RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: B #84 (41 mer)
Target: Streptomycin
Type of nucleic acid: ssRNA
Sequence: 5'AUCACCUCAAGGAAAACGCUUCAGAAAGGGACUUAGGUGAU3'
Sequence length: 41
GC content: 0.4390243902439024
Affinity: Not reported
Pool type: 5'-GGAGCUCAGCCUUCACUGC-N74-GGCACCACGGUCGGAUCCAC3'
Pool random region: 74
Binding buffer/conditions: 5 mM MgCl2, 50 mM Tris-HCl, pH 7.6, 250 mM NaCl
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Pb21-induced cleavage of b #84
Application as quoted in the referenced paper: Drug Development: "A growing body of evidence points to RNA as a crucial target for antibacterial and antiviral drugs. For example, the aminocyclitol antibiotic streptomycin interacts with the 16S ribosomal RNA and, in addition, inhibits group I intron splicing. To understand the mode of binding of streptomycin to RNA, we isolated small, streptomycin-binding RNA aptamers via in vitro selection"
Reference (1998, RNA ): Wallace, S. T., & Schroeder, R. (1998). In vitro selection and characterization of streptomycin-binding RNAs: recognition discrimination between antibiotics. RNA (New York, N.Y.), 4(1), 112–123.
Aptamer: clone 488
Target: SelB protein, Escherichia coli
Type of nucleic acid: ssRNA
Sequence: 5'GCGCUAAGUCCUCGCUCAGCCCAUAAGUUGUCCCAAGUCUUGGGCGCAAAUACAUCCCACGCGCGACUCGGAUCCG3'
Sequence length: 76
GC content: 0.5921052631578947
Affinity: Not reported
Pool type: 5'-GCGCTAAGTCCTCGCTCA-N40-ACGCGCGACTCGGATCCG-3'
Pool random region: 40
Binding buffer/conditions: 50 mM potassium phosphate, pH 7.0, 5 mM Mg(OAc)2, 0.1 mM EDTA, 1 mM DTT, 0.5 mM GTP, 0.02% Tween 20, 400 U/mL RNAsin
Buffer type: PBS/phosphate buffers
pH: 7
Molecular weight of target: 17 kDa
Application as quoted in the referenced paper: Research: " Domain mapping for SelB-binding aptamers showed that despite the different RNA-binding sites in the protein, the vast majority of aptamers bound to the ultimate C-terminus of SelB, the domain responsible for mRNA hairpin binding.Although the selected aptamers may be biologically inactive for selenocysteine incorporation, they may prove to be highly efficient inhibitors of this process in vivo, offering alternative ways of analyzing the interactions involved+"
Additional information: This RNA has exactly the same 59-CAAGUCUUG-39 sequence in the apical loop (AGUCU) and adjacent stem as the mRNA hairpin of the E. coli fdnG gene (Fig+ 5B)+ T, DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, RNA ): Klug, S. J., Hüttenhofer, A., & Famulok, M. (1999). In vitro selection of RNA aptamers that bind special elongation factor SelB, a protein with multiple RNA-binding sites, reveals one major interaction domain at the carboxyl terminus. RNA (New York, N.Y.), 5(9), 1180–1190. https://doi.org/10.1017/s135583829999088x
Aptamer: B3
Target: Phenylalanine tRNA, Yeast
Type of nucleic acid: ssRNA
Sequence: 5'GGGAAUUCCGCGUGUGCAAGCCUGUCGUGUGAACCUUGGUAGUCUUCAGAUACCAUUCUAGCCACGAGAGACUACGACACUGCUCCGUCGCCCGUCCGUUCGGGAUCCUC3'
Sequence length: 110
GC content: 0.5727272727272728
Affinity: binding efficiency: recovery as percentage of load: 55%; Kd: 26 ± 1.4 nM
Pool type: 5'-GGGAATTCCGCGTGTGC-N80-GTCCGTTCGGGATCCTC-3'
Pool random region: 80
Binding buffer/conditions: 0.25 M NaCl, 50 mM Tris–HCl pH 7.5, 10 mM MgCl2, 2 mM spermidine, 0.2 mM EDTA
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Six RNA aptamers that bind to yeast phenylalanine tRNA were identified by in vitro selection from a random-sequence pool. The in vitro selection approach can be employed to address experimentally how prevalent different kinds of binding partners are for various target RNAs in unbiased searches of RNA sequence space"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, EMBO J ): Scarabino, D., Crisari, A., Lorenzini, S., Williams, K., & Tocchini-Valentini, G. P. (1999). tRNA prefers to kiss. The EMBO journal, 18(16), 4571–4578. https://doi.org/10.1093/emboj/18.16.4571
Aptamer: B4
Target: Phenylalanine tRNA, Yeast
Type of nucleic acid: ssRNA
Sequence: 5'GGGAAUUCCGCGUGUGCUCGGUCACGCAUCUUCACGUCGAAAGCUACAUCGGUCUGCUGACGGUGAUGGCAUUUGCGCGGCUUACGCCGGUCGUGGUCCGUUCGGGAUCCUC3'
Sequence length: 112
GC content: 0.6071428571428571
Affinity: binding efficiency: recovery as percentage of load: 40%
Pool type: 5'-GGGAATTCCGCGTGTGC-N80-GTCCGTTCGGGATCCTC-3'
Pool random region: 80
Binding buffer/conditions: 0.25 M NaCl, 50 mM Tris–HCl pH 7.5, 10 mM MgCl2, 2 mM spermidine, 0.2 mM EDTA
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Six RNA aptamers that bind to yeast phenylalanine tRNA were identified by in vitro selection from a random-sequence pool. The in vitro selection approach can be employed to address experimentally how prevalent different kinds of binding partners are for various target RNAs in unbiased searches of RNA sequence space"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, EMBO J ): Scarabino, D., Crisari, A., Lorenzini, S., Williams, K., & Tocchini-Valentini, G. P. (1999). tRNA prefers to kiss. The EMBO journal, 18(16), 4571–4578. https://doi.org/10.1093/emboj/18.16.4571
Aptamer: B6
Target: Phenylalanine tRNA, Yeast
Type of nucleic acid: ssRNA
Sequence: 5'GGGAAUUCCGCGUGUGCAGAGUGGCCGGGCCUCCAUUCGGGGGUUAUCUUCACCUACGGGCCCCACGCGUUAUUUAGUGUUGUACCGUAGGGCUGUGUCCGUUCGGGAUCCUC3'
Sequence length: 113
GC content: 0.6017699115044248
Affinity: binding efficiency: recovery as percentage of load: 37%
Pool type: 5'-GGGAATTCCGCGTGTGC-N80-GTCCGTTCGGGATCCTC-3'
Pool random region: 80
Binding buffer/conditions: 0.25 M NaCl, 50 mM Tris–HCl pH 7.5, 10 mM MgCl2, 2 mM spermidine, 0.2 mM EDTA
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Six RNA aptamers that bind to yeast phenylalanine tRNA were identified by in vitro selection from a random-sequence pool. The in vitro selection approach can be employed to address experimentally how prevalent different kinds of binding partners are for various target RNAs in unbiased searches of RNA sequence space"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, EMBO J ): Scarabino, D., Crisari, A., Lorenzini, S., Williams, K., & Tocchini-Valentini, G. P. (1999). tRNA prefers to kiss. The EMBO journal, 18(16), 4571–4578. https://doi.org/10.1093/emboj/18.16.4571
Aptamer: B7
Target: Phenylalanine tRNA, Yeast
Type of nucleic acid: ssRNA
Sequence: 5'GGGAAUUCCGCGUGUGCGGGUCUUCACAGACUUGGCAAUUACCAGAACAUGUGCCUGGUAUACGUCAAUACGUCUGGUGGUUAAUACCGCCGUGGUCCGUUCGGGAUCCUC3'
Sequence length: 111
GC content: 0.5405405405405406
Affinity: binding efficiency: recovery as percentage of load: 41%
Pool type: 5'-GGGAATTCCGCGTGTGC-N80-GTCCGTTCGGGATCCTC-3'
Pool random region: 80
Binding buffer/conditions: 0.25 M NaCl, 50 mM Tris–HCl pH 7.5, 10 mM MgCl2, 2 mM spermidine, 0.2 mM EDTA
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Six RNA aptamers that bind to yeast phenylalanine tRNA were identified by in vitro selection from a random-sequence pool. The in vitro selection approach can be employed to address experimentally how prevalent different kinds of binding partners are for various target RNAs in unbiased searches of RNA sequence space"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, EMBO J ): Scarabino, D., Crisari, A., Lorenzini, S., Williams, K., & Tocchini-Valentini, G. P. (1999). tRNA prefers to kiss. The EMBO journal, 18(16), 4571–4578. https://doi.org/10.1093/emboj/18.16.4571
Aptamer: B1
Target: Phenylalanine tRNA, Yeast
Type of nucleic acid: ssRNA
Sequence: 5'GGGAAUUCCGCGUGUGCAUCACGGGUGUAUGCAAGACUCAGCAGUGGGCCAUAUGGUCGGAUCGAGGCUAGCUAAGUCUCCCAAUUGCACCUUCGUGGUCCGUUCGGGAUCCUC3'
Sequence length: 114
GC content: 0.5701754385964912
Affinity: binding efficiency: recovery as percentage of load: 16%
Pool type: 5'-GGGAATTCCGCGTGTGC-N80-GTCCGTTCGGGATCCTC-3'
Pool random region: 80
Binding buffer/conditions: 0.25 M NaCl, 50 mM Tris–HCl pH 7.5, 10 mM MgCl2, 2 mM spermidine, 0.2 mM EDTA
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Six RNA aptamers that bind to yeast phenylalanine tRNA were identified by in vitro selection from a random-sequence pool. The in vitro selection approach can be employed to address experimentally how prevalent different kinds of binding partners are for various target RNAs in unbiased searches of RNA sequence space"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, EMBO J ): Scarabino, D., Crisari, A., Lorenzini, S., Williams, K., & Tocchini-Valentini, G. P. (1999). tRNA prefers to kiss. The EMBO journal, 18(16), 4571–4578. https://doi.org/10.1093/emboj/18.16.4571
Aptamer: D20
Target: Cytoplasmic domain of CD18
Type of nucleic acid: ssRNA
Sequence: 5′GGGCGCUAAGUCCUCGCUCAUGCGCGUCCCAUGGGGUAUAGAGGGGUCGAAGUGGACGCGCGACUCGGAUCCUAC3′
Sequence length: 75
GC content: 0.64
Affinity: Kd: between 500 and 1,000 nM
Pool type: 5′-TCGGCGCTAAGTCCTCGCTCA-N40-ACGCGCGACTCGGATCCT-3′
Pool random region: 40
Binding buffer/conditions: 4.3 mM K2HPO4, 1.4 mM NaH2PO4, 150 mM NaCl, 1.0 mM MgCl2, 0.1 μM CaCl2
Divalent salt: MgCl/CaCl
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Reasearch: " the development and application of a system allowing high-level expression of aptamers within the cytoplasm of leukocytes, and investigation into their biological effects in the context of the living cell; cytoplasmic aptamers are capable of targeting receptors that are anchored in the plasma membrane compartment, thus opening an even wider application potential for aptamer technology compared with what are already a number of significant studies on nuclear aptamer expression or translational regulation"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, Proc Natl Acad Sci U S A ): Blind, M., Kolanus, W., & Famulok, M. (1999). Cytoplasmic RNA modulators of an inside-out signal-transduction cascade. Proceedings of the National Academy of Sciences of the United States of America, 96(7), 3606–3610. https://doi.org/10.1073/pnas.96.7.3606
Aptamer: D28
Target: Cytoplasmic domain of CD18
Type of nucleic acid: ssRNA
Sequence: 5′GGGCGCUAAGUCCUCGCUCAUACAACGAGGGGUCGUGUAGGGAUGUAUGGGCUUGGACACACGCGCGACUCGGAUCCUAC3′
Sequence length: 80
GC content: 0.6
Affinity: Kd: between 500 and 1,000 nM
Pool type: 5′-TCGGCGCTAAGTCCTCGCTCA-N40-ACGCGCGACTCGGATCCT-3′
Pool random region: 40
Binding buffer/conditions: 4.3 mM K2HPO4, 1.4 mM NaH2PO4, 150 mM NaCl, 1.0 mM MgCl2, 0.1 μM CaCl2
Divalent salt: MgCl/CaCl
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Reasearch: " the development and application of a system allowing high-level expression of aptamers within the cytoplasm of leukocytes, and investigation into their biological effects in the context of the living cell; cytoplasmic aptamers are capable of targeting receptors that are anchored in the plasma membrane compartment, thus opening an even wider application potential for aptamer technology compared with what are already a number of significant studies on nuclear aptamer expression or translational regulation"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, Proc Natl Acad Sci U S A ): Blind, M., Kolanus, W., & Famulok, M. (1999). Cytoplasmic RNA modulators of an inside-out signal-transduction cascade. Proceedings of the National Academy of Sciences of the United States of America, 96(7), 3606–3610. https://doi.org/10.1073/pnas.96.7.3606
Aptamer: D31
Target: Cytoplasmic domain of CD18
Type of nucleic acid: ssRNA
Sequence: 5′GGGCGCUAAGUCCUCGCUCACAAGGUGCAAUGCAAUAUGUGAGUGCGCCGCCCUUUCUCUCGCGCGACUCGGAUCCUAC3′
Sequence length: 79
GC content: 0.5949367088607594
Affinity: Kd: between 500 and 1,000 nM
Pool type: 5′-TCGGCGCTAAGTCCTCGCTCA-N40-ACGCGCGACTCGGATCCT-3′
Pool random region: 40
Binding buffer/conditions: 4.3 mM K2HPO4, 1.4 mM NaH2PO4, 150 mM NaCl, 1.0 mM MgCl2, 0.1 μM CaCl2
Divalent salt: MgCl/CaCl
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Reasearch: " the development and application of a system allowing high-level expression of aptamers within the cytoplasm of leukocytes, and investigation into their biological effects in the context of the living cell; cytoplasmic aptamers are capable of targeting receptors that are anchored in the plasma membrane compartment, thus opening an even wider application potential for aptamer technology compared with what are already a number of significant studies on nuclear aptamer expression or translational regulation"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, Proc Natl Acad Sci U S A ): Blind, M., Kolanus, W., & Famulok, M. (1999). Cytoplasmic RNA modulators of an inside-out signal-transduction cascade. Proceedings of the National Academy of Sciences of the United States of America, 96(7), 3606–3610. https://doi.org/10.1073/pnas.96.7.3606
Aptamer: RNA-1
Target: Subtilisin BPN
Type of nucleic acid: ssRNA
Sequence: 5'GGGCGAAUUCGAGCUCGGGCCACUCGCUCAACACGGUAAGUAGAGACCUAGUGGUACAUAAAGGACUGCAGGCAUGCAAGCU3'
Sequence length: 82
GC content: 0.5487804878048781
Affinity: Ki: 2.5 µM
Pool type: 5'-AAGCTTGCATGCCTGCAG-N47-CCGAGCTCGAATTCGCCCTATAGTGAGTCGTATTA-3'
Pool random region: 47
Binding buffer/conditions: 50 mM Tris-HCl, pH 7.5, 50 mM NaCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " RNA ligands (RNA aptamers) to a protease subtilisin were selected from pools of random RNA by SELEX (systematic evolution of ligands by exponential enrichment) and by use of a subtilisin-immobilized Sepharose column. . After eight rounds of selection, RNA aptamers were isolated by cloning to a plasmid vector. This RNA aptamer displayed specific inhibition toward the subtilisin activity. These findings indicate that this RNA can differentially recognize the surfaces of similar proteases"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, J Biochem ): Takeno, H., Yamamoto, S., Tanaka, T., Sakano, Y., & Kikuchi, Y. (1999). Selection of an RNA molecule that specifically inhibits the protease activity of subtilisin. Journal of biochemistry, 125(6), 1115–1119. https://doi.org/10.1093/oxfordjournals.jbchem.a022393
Aptamer: 85
Target: Unr (Upstream of N-Ras) protein, Human
Type of nucleic acid: ssRNA
Sequence: 5′GGGCCACCAACGACAUUGAAUGAGAGAGAAGUAAAAGGUUGAUAUAAAUAGUGCCCA3′
Sequence length: 57
GC content: 0.4210526315789473
Affinity: Kd: 11 nM
Pool type: 5′-CCCGGTGGTTGCTGTAA-N20-CAACTATATTTATCACGGGT-3′
Pool random region: 20
Binding buffer/conditions: 25 µg/ml BSA, 25 µg/ml tRNA, 5 U/ml RNAguard (Pharmacia), 1 mM PMSF, 1 mM β-mercaptoethanol and 1 µg/ml of leupeptin, antipain and aprotinin, in TNG buffer
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 85 kDa
Application as quoted in the referenced paper: Research: " In our initial characterization of the human Unr protein, we have determined that it has the capacity to interact in vitro with single-stranded RNA and DNA; To further characterize the RNA-binding specificity of Unr and eventually identify RNA ligands, we have used an in vitro selection/amplification approach"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, Nucleic Acids Res ): Triqueneaux, G., Velten, M., Franzon, P., Dautry, F., & Jacquemin-Sablon, H. (1999). RNA binding specificity of Unr, a protein with five cold shock domains. Nucleic acids research, 27(8), 1926–1934. https://doi.org/10.1093/nar/27.8.1926
Aptamer: 88
Target: Unr (Upstream of N-Ras) protein, Human
Type of nucleic acid: ssRNA
Sequence: 5′GGGCCACCAACGACAUUUCGAAAGAAAAGAGUAACUGGUUGAUAUAAAUAGUGCCCA3′
Sequence length: 57
GC content: 0.4210526315789473
Affinity: Kd: 10 nM
Pool type: 5′-CCCGGTGGTTGCTGTAA-N20-CAACTATATTTATCACGGGT-3′
Pool random region: 20
Binding buffer/conditions: 25 µg/ml BSA, 25 µg/ml tRNA, 5 U/ml RNAguard (Pharmacia), 1 mM PMSF, 1 mM β-mercaptoethanol and 1 µg/ml of leupeptin, antipain and aprotinin, in TNG buffer
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 85 kDa
Application as quoted in the referenced paper: Research: " In our initial characterization of the human Unr protein, we have determined that it has the capacity to interact in vitro with single-stranded RNA and DNA; To further characterize the RNA-binding specificity of Unr and eventually identify RNA ligands, we have used an in vitro selection/amplification approach"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, Nucleic Acids Res ): Triqueneaux, G., Velten, M., Franzon, P., Dautry, F., & Jacquemin-Sablon, H. (1999). RNA binding specificity of Unr, a protein with five cold shock domains. Nucleic acids research, 27(8), 1926–1934. https://doi.org/10.1093/nar/27.8.1926
Aptamer: 76
Target: Unr (Upstream of N-Ras) protein, Human
Type of nucleic acid: ssRNA
Sequence: 5′GGGCCACCAACGACAUUAAGAGAAGAAGUACCCGAGCGUUGAUAUAAAUAGUGCCCA3′
Sequence length: 57
GC content: 0.4736842105263157
Affinity: Kd: 10 nM
Pool type: 5′-CCCGGTGGTTGCTGTAA-N20-CAACTATATTTATCACGGGT-3′
Pool random region: 20
Binding buffer/conditions: 25 µg/ml BSA, 25 µg/ml tRNA, 5 U/ml RNAguard (Pharmacia), 1 mM PMSF, 1 mM β-mercaptoethanol and 1 µg/ml of leupeptin, antipain and aprotinin, in TNG buffer
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 85 kDa
Application as quoted in the referenced paper: Research: " In our initial characterization of the human Unr protein, we have determined that it has the capacity to interact in vitro with single-stranded RNA and DNA; To further characterize the RNA-binding specificity of Unr and eventually identify RNA ligands, we have used an in vitro selection/amplification approach"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, Nucleic Acids Res ): Triqueneaux, G., Velten, M., Franzon, P., Dautry, F., & Jacquemin-Sablon, H. (1999). RNA binding specificity of Unr, a protein with five cold shock domains. Nucleic acids research, 27(8), 1926–1934. https://doi.org/10.1093/nar/27.8.1926
Aptamer: 98
Target: Unr (Upstream of N-Ras) protein, Human
Type of nucleic acid: ssRNA
Sequence: 5′GGGCCACCAACGACAUUGAUGAAGUAAAAAGCGAUGAGUUGAUAUAAAUAGUGCCCA3′
Sequence length: 57
GC content: 0.4210526315789473
Affinity: Kd: 21 nM
Pool type: 5′-CCCGGTGGTTGCTGTAA-N20-CAACTATATTTATCACGGGT-3′
Pool random region: 20
Binding buffer/conditions: 25 µg/ml BSA, 25 µg/ml tRNA, 5 U/ml RNAguard (Pharmacia), 1 mM PMSF, 1 mM β-mercaptoethanol and 1 µg/ml of leupeptin, antipain and aprotinin, in TNG buffer
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 85 kDa
Application as quoted in the referenced paper: Research: " In our initial characterization of the human Unr protein, we have determined that it has the capacity to interact in vitro with single-stranded RNA and DNA; To further characterize the RNA-binding specificity of Unr and eventually identify RNA ligands, we have used an in vitro selection/amplification approach"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, Nucleic Acids Res ): Triqueneaux, G., Velten, M., Franzon, P., Dautry, F., & Jacquemin-Sablon, H. (1999). RNA binding specificity of Unr, a protein with five cold shock domains. Nucleic acids research, 27(8), 1926–1934. https://doi.org/10.1093/nar/27.8.1926
Aptamer: 58
Target: Unr (Upstream of N-Ras) protein, Human
Type of nucleic acid: ssRNA
Sequence: 5′GGGCCACCAACGACAUUGGGAGGCAGAAAGGAAAAAGUGUUGAUAUAAAUAGUGCCCA3′
Sequence length: 58
GC content: 0.4655172413793103
Affinity: Kd: 13 nM
Pool type: 5′-CCCGGTGGTTGCTGTAA-N20-CAACTATATTTATCACGGGT-3′
Pool random region: 20
Binding buffer/conditions: 25 µg/ml BSA, 25 µg/ml tRNA, 5 U/ml RNAguard (Pharmacia), 1 mM PMSF, 1 mM β-mercaptoethanol and 1 µg/ml of leupeptin, antipain and aprotinin, in TNG buffer
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 85 kDa
Application as quoted in the referenced paper: Research: " In our initial characterization of the human Unr protein, we have determined that it has the capacity to interact in vitro with single-stranded RNA and DNA; To further characterize the RNA-binding specificity of Unr and eventually identify RNA ligands, we have used an in vitro selection/amplification approach"
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
Reference (1999, Nucleic Acids Res ): Triqueneaux, G., Velten, M., Franzon, P., Dautry, F., & Jacquemin-Sablon, H. (1999). RNA binding specificity of Unr, a protein with five cold shock domains. Nucleic acids research, 27(8), 1926–1934. https://doi.org/10.1093/nar/27.8.1926