40-CAGACGACTCGCCCGA-3'
Pool random region: 40
Binding buffer/conditions: 110 mM NaCl, 1 mM MgCl2, 20 mM HEPES, pH 7.0, 1 mM CaCl2, 5 mM KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Includes t7 promoter
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "The C44 aptamer was the only RNA molecule identified capable of antagonizing both the human and the mouse CXCL10, making this aptamer an excellent tool for target validation and potentially a candidate for therapeutic use. This aptamer was shown to be functional in assays against both mouse and human CXCL10."
Additional information: C” aptamers were generated by the mCXCL10 SELEX. A Potent Antagonist against Both mCXCL10 and hCXCL10 Orthologues.
Reference (2005, Biochemistry ): Marro, M. L., Daniels, D. A., McNamee, A., Andrew, D. P., Chapman, T. D., Jiang, M. S., Wu, Z., Smith, J. L., Patel, K. K., & Gearing, K. L. (2005). Identification of potent and selective RNA antagonists of the IFN-gamma-inducible CXCL10 chemokine. Biochemistry, 44(23), 8449–8460. https://doi.org/10.1021/bi048145w
Aptamer: C44-38
Target: IFN-gamma-inducible (IFN-γ-Inducible) mCXCL10 Chemokine (also known as IP-10 in humans and CRG-2 in mice)
Type of nucleic acid: ssRNA
Sequence: 5'UCUGACCUACGUGCCAAGCAUUUGUGUAACCCGUCAGA3'
Sequence length: 38
GC content: 0.5
Affinity: IC50 = 29.3 nM
Pool type: 5'-GGAGGACGATGCGG-N40-CAGACGACTCGCCCGA-3'
Pool random region: 40
Binding buffer/conditions: 110 mM NaCl, 1 mM MgCl2, 20 mM HEPES, pH 7.0, 1 mM CaCl2, 5 mM KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated c44
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "The C44 aptamer was the only RNA molecule identified capable of antagonizing both the human and the mouse CXCL10, making this aptamer an excellent tool for target validation and potentially a candidate for therapeutic use. This aptamer was shown to be functional in assays against both mouse and human CXCL10."
Additional information: C” aptamers were generated by the mCXCL10 SELEX
Reference (2005, Biochemistry ): Marro, M. L., Daniels, D. A., McNamee, A., Andrew, D. P., Chapman, T. D., Jiang, M. S., Wu, Z., Smith, J. L., Patel, K. K., & Gearing, K. L. (2005). Identification of potent and selective RNA antagonists of the IFN-gamma-inducible CXCL10 chemokine. Biochemistry, 44(23), 8449–8460. https://doi.org/10.1021/bi048145w
Aptamer: P31
Target: IFN-gamma-inducible (IFN-γ-Inducible) mCXCL10 Chemokine (also known as IP-10 in humans and CRG-2 in mice)
Type of nucleic acid: ssRNA
Sequence: 5'UAAUACGACUCACUAUAGGGAGGACGAUGCGGAGUUUCUUCUGAGGUCUGAACCUUUCGAAAGCUGGCGCUCAGACGACUCGCCCGA3'
Sequence length: 87
GC content: 0.5287356321839081
Affinity: Kd: 1.53 nM
Pool type: 5'-GGAGGACGATGCGG-N40-CAGACGACTCGCCCGA-3'
Pool random region: 40
Binding buffer/conditions: 110 mM NaCl, 1 mM MgCl2, 20 mM HEPES, pH 7.0, 1 mM CaCl2, 5 mM KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Includes t7 promoter
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "The C44 aptamer was the only RNA molecule identified capable of antagonizing both the human and the mouse CXCL10, making this aptamer an excellent tool for target validation and potentially a candidate for therapeutic use. This aptamer was shown to be functional in assays against both mouse and human CXCL10."
Additional information: “P” aptamers were generated by the hCXCL10 SELEX. In summary, the anti-hCXCL10 aptamers demonstrated high specificity and selectivity by functionally antagonizing hCXCL10 but not mCXCL10, hCXCL9, hCXCL11, hCCL1, or hCCL22 chemokines.
Reference (2005, Biochemistry ): Marro, M. L., Daniels, D. A., McNamee, A., Andrew, D. P., Chapman, T. D., Jiang, M. S., Wu, Z., Smith, J. L., Patel, K. K., & Gearing, K. L. (2005). Identification of potent and selective RNA antagonists of the IFN-gamma-inducible CXCL10 chemokine. Biochemistry, 44(23), 8449–8460. https://doi.org/10.1021/bi048145w
Aptamer: P12
Target: IFN-gamma-inducible (IFN-γ-Inducible) mCXCL10 Chemokine (also known as IP-10 in humans and CRG-2 in mice)
Type of nucleic acid: ssRNA
Sequence: 5'UAAUACGACUCACUAUAGGGAGGACGAUGCGGACUGAACCUAAUUUGAAAUUGGCUGGCGCGCAUAUUCCGUCAGACGACUCGCCCGA3'
Sequence length: 88
GC content: 0.5113636363636364
Affinity: Kd: 1.76 nM
Pool type: 5'-GGAGGACGATGCGG-N40-CAGACGACTCGCCCGA-3'
Pool random region: 40
Binding buffer/conditions: 110 mM NaCl, 1 mM MgCl2, 20 mM HEPES, pH 7.0, 1 mM CaCl2, 5 mM KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Includes t7 promoter
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "The C44 aptamer was the only RNA molecule identified capable of antagonizing both the human and the mouse CXCL10, making this aptamer an excellent tool for target validation and potentially a candidate for therapeutic use. This aptamer was shown to be functional in assays against both mouse and human CXCL10."
Additional information: “P” aptamers were generated by the hCXCL10 SELEX. In summary, the anti-hCXCL10 aptamers demonstrated high specificity and selectivity by functionally antagonizing hCXCL10 but not mCXCL10, hCXCL9, hCXCL11, hCCL1, or hCCL22 chemokines.
Reference (2005, Biochemistry ): Marro, M. L., Daniels, D. A., McNamee, A., Andrew, D. P., Chapman, T. D., Jiang, M. S., Wu, Z., Smith, J. L., Patel, K. K., & Gearing, K. L. (2005). Identification of potent and selective RNA antagonists of the IFN-gamma-inducible CXCL10 chemokine. Biochemistry, 44(23), 8449–8460. https://doi.org/10.1021/bi048145w
Aptamer: not reported
Target: Autonomously replicating sequence‐binding factor 1 (ABF1) protein
Type of nucleic acid: ssDNA
Sequence: 5′GACCCGTAGGGCAGTGAATTCAGATACGTAACTAACGACGATCCCCTACGTTAGCAAGCTTGGACGTGTGTGCG3'
Sequence length: 74
GC content: 0.527027027027027
Affinity: Kd: 4.7 ± 1.1 nM
Pool type: 5′‐GACCCGTAGGGCAGTGAATTCAG‐N30‐GCAAGCTTGGACGTGTGTGCG-3'
Pool random region: 30
Binding buffer/conditions: 25 mM HEPES, pH 7.5, 25 μM ZnCl2, 2 mM β‐mercaptoethanol, 5% glycerol, 75 mM NaCl, 0.1 mg/ml poly(dI‐dC) and 0.1 mg/ml BSA
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Detection: " DNA sequences that are bound by ABF1 with nearly two-magnitude higher affinity as compared to the hitherto accepted ABF1 consensus sequence. The autonomously replicating sequence-binding factor 1 (ABF1) from Sacchramoyces cerevisiae is known as a multifunctional DNA binding protein that is involved in transcriptional regulation, DNA-replication, and in restructuring of chromatin via nucleosome remodelling."
Reference (2005, FEBS Lett ): Beinoraviciūte-Kellner, R., Lipps, G., & Krauss, G. (2005). In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS letters, 579(20), 4535–4540. https://doi.org/10.1016/j.febslet.2005.07.009
Aptamer: not reported
Target: Autonomously replicating sequence‐binding factor 1 (ABF1) protein
Type of nucleic acid: ssDNA
Sequence: 5′GACCCGTAGGGCAGTGAATTCAGATCGATGACCCGTAGTGCAGTGAATTACGTGCAAGCTTGGACGTGTGTGCG3'
Sequence length: 74
GC content: 0.5405405405405406
Affinity: Kd: 250.8 ± 9.8 nM
Pool type: 5′‐GACCCGTAGGGCAGTGAATTCAG‐N30‐GCAAGCTTGGACGTGTGTGCG-3'
Pool random region: 30
Binding buffer/conditions: 25 mM HEPES, pH 7.5, 25 μM ZnCl2, 2 mM β‐mercaptoethanol, 5% glycerol, 75 mM NaCl, 0.1 mg/ml poly(dI‐dC) and 0.1 mg/ml BSA
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Detection: " DNA sequences that are bound by ABF1 with nearly two-magnitude higher affinity as compared to the hitherto accepted ABF1 consensus sequence. The autonomously replicating sequence-binding factor 1 (ABF1) from Sacchramoyces cerevisiae is known as a multifunctional DNA binding protein that is involved in transcriptional regulation, DNA-replication, and in restructuring of chromatin via nucleosome remodelling."
Reference (2005, FEBS Lett ): Beinoraviciūte-Kellner, R., Lipps, G., & Krauss, G. (2005). In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS letters, 579(20), 4535–4540. https://doi.org/10.1016/j.febslet.2005.07.009
Aptamer: Apt- 83
Target: Autonomously replicating sequence‐binding factor 1 (ABF1) protein
Type of nucleic acid: ssDNA
Sequence: 5′GACCCGTAGGGCAGTGAATTCAGCCACAGTACTACCGTATAACATGATGTCAAGCAAGCTTGGACGTGTGTGCG3'
Sequence length: 74
GC content: 0.5135135135135135
Affinity: Kd: 0.06 ± 0.02 nM
Pool type: 5′‐GACCCGTAGGGCAGTGAATTCAG‐N30‐GCAAGCTTGGACGTGTGTGCG-3'
Pool random region: 30
Binding buffer/conditions: 25 mM HEPES, pH 7.5, 25 μM ZnCl2, 2 mM β‐mercaptoethanol, 5% glycerol, 75 mM NaCl, 0.1 mg/ml poly(dI‐dC) and 0.1 mg/ml BSA
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: Detection: " DNA sequences that are bound by ABF1 with nearly two-magnitude higher affinity as compared to the hitherto accepted ABF1 consensus sequence. The autonomously replicating sequence-binding factor 1 (ABF1) from Sacchramoyces cerevisiae is known as a multifunctional DNA binding protein that is involved in transcriptional regulation, DNA-replication, and in restructuring of chromatin via nucleosome remodelling."
Additional information: inconsistencies in reporting aptamer sequence
Reference (2005, FEBS Lett ): Beinoraviciūte-Kellner, R., Lipps, G., & Krauss, G. (2005). In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS letters, 579(20), 4535–4540. https://doi.org/10.1016/j.febslet.2005.07.009
Aptamer: Apt-78
Target: Autonomously replicating sequence‐binding factor 1 (ABF1) protein
Type of nucleic acid: ssDNA
Sequence: 5′GACCCGTAGGGCAGTGAATTCAGTAGTGATGTTCGTGGCGAATGATACACTTAGCAAGCTTGGACGTGTGTGCG3'
Sequence length: 74
GC content: 0.5135135135135135
Affinity: Kd: 0.44 ± 0.11 nM
Pool type: 5′‐GACCCGTAGGGCAGTGAATTCAG‐N30‐GCAAGCTTGGACGTGTGTGCG-3'
Pool random region: 30
Binding buffer/conditions: 25 mM HEPES, pH 7.5, 25 μM ZnCl2, 2 mM β‐mercaptoethanol, 5% glycerol, 75 mM NaCl, 0.1 mg/ml poly(dI‐dC) and 0.1 mg/ml BSA
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: Detection: " DNA sequences that are bound by ABF1 with nearly two-magnitude higher affinity as compared to the hitherto accepted ABF1 consensus sequence. The autonomously replicating sequence-binding factor 1 (ABF1) from Sacchramoyces cerevisiae is known as a multifunctional DNA binding protein that is involved in transcriptional regulation, DNA-replication, and in restructuring of chromatin via nucleosome remodelling."
Reference (2005, FEBS Lett ): Beinoraviciūte-Kellner, R., Lipps, G., & Krauss, G. (2005). In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS letters, 579(20), 4535–4540. https://doi.org/10.1016/j.febslet.2005.07.009
Aptamer: Apt-77
Target: Autonomously replicating sequence‐binding factor 1 (ABF1) protein
Type of nucleic acid: ssDNA
Sequence: 5′GACCCGTAGGGCAGTGAATTCAGTGTATCGTATTTGGTGATGTTTGGTGTTCAGCAAGCTTGGACGTGTGTGCG3'
Sequence length: 74
GC content: 0.5
Affinity: Kd: 2.1 ± 0.2 nM
Pool type: 5′‐GACCCGTAGGGCAGTGAATTCAG‐N30‐GCAAGCTTGGACGTGTGTGCG-3'
Pool random region: 30
Binding buffer/conditions: 25 mM HEPES, pH 7.5, 25 μM ZnCl2, 2 mM β‐mercaptoethanol, 5% glycerol, 75 mM NaCl, 0.1 mg/ml poly(dI‐dC) and 0.1 mg/ml BSA
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: Detection: " DNA sequences that are bound by ABF1 with nearly two-magnitude higher affinity as compared to the hitherto accepted ABF1 consensus sequence. The autonomously replicating sequence-binding factor 1 (ABF1) from Sacchramoyces cerevisiae is known as a multifunctional DNA binding protein that is involved in transcriptional regulation, DNA-replication, and in restructuring of chromatin via nucleosome remodelling."
Reference (2005, FEBS Lett ): Beinoraviciūte-Kellner, R., Lipps, G., & Krauss, G. (2005). In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS letters, 579(20), 4535–4540. https://doi.org/10.1016/j.febslet.2005.07.009