RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: 10.10q aptamer
Target: Daunomycin
Type of nucleic acid: ssDNA
Sequence: 5'AGGGGTAAGGGGTGGGGGTGGGT3'
Sequence length: 23
GC content: 0.6956521739130435
Affinity: Not reported
Pool type: 5'-GGGAATTCGAGCTCGGTACC-N40-CTGCAGGCATGCAAGCTTGG-3'
Pool random region: 40
Binding buffer/conditions: 20 mM Tris–HCl [pH 7.4], 140 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2, and 0.05% [v/v] Tween 20
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: 10.10Q was empirically shortened to obtain only the g-rich sequence
Application as quoted in the referenced paper: Detection: " We describe the characterization of a DNA aptamer that displays high affinity and specificity for the anthracyclines daunomycin and doxorubicin, both of which are frequently used in chemotherapy. This not only allows the determination of the aptamer's specificity but also allows the quantification of as little as 8.4 microg/L daunomycin and doxorubicin."
Reference (2008, Anal Biochem ): Wochner, A., Menger, M., Orgel, D., Cech, B., Rimmele, M., Erdmann, V. A., & Glökler, J. (2008). A DNA aptamer with high affinity and specificity for therapeutic anthracyclines. Analytical biochemistry, 373(1), 34–42. https://doi.org/10.1016/j.ab.2007.09.007
Aptamer: S1
Target: Recombinant human 14-3-3 gamma (14-3-3γ)
Type of nucleic acid: ssDNA
Sequence: 5′CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACTAGCGCCGGTGGTGGGGGTTGTTGTTACGCGGTATTATACTTGAGCAAAATCACCTGCAGGGG3′
Sequence length: 111
GC content: 0.5135135135135135
Affinity: Kd: 5.4 μM
Pool type: 5′-CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACT-N40-ACTTGAGCAAAATCACCTGCAGGGG-3′
Pool random region: 40
Binding buffer/conditions: Tris–Cl (50 mM, pH 7.5), Triton X-100 (0.05% w/v), NaCl (0.5 M), imidazole (20 mM)
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: Detection and Diagnostic: "We describe identification of a synthetic ssDNA aptamer which binds to undenatured 14-3-3 proteins and its application to the affinity precipitation of 14-3-3 from the cerebral spinal fluid of a scrapie infected sheep. Detection of 14-3-3 proteins is used in the diagnosis of sporadic Creutzfeld–Jacob disease (sCJD) in humans"
Reference (2008, Bioorg Chem ): Stevenson, R., Baxter, H. C., Aitken, A., Brown, T., & Baxter, R. L. (2008). Binding of 14-3-3 proteins to a single stranded oligodeoxynucleotide aptamer. Bioorganic chemistry, 36(5), 215–219. https://doi.org/10.1016/j.bioorg.2007.12.005
Aptamer: S2
Target: Recombinant human 14-3-3 gamma (14-3-3γ)
Type of nucleic acid: ssDNA
Sequence: 5′CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACTCGAGGCGTGTGCAAGGCGTGTTGTTCAAAGGTGTGTGTGTACTTGAGCAAAATCACCTGCAGGGG3′
Sequence length: 114
GC content: 0.5087719298245614
Affinity: Kd: 0.56 μM
Pool type: 5′-CCGAAGCTTAATACGACTCACTATAGGGATCCGCCTGATTAGCGATACT-N40-ACTTGAGCAAAATCACCTGCAGGGG-3′
Pool random region: 40
Binding buffer/conditions: Tris–Cl (50 mM, pH 7.5), Triton X-100 (0.05% w/v), NaCl (0.5 M), imidazole (20 mM)
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: Detection and Diagnostic: "We describe identification of a synthetic ssDNA aptamer which binds to undenatured 14-3-3 proteins and its application to the affinity precipitation of 14-3-3 from the cerebral spinal fluid of a scrapie infected sheep. Detection of 14-3-3 proteins is used in the diagnosis of sporadic Creutzfeld–Jacob disease (sCJD) in humans"
Reference (2008, Bioorg Chem ): Stevenson, R., Baxter, H. C., Aitken, A., Brown, T., & Baxter, R. L. (2008). Binding of 14-3-3 proteins to a single stranded oligodeoxynucleotide aptamer. Bioorganic chemistry, 36(5), 215–219. https://doi.org/10.1016/j.bioorg.2007.12.005
Aptamer: TLS1
Target: Liver cancer cell line BNL 1ME A.7R.1 (MEAR) (T-cell acute lymphoblastic leukemia cell line, CCRF-CEM)
Type of nucleic acid: ssDNA
Sequence: 5'ACGCTCGGATGCCACTACAGAGTGATGGTTGTTATCTGGCCTCAGAGGTTCTCGGGTGTGGTCACTCATGGACGTGCTGGTGAC3'
Sequence length: 84
GC content: 0.5595238095238095
Affinity: Kd: 10.34 ± 0.96 nM
Pool type: 5'-ACGCTCGGATGCCACTACAG-N45-CTCATGGACGTGCTGGTGAC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline with calcium chloride and magnesium chloride (Sigma); yeast tRNA (0.1 mg/mL; Sigma) and BSA (1 mg/mL; Fisher)
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 Detection: "The cell-SELEX shows that the newly generated aptamers could be effective molecular probes for liver cancer analysis. The close relationship between MEAR cells and BNL cells indicated that cell-SELEX can be used to identify minor molecular-level differences among cells. It further indicates that the target molecules would be specific biomarkers for this kind of liver cancer and would provide useful information for explaining the mechanism of oncogenesis."
Reference (2008, Anal Chem ): Shangguan, D., Meng, L., Cao, Z. C., Xiao, Z., Fang, X., Li, Y., Cardona, D., Witek, R. P., Liu, C., & Tan, W. (2008). Identification of liver cancer-specific aptamers using whole live cells. Analytical chemistry, 80(3), 721–728. https://doi.org/10.1021/ac701962v
Aptamer: TLS1c
Target: Liver cancer cell line BNL 1ME A.7R.1 (MEAR) (T-cell acute lymphoblastic leukemia cell line, CCRF-CEM)
Type of nucleic acid: ssDNA
Sequence: 5'ACAGGAGTGATGGTTGTTATCTGGCCTCAGAGGTTCTCGGGTGTGGTCACTCCTG3'
Sequence length: 55
GC content: 0.5454545454545454
Affinity: Kd: 9.79 ± 0.30 nM
Pool type: 5'-ACGCTCGGATGCCACTACAG-N45-CTCATGGACGTGCTGGTGAC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline with calcium chloride and magnesium chloride (Sigma); yeast tRNA (0.1 mg/mL; Sigma) and BSA (1 mg/mL; Fisher)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Optimized truncated version of tls1 aptamer
Application as quoted in the referenced paper: Diagnostic and Detection: "The cell-SELEX shows that the newly generated aptamers could be effective molecular probes for liver cancer analysis. The close relationship between MEAR cells and BNL cells indicated that cell-SELEX can be used to identify minor molecular-level differences among cells. It further indicates that the target molecules would be specific biomarkers for this kind of liver cancer and would provide useful information for explaining the mechanism of oncogenesis."
Reference (2008, Anal Chem ): Shangguan, D., Meng, L., Cao, Z. C., Xiao, Z., Fang, X., Li, Y., Cardona, D., Witek, R. P., Liu, C., & Tan, W. (2008). Identification of liver cancer-specific aptamers using whole live cells. Analytical chemistry, 80(3), 721–728. https://doi.org/10.1021/ac701962v
Aptamer: TLS3
Target: Liver cancer cell line BNL 1ME A.7R.1 (MEAR) (T-cell acute lymphoblastic leukemia cell line, CCRF-CEM)
Type of nucleic acid: ssDNA
Sequence: 5'ACGCTCGGATGCCACTACAGTGGGAATATTAGTACCGTTATTCGGACTCCGCCATGACAATCTGGCTCATGGACGTGCTGGTGAC3'
Sequence length: 85
GC content: 0.5294117647058824
Affinity: Kd: 10.9 ± 1.8 nM
Pool type: 5'-ACGCTCGGATGCCACTACAG-N45-CTCATGGACGTGCTGGTGAC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline with calcium chloride and magnesium chloride (Sigma); yeast tRNA (0.1 mg/mL; Sigma) and BSA (1 mg/mL; Fisher)
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 Detection: "The cell-SELEX shows that the newly generated aptamers could be effective molecular probes for liver cancer analysis. The close relationship between MEAR cells and BNL cells indicated that cell-SELEX can be used to identify minor molecular-level differences among cells. It further indicates that the target molecules would be specific biomarkers for this kind of liver cancer and would provide useful information for explaining the mechanism of oncogenesis."
Reference (2008, Anal Chem ): Shangguan, D., Meng, L., Cao, Z. C., Xiao, Z., Fang, X., Li, Y., Cardona, D., Witek, R. P., Liu, C., & Tan, W. (2008). Identification of liver cancer-specific aptamers using whole live cells. Analytical chemistry, 80(3), 721–728. https://doi.org/10.1021/ac701962v
Aptamer: TLS4
Target: Liver cancer cell line BNL 1ME A.7R.1 (MEAR) (T-cell acute lymphoblastic leukemia cell line, CCRF-CEM)
Type of nucleic acid: ssDNA
Sequence: 5'ACGCTCGGATGCCACTACAGACGGTGGTCGTACACGGCCATTTTATTCCCGGAATATTTGTCAACCTCATGGACGTGCTGGTGAC3'
Sequence length: 85
GC content: 0.5294117647058824
Affinity: Kd: 33.9 ± 2.3 nM
Pool type: 5'-ACGCTCGGATGCCACTACAG-N45-CTCATGGACGTGCTGGTGAC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline with calcium chloride and magnesium chloride (Sigma); yeast tRNA (0.1 mg/mL; Sigma) and BSA (1 mg/mL; Fisher)
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 Detection: "The cell-SELEX shows that the newly generated aptamers could be effective molecular probes for liver cancer analysis. The close relationship between MEAR cells and BNL cells indicated that cell-SELEX can be used to identify minor molecular-level differences among cells. It further indicates that the target molecules would be specific biomarkers for this kind of liver cancer and would provide useful information for explaining the mechanism of oncogenesis."
Reference (2008, Anal Chem ): Shangguan, D., Meng, L., Cao, Z. C., Xiao, Z., Fang, X., Li, Y., Cardona, D., Witek, R. P., Liu, C., & Tan, W. (2008). Identification of liver cancer-specific aptamers using whole live cells. Analytical chemistry, 80(3), 721–728. https://doi.org/10.1021/ac701962v
Aptamer: TLS6
Target: Liver cancer cell line BNL 1ME A.7R.1 (MEAR) (T-cell acute lymphoblastic leukemia cell line, CCRF-CEM)
Type of nucleic acid: ssDNA
Sequence: 5'ACGCTCGGATGCCACTACAGATACGGCCTGGGTCTTTATTCGCCCCGAATATTTCTTAACGTCGGCTCATGGACGTGCTGGTGAC3'
Sequence length: 85
GC content: 0.5411764705882353
Affinity: Kd: 157.0 ± 16.9 nM
Pool type: 5'-ACGCTCGGATGCCACTACAG-N45-CTCATGGACGTGCTGGTGAC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline with calcium chloride and magnesium chloride (Sigma); yeast tRNA (0.1 mg/mL; Sigma) and BSA (1 mg/mL; Fisher)
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 Detection: "The cell-SELEX shows that the newly generated aptamers could be effective molecular probes for liver cancer analysis. The close relationship between MEAR cells and BNL cells indicated that cell-SELEX can be used to identify minor molecular-level differences among cells. It further indicates that the target molecules would be specific biomarkers for this kind of liver cancer and would provide useful information for explaining the mechanism of oncogenesis."
Reference (2008, Anal Chem ): Shangguan, D., Meng, L., Cao, Z. C., Xiao, Z., Fang, X., Li, Y., Cardona, D., Witek, R. P., Liu, C., & Tan, W. (2008). Identification of liver cancer-specific aptamers using whole live cells. Analytical chemistry, 80(3), 721–728. https://doi.org/10.1021/ac701962v
Aptamer: TLS7
Target: Liver cancer cell line BNL 1ME A.7R.1 (MEAR) (T-cell acute lymphoblastic leukemia cell line, CCRF-CEM)
Type of nucleic acid: ssDNA
Sequence: 5'ACGCTCGGATGCCACTACAGTGCGCCCAAAGTTCCCATATTGCTTCCCTGTTGGTGAGTGCCGATCTCATGGACGTGCTGGTGAC3'
Sequence length: 85
GC content: 0.5647058823529412
Affinity: Kd: 68.1 ± 7.6 nM
Pool type: 5'-ACGCTCGGATGCCACTACAG-N45-CTCATGGACGTGCTGGTGAC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline with calcium chloride and magnesium chloride (Sigma); yeast tRNA (0.1 mg/mL; Sigma) and BSA (1 mg/mL; Fisher)
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 Detection: "The cell-SELEX shows that the newly generated aptamers could be effective molecular probes for liver cancer analysis. The close relationship between MEAR cells and BNL cells indicated that cell-SELEX can be used to identify minor molecular-level differences among cells. It further indicates that the target molecules would be specific biomarkers for this kind of liver cancer and would provide useful information for explaining the mechanism of oncogenesis."
Reference (2008, Anal Chem ): Shangguan, D., Meng, L., Cao, Z. C., Xiao, Z., Fang, X., Li, Y., Cardona, D., Witek, R. P., Liu, C., & Tan, W. (2008). Identification of liver cancer-specific aptamers using whole live cells. Analytical chemistry, 80(3), 721–728. https://doi.org/10.1021/ac701962v
Aptamer: TLS11a
Target: Liver cancer cell line BNL 1ME A.7R.1 (MEAR) (T-cell acute lymphoblastic leukemia cell line, CCRF-CEM)
Type of nucleic acid: ssDNA
Sequence: 5'ACAGCATCCCCATGTGAACAATCGCATTGTGATTGTTACGGTTTCCGCCTCATGGACGTGCTG3'
Sequence length: 63
GC content: 0.5079365079365079
Affinity: Kd: 4.51 ± 0.39 nM
Pool type: 5'-ACGCTCGGATGCCACTACAG-N45-CTCATGGACGTGCTGGTGAC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline with calcium chloride and magnesium chloride (Sigma); yeast tRNA (0.1 mg/mL; Sigma) and BSA (1 mg/mL; Fisher)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Optimized truncated version of tls11 aptamer (sequence not provided)
Application as quoted in the referenced paper: Diagnostic and Detection: "The cell-SELEX shows that the newly generated aptamers could be effective molecular probes for liver cancer analysis. The close relationship between MEAR cells and BNL cells indicated that cell-SELEX can be used to identify minor molecular-level differences among cells. It further indicates that the target molecules would be specific biomarkers for this kind of liver cancer and would provide useful information for explaining the mechanism of oncogenesis."
Reference (2008, Anal Chem ): Shangguan, D., Meng, L., Cao, Z. C., Xiao, Z., Fang, X., Li, Y., Cardona, D., Witek, R. P., Liu, C., & Tan, W. (2008). Identification of liver cancer-specific aptamers using whole live cells. Analytical chemistry, 80(3), 721–728. https://doi.org/10.1021/ac701962v
Aptamer: 85A
Target: Fibrinogen
Type of nucleic acid: ssDNA
Sequence: 5'CCTTCGTTGTCTGCCTTCGTAGCGGATCGAATTACGCGTTAACGGCAACCGATAACGGGACCGATTGCACACCCTTCAGAATTCGCACCA3'
Sequence length: 90
GC content: 0.5333333333333333
Affinity: Kd: 102 ± 39.7
Pool type: 5'-CCTTCGTTGTCTGCCTTCGT-N50-ACCCTTCAGAATTCGCACCA-3'
Pool random region: 50
Binding buffer/conditions: 300 mM NaCl, 5 mM MgCl2, 20 mM Tris-HCl at pH 7.6
Divalent salt: MgCl
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: " Using fibrinogen as a model, we have selected boronic acid-modified DNA aptamers that have high affinities (low nM Kd) and the ability to recognize changes in the glycosylation site. The method developed should also be applicable to the development of aptamers for other glyco-products, such as glycolipids and glycopeptides."
Additional information: boronic acid-labeled
Reference (2008, J Am Chem Soc ): Li, M., Lin, N., Huang, Z., Du, L., Altier, C., Fang, H., & Wang, B. (2008). Selecting aptamers for a glycoprotein through the incorporation of the boronic acid moiety. Journal of the American Chemical Society, 130(38), 12636–12638. https://doi.org/10.1021/ja801510d
Aptamer: 85B
Target: Fibrinogen
Type of nucleic acid: ssDNA
Sequence: 5'CCTTCGTTGTCTGCCTTCGTTAGGACCGCAGACATCGACGCAGGGAAATTCCGCAAGTCCAGCCAAATGCCACCCTTCAGAATTCGCACCA3'
Sequence length: 91
GC content: 0.5494505494505495
Affinity: Kd: 6.4±0.81 nM
Pool type: 5'-CCTTCGTTGTCTGCCTTCGT-N50-ACCCTTCAGAATTCGCACCA-3'
Pool random region: 50
Binding buffer/conditions: 300 mM NaCl, 5 mM MgCl2, 20 mM Tris-HCl at pH 7.6
Divalent salt: MgCl
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: " Using fibrinogen as a model, we have selected boronic acid-modified DNA aptamers that have high affinities (low nM Kd) and the ability to recognize changes in the glycosylation site. The method developed should also be applicable to the development of aptamers for other glyco-products, such as glycolipids and glycopeptides."
Additional information: boronic acid-labeled
Reference (2008, J Am Chem Soc ): Li, M., Lin, N., Huang, Z., Du, L., Altier, C., Fang, H., & Wang, B. (2008). Selecting aptamers for a glycoprotein through the incorporation of the boronic acid moiety. Journal of the American Chemical Society, 130(38), 12636–12638. https://doi.org/10.1021/ja801510d
Aptamer: 85C
Target: Fibrinogen
Type of nucleic acid: ssDNA
Sequence: 5'CCTTCGTTGTCTGCCTTCGTAGTCGACTCTGACGCATGGACGTATCCTGTGCGTATGCATTATGAAGCACACCCTTCAGAATTCGCACCA3'
Sequence length: 90
GC content: 0.5111111111111111
Affinity: Kd: 17.1±2.1 nM
Pool type: 5'-CCTTCGTTGTCTGCCTTCGT-N50-ACCCTTCAGAATTCGCACCA-3'
Pool random region: 50
Binding buffer/conditions: 300 mM NaCl, 5 mM MgCl2, 20 mM Tris-HCl at pH 7.6
Divalent salt: MgCl
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: " Using fibrinogen as a model, we have selected boronic acid-modified DNA aptamers that have high affinities (low nM Kd) and the ability to recognize changes in the glycosylation site. The method developed should also be applicable to the development of aptamers for other glyco-products, such as glycolipids and glycopeptides."
Additional information: boronic acid-labeled
Reference (2008, J Am Chem Soc ): Li, M., Lin, N., Huang, Z., Du, L., Altier, C., Fang, H., & Wang, B. (2008). Selecting aptamers for a glycoprotein through the incorporation of the boronic acid moiety. Journal of the American Chemical Society, 130(38), 12636–12638. https://doi.org/10.1021/ja801510d
Aptamer: C13
Target: G-protein-coupled receptor kinase 2 (GRK2)
Type of nucleic acid: ssRNA
Sequence: 5′CUGCAGUUCGGGUAGCACAGACCAUACGGGAGAGAAACUUGUGCAACCCGGGGCUAC3′
Sequence length: 57
GC content: 0.5789473684210527
Affinity: Kd: 78.2 nM ± 2.6 nM
Pool type: 5′-CTGCAGTTCGGGTAGCACA-N20-TGTGCAACCCGGGGCTAC-3′
Pool random region: 20
Binding buffer/conditions: PBS/3 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: Detection: " This RNA aptamer represents the most potent inhibitor of GRK2 activity reported so far. More importantly, the aptamer possesses a high specificity for GRK function, and thus it might allow the precise functional characterization of GRK2 both in cell culture and in vivo."
Reference (2008, RNA ): Mayer, G., Wulffen, B., Huber, C., Brockmann, J., Flicke, B., Neumann, L., Hafenbradl, D., Klebl, B. M., Lohse, M. J., Krasel, C., & Blind, M. (2008). An RNA molecule that specifically inhibits G-protein-coupled receptor kinase 2 in vitro. RNA (New York, N.Y.), 14(3), 524–534. https://doi.org/10.1261/rna.821908
Aptamer: C13.51
Target: G-protein-coupled receptor kinase 2 (GRK2)
Type of nucleic acid: ssRNA
Sequence: 5'GGUUCGGGUAGCACAGACCAUACGGGAGAGAAACUUGUGCAACCCGGGGCU3'
Sequence length: 51
GC content: 0.5882352941176471
Affinity: Kd: 101.2 nM ± 7.2 nM
Pool type: 5′-CTGCAGTTCGGGTAGCACA-N20-TGTGCAACCCGGGGCTAC-3′
Pool random region: 20
Binding buffer/conditions: PBS/3 mM MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated variant of c13 consisting of 51 nt, termed c13.51
Application as quoted in the referenced paper: Detection: " This RNA aptamer represents the most potent inhibitor of GRK2 activity reported so far. More importantly, the aptamer possesses a high specificity for GRK function, and thus it might allow the precise functional characterization of GRK2 both in cell culture and in vivo."
Reference (2008, RNA ): Mayer, G., Wulffen, B., Huber, C., Brockmann, J., Flicke, B., Neumann, L., Hafenbradl, D., Klebl, B. M., Lohse, M. J., Krasel, C., & Blind, M. (2008). An RNA molecule that specifically inhibits G-protein-coupled receptor kinase 2 in vitro. RNA (New York, N.Y.), 14(3), 524–534. https://doi.org/10.1261/rna.821908
Aptamer: T7
Target: Tetracycline (TET), oxytetracycline (OTC), doxycycline (DOX)
Type of nucleic acid: ssDNA
Sequence: 5'CGTACGGAATTCGCTAGCGGGCAGCGGTGGTGTGGCGGGATCTGGGGTTgtgcGGTGTGGATCCGAGCTCCACGTG3'
Sequence length: 76
GC content: 0.6578947368421053
Affinity: Kd: 357.8 nM
Pool type: 5'-CGTACGGAATTCGCTAGC-N40-GGATCCGAGCTCCACGTG-3'
Pool random region: 40
Binding buffer/conditions: NaCl (100 mM), Tris–HCl (20 mM, pH 7.6), MgCl2(2 mM), KCl(5 mM), CaCl2(1 mM), and Tween 20 (0.02%)
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: Drug Delivery: "Tetracyclines (TCs) are a group of antibiotics comprising of a common tetracycline (TET) nucleus with variable X(1) and X(2) positions on 5 and 6 carbon atoms, such as oxytetracycline (OTC) and doxycycline (DOX). TGS-aptamers have potential applications such as target drug delivery, and detection of TCs in pharmaceutical preparations and contaminated food products."
Additional information: ssDNA aptamers were identified by modified SELEX method by employing tosylactivated magnetic beads (TMB) coated with OTC, TET, and DOX,respectively, as targets and counter targets
The T/GTGCT conserved motif was specifically found in TGS-aptamers, which is predicted to be crucial for group specificity because this motif was absent in aptamers specific for OTC as reported in our previous studies.
Reference (2008, Bioorg Med Chem ): Niazi, J. H., Lee, S. J., & Gu, M. B. (2008). Single-stranded DNA aptamers specific for antibiotics tetracyclines. Bioorganic & medicinal chemistry, 16(15), 7245–7253.