RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: SL-18
Target: Sialyllactose
Type of nucleic acid: ssDNA
Sequence: 5′GTACGAATTCACGAGGTTGCCGAGGTCGGGGGGGGCCCTGTACGAATTCACGAGGTTGGGAGCATGGAGTCGGATCCTCTA3′
Sequence length: 81
GC content: 0.5925925925925926
Affinity: Not reported
Pool type: 5′-GTACGAATTCACGAGGTTGCC-N60-AGCATGGAGTCGGATCCTCTA-3′
Pool random region: 60
Binding buffer/conditions: Tris–HCl buffer (50 mM, pH 7.6) containing 250 mM NaCl and 5 mM MgCl2
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: Therapeutic: " To our knowledge, this is the first report on the selection of a modified DNA aptamer that has micromolar affinity for sialyllactose, the cell surface carbohydrate. The highaffinity sialyllactose-specific DNA aptamer might be useful for studies of cell adhesion and the development of a lead molecule for cell-adhesion-blocking anti-viral therapy."
Reference (2004, Bioorg Med Chem ): Masud, M. M., Kuwahara, M., Ozaki, H., & Sawai, H. (2004). Sialyllactose-binding modified DNA aptamer bearing additional functionality by SELEX. Bioorganic & medicinal chemistry, 12(5), 1111–1120. https://doi.org/10.1016/j.bmc.2003.12.009
Aptamer: RNA aptamer #1
Target: Nuclear factor of activated T cells DNA binding domain (NFAT DBD)
Type of nucleic acid: ssRNA
Sequence: 5′GGGAGAGCGGAAGCGUGCUGGGCCGAUAUGAAGGAGUGGAGAGGGUGGCAGCAUGGUCCGGAUCCAUAACCCAGAGGUCGAUGGAUCCCCCC3′
Sequence length: 92
GC content: 0.6304347826086957
Affinity: Kd: 11.1 nM
Pool type: 5′-GGGAGAGCGGAAGCGUGCUGGGCC-N40-CAUAACCCAGAGGUCGAUGGAUCCCCCC-3′
Pool random region: 40
Binding buffer/conditions: 30 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1.5 mM MgCl2, 2 mM dithiothreitol, and 1% BSA
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: " Nuclear factor of activated T cells (NFAT) plays a central role in the immune response, and the immunosuppressive drugs, cyclosporin A and FK-506, have been developed to inhibit it. However, due to the toxic effects of these drugs, which derive from their ability to inhibit calcineurin in non-immune tissues, the identification of small compounds that target NFAT directly could be an approach to developing less toxic immunosuppressive therapy."
Reference (2004, Mol Cells ): Cho, J. S., Lee, Y. J., Shin, K. S., Jeong, S., Park, J., & Lee, S. W. (2004). In vitro selection of specific RNA aptamers for the NFAT DNA binding domain. Molecules and cells, 18(1), 17–23.
Aptamer: RNA aptamer #2
Target: Nuclear factor of activated T cells DNA binding domain (NFAT DBD)
Type of nucleic acid: ssRNA
Sequence: 5′GGGAGAGCGGAAGCGUGCUGGGCCGAGGGAGGCGAUAUGAAGGUGUAGAGAGGCCUCCUGGACACAUAACCCAGAGGUCGAUGGAUCCCCCC3′
Sequence length: 92
GC content: 0.6304347826086957
Affinity: Kd: 120 nM
Pool type: 5′-GGGAGAGCGGAAGCGUGCUGGGCC-N40-CAUAACCCAGAGGUCGAUGGAUCCCCCC-3′
Pool random region: 40
Binding buffer/conditions: 30 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1.5 mM MgCl2, 2 mM dithiothreitol, and 1% BSA
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: " Nuclear factor of activated T cells (NFAT) plays a central role in the immune response, and the immunosuppressive drugs, cyclosporin A and FK-506, have been developed to inhibit it. However, due to the toxic effects of these drugs, which derive from their ability to inhibit calcineurin in non-immune tissues, the identification of small compounds that target NFAT directly could be an approach to developing less toxic immunosuppressive therapy."
Reference (2004, Mol Cells ): Cho, J. S., Lee, Y. J., Shin, K. S., Jeong, S., Park, J., & Lee, S. W. (2004). In vitro selection of specific RNA aptamers for the NFAT DNA binding domain. Molecules and cells, 18(1), 17–23.
Aptamer: F1-1
Target: C-terminal ribonuclease domain of colicin E3 (CRD of colicin E3)
Type of nucleic acid: ssRNA
Sequence: 5‘GGGAGAAUUCCGACCAGAAGCUUACUGUCCUCCCUUCAGAGAGCGCGGGACCCUUAACUUGGGGCCCACGAACAGCUUCAGUUCCGUCUCGGCGUCAUAUGUGCGUCUACAUGGAUCCUCA3‘
Sequence length: 121
GC content: 0.5619834710743802
Affinity: Kd: 2±11 nM
Pool type: 5‘-GGTAATACGACTCACTATAGGGAGAATTCCGACCAGAAGCTT-N72-CATATGTGCGTCTACATGGATCCTCA-3‘
Pool random region: 72
Binding buffer/conditions: 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, and 30 mM NH4Cl
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: " Aptamer F2-1 could be used for the structural analysis of the interaction with colicin E3, in place of 16S rRNA. Furthermore, the aptamers work as analogues of the colicin E3 immunity protein, and the expression of the aptamers in a colicin-sensitive cell could confer resistance to colicin E3. This implies that the aptamers could be used as selection markers, such as anti-aminoglycoside aptamers, for the isolation of certain E. coli mutants (45).
"
Reference (2004, Biochemistry ): Hirao, I., Harada, Y., Nojima, T., Osawa, Y., Masaki, H., & Yokoyama, S. (2004). In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA. Biochemistry, 43(11), 3214–3221. https://doi.org/10.1021/bi0356146
Aptamer: F2-1
Target: C-terminal ribonuclease domain of colicin E3 (CRD of colicin E3)
Type of nucleic acid: ssRNA
Sequence: 5‘GGGAGAAUUCCGACCAGAAGCUUUCCCUGGCCCAAGAUCCUAAUAAAGUUUUUUCGGACCGGAGCGAAACCACUAUCCUCUUAAGCAAUCUGUCAUAUGUGCGUCUACAUGGAUCCUCA3‘
Sequence length: 119
GC content: 0.4705882352941176
Affinity: Kd: 14±2 nM
Pool type: 5‘-GGTAATACGACTCACTATAGGGAGAATTCCGACCAGAAGCTT-N72-CATATGTGCGTCTACATGGATCCTCA-3‘
Pool random region: 72
Binding buffer/conditions: 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, and 30 mM NH4Cl
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: " Aptamer F2-1 could be used for the structural analysis of the interaction with colicin E3, in place of 16S rRNA. Furthermore, the aptamers work as analogues of the colicin E3 immunity protein, and the expression of the aptamers in a colicin-sensitive cell could confer resistance to colicin E3. This implies that the aptamers could be used as selection markers, such as anti-aminoglycoside aptamers, for the isolation of certain E. coli mutants (45).
"
Reference (2004, Biochemistry ): Hirao, I., Harada, Y., Nojima, T., Osawa, Y., Masaki, H., & Yokoyama, S. (2004). In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA. Biochemistry, 43(11), 3214–3221. https://doi.org/10.1021/bi0356146
Aptamer: F3-1
Target: C-terminal ribonuclease domain of colicin E3 (CRD of colicin E3)
Type of nucleic acid: ssRNA
Sequence: 5‘GGGAGAAUUCCGACCAGAAGCUUGUACAACACAUCAUUACGGCUGCUAUUGGCUCCAAGCGUCUUUCUCCCUGGUCAAUAGUCCAGCCACCACGCAUAUGUGCGUCUACAUGGAUCCUCA3‘
Sequence length: 120
GC content: 0.5083333333333333
Affinity: Kd: 4±15 nM
Pool type: 5‘-GGTAATACGACTCACTATAGGGAGAATTCCGACCAGAAGCTT-N72-CATATGTGCGTCTACATGGATCCTCA-3‘
Pool random region: 72
Binding buffer/conditions: 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, and 30 mM NH4Cl
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: " Aptamer F2-1 could be used for the structural analysis of the interaction with colicin E3, in place of 16S rRNA. Furthermore, the aptamers work as analogues of the colicin E3 immunity protein, and the expression of the aptamers in a colicin-sensitive cell could confer resistance to colicin E3. This implies that the aptamers could be used as selection markers, such as anti-aminoglycoside aptamers, for the isolation of certain E. coli mutants (45).
"
Reference (2004, Biochemistry ): Hirao, I., Harada, Y., Nojima, T., Osawa, Y., Masaki, H., & Yokoyama, S. (2004). In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA. Biochemistry, 43(11), 3214–3221. https://doi.org/10.1021/bi0356146
Aptamer: F4-1
Target: C-terminal ribonuclease domain of colicin E3 (CRD of colicin E3)
Type of nucleic acid: ssRNA
Sequence: 5‘GGGAGAAUUCCGACCAGAAGCUUGACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGAGGGCUCGGACUCUGAUUGCCUCCCCGCACCCAUAUGUGCGUCUACAUGGAUCCUCA3‘
Sequence length: 119
GC content: 0.5126050420168067
Affinity: Kd: 7±1 nM
Pool type: 5‘-GGTAATACGACTCACTATAGGGAGAATTCCGACCAGAAGCTT-N72-CATATGTGCGTCTACATGGATCCTCA-3‘
Pool random region: 72
Binding buffer/conditions: 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, and 30 mM NH4Cl
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: " Aptamer F2-1 could be used for the structural analysis of the interaction with colicin E3, in place of 16S rRNA. Furthermore, the aptamers work as analogues of the colicin E3 immunity protein, and the expression of the aptamers in a colicin-sensitive cell could confer resistance to colicin E3. This implies that the aptamers could be used as selection markers, such as anti-aminoglycoside aptamers, for the isolation of certain E. coli mutants (45).
"
Reference (2004, Biochemistry ): Hirao, I., Harada, Y., Nojima, T., Osawa, Y., Masaki, H., & Yokoyama, S. (2004). In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA. Biochemistry, 43(11), 3214–3221. https://doi.org/10.1021/bi0356146
Aptamer: F4-2
Target: C-terminal ribonuclease domain of colicin E3 (CRD of colicin E3)
Type of nucleic acid: ssRNA
Sequence: 5‘GGGAGAAUUCCGACCAGAAGCUUGACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGGGGGCUCGGACUCUGAUUGCCUCCCCGCACCCAUAUGUGCGUCUACAUGGAUCCUCA3‘
Sequence length: 119
GC content: 0.5210084033613446
Affinity: Kd: 294±170 nM
Pool type: 5‘-GGTAATACGACTCACTATAGGGAGAATTCCGACCAGAAGCTT-N72-CATATGTGCGTCTACATGGATCCTCA-3‘
Pool random region: 72
Binding buffer/conditions: 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, and 30 mM NH4Cl
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: " Aptamer F2-1 could be used for the structural analysis of the interaction with colicin E3, in place of 16S rRNA. Furthermore, the aptamers work as analogues of the colicin E3 immunity protein, and the expression of the aptamers in a colicin-sensitive cell could confer resistance to colicin E3. This implies that the aptamers could be used as selection markers, such as anti-aminoglycoside aptamers, for the isolation of certain E. coli mutants (45).
"
Reference (2004, Biochemistry ): Hirao, I., Harada, Y., Nojima, T., Osawa, Y., Masaki, H., & Yokoyama, S. (2004). In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA. Biochemistry, 43(11), 3214–3221. https://doi.org/10.1021/bi0356146
Aptamer: F5-1
Target: C-terminal ribonuclease domain of colicin E3 (CRD of colicin E3)
Type of nucleic acid: ssRNA
Sequence: 5‘GGGAGAAUUCCGACCAGAAGCUUGUCAGCUGCUCGCGGGAUCGAUCCAUUCGGUGGCCAUGCUCCGGAAGACGGGCCGGCUUCGCAAGACUCAGGCAUAUGUGCGUCUACAUGGAUCCUCA3‘
Sequence length: 121
GC content: 0.5867768595041323
Affinity: Kd: 10±1 nM
Pool type: 5‘-GGTAATACGACTCACTATAGGGAGAATTCCGACCAGAAGCTT-N72-CATATGTGCGTCTACATGGATCCTCA-3‘
Pool random region: 72
Binding buffer/conditions: 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, and 30 mM NH4Cl
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: " Aptamer F2-1 could be used for the structural analysis of the interaction with colicin E3, in place of 16S rRNA. Furthermore, the aptamers work as analogues of the colicin E3 immunity protein, and the expression of the aptamers in a colicin-sensitive cell could confer resistance to colicin E3. This implies that the aptamers could be used as selection markers, such as anti-aminoglycoside aptamers, for the isolation of certain E. coli mutants."
Reference (2004, Biochemistry ): Hirao, I., Harada, Y., Nojima, T., Osawa, Y., Masaki, H., & Yokoyama, S. (2004). In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA. Biochemistry, 43(11), 3214–3221. https://doi.org/10.1021/bi0356146
Aptamer: E1
Target: Escherichia coli (E. coli) core bacterial RNA polymerase (RNAP)
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGCTCAGAATAAACGCTCAATTCGGGGAGGTGGCATGGGGGGGAGGCAGTTATTCGACATGAGGCCCGGATC3'
Sequence length: 75
GC content: 0.5866666666666667
Affinity: Kd: 0.13 nM
Pool type: 5'-GGGAGCTCAGAATAAACGCTCAA-N32-TTCGACATGAGGCCCGGATC-3'
Pool random region: 32
Binding buffer/conditions: 20 mM Tris/HCl pH 7.9, 10 mM MgCl2, 300 mM NaCl, 30 mM KCl; in subsequent rounds NaCl and KCl concentrations were increased to 400 and 40 mM, respectively
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.9
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Bacterial RNA polymerase (RNAP) is the central enzyme of gene expression that is responsible for the synthesis of all types of cellular RNAs. The goal of this work was to obtain novel ligands to RNAP which would target different epitopes of the enzyme and serve as specific probes to study the mechanism of transcription and conformational flexibility of RNAP. We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme."
Reference (2004, Eur J Biochem ): Kulbachinskiy, A., Feklistov, A., Krasheninnikov, I., Goldfarb, A., & Nikiforov, V. (2004). Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. European journal of biochemistry, 271(23-24), 4921–4931. https://doi.org/10.1111/j.1432-1033.2004.04461.x
Aptamer: E2
Target: Escherichia coli (E. coli) core bacterial RNA polymerase (RNAP)
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGCTCAGAATAAACGCTCAAAACGCACCGGAGGGAGGACTTTGGGCCATCCTTTCGACATGAGGCCCGGATC3'
Sequence length: 75
GC content: 0.5733333333333334
Affinity: Kd: 1.04 nM
Pool type: 5'-GGGAGCTCAGAATAAACGCTCAA-N32-TTCGACATGAGGCCCGGATC-3'
Pool random region: 32
Binding buffer/conditions: 20 mM Tris/HCl pH 7.9, 10 mM MgCl2, 300 mM NaCl, 30 mM KCl; in subsequent rounds NaCl and KCl concentrations were increased to 400 and 40 mM, respectively
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.9
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Bacterial RNA polymerase (RNAP) is the central enzyme of gene expression that is responsible for the synthesis of all types of cellular RNAs. The goal of this work was to obtain novel ligands to RNAP which would target different epitopes of the enzyme and serve as specific probes to study the mechanism of transcription and conformational flexibility of RNAP. We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme."
Reference (2004, Eur J Biochem ): Kulbachinskiy, A., Feklistov, A., Krasheninnikov, I., Goldfarb, A., & Nikiforov, V. (2004). Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. European journal of biochemistry, 271(23-24), 4921–4931. https://doi.org/10.1111/j.1432-1033.2004.04461.x
Aptamer: E3
Target: Escherichia coli (E. coli) core bacterial RNA polymerase (RNAP)
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGCTCAGAATAAACGCTCAACGCAGGCCAGCGGGCGAGGATGGGCCACCCCTATCGACATGAGGCCCGGATC3'
Sequence length: 75
GC content: 0.64
Affinity: Kd: 1.23 nM
Pool type: 5'-GGGAGCTCAGAATAAACGCTCAA-N32-TTCGACATGAGGCCCGGATC-3'
Pool random region: 32
Binding buffer/conditions: 20 mM Tris/HCl pH 7.9, 10 mM MgCl2, 300 mM NaCl, 30 mM KCl; in subsequent rounds NaCl and KCl concentrations were increased to 400 and 40 mM, respectively
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.9
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Bacterial RNA polymerase (RNAP) is the central enzyme of gene expression that is responsible for the synthesis of all types of cellular RNAs. The goal of this work was to obtain novel ligands to RNAP which would target different epitopes of the enzyme and serve as specific probes to study the mechanism of transcription and conformational flexibility of RNAP. We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme."
Additional information: Substitution of T with A at the first position of the right constant region
Reference (2004, Eur J Biochem ): Kulbachinskiy, A., Feklistov, A., Krasheninnikov, I., Goldfarb, A., & Nikiforov, V. (2004). Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. European journal of biochemistry, 271(23-24), 4921–4931. https://doi.org/10.1111/j.1432-1033.2004.04461.x
Aptamer: E4
Target: Escherichia coli (E. coli) core bacterial RNA polymerase (RNAP)
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGCTCAGAATAAACGCTCAATGGGTTGTGCAGGAGGGGGTGCCCGTTTAGGTTTCGACATGAGGCCCGGATC3'
Sequence length: 75
GC content: 0.5733333333333334
Affinity: Kd: 2.23 nM
Pool type: 5'-GGGAGCTCAGAATAAACGCTCAA-N32-TTCGACATGAGGCCCGGATC-3'
Pool random region: 32
Binding buffer/conditions: 20 mM Tris/HCl pH 7.9, 10 mM MgCl2, 300 mM NaCl, 30 mM KCl; in subsequent rounds NaCl and KCl concentrations were increased to 400 and 40 mM, respectively
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.9
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Bacterial RNA polymerase (RNAP) is the central enzyme of gene expression that is responsible for the synthesis of all types of cellular RNAs. The goal of this work was to obtain novel ligands to RNAP which would target different epitopes of the enzyme and serve as specific probes to study the mechanism of transcription and conformational flexibility of RNAP. We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme."
Reference (2004, Eur J Biochem ): Kulbachinskiy, A., Feklistov, A., Krasheninnikov, I., Goldfarb, A., & Nikiforov, V. (2004). Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. European journal of biochemistry, 271(23-24), 4921–4931. https://doi.org/10.1111/j.1432-1033.2004.04461.x
Aptamer: E5
Target: Escherichia coli (E. coli) core bacterial RNA polymerase (RNAP)
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGCTCAGAATAAACGCTCAAGGGTGGGCGGGAAGAGTGGGGTGGAAGAGCGTTTCGACATGAGGCCCGGATC3'
Sequence length: 75
GC content: 0.6
Affinity: Kd: 0.72 nM
Pool type: 5'-GGGAGCTCAGAATAAACGCTCAA-N32-TTCGACATGAGGCCCGGATC-3'
Pool random region: 32
Binding buffer/conditions: 20 mM Tris/HCl pH 7.9, 10 mM MgCl2, 300 mM NaCl, 30 mM KCl; in subsequent rounds NaCl and KCl concentrations were increased to 400 and 40 mM, respectively
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.9
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Bacterial RNA polymerase (RNAP) is the central enzyme of gene expression that is responsible for the synthesis of all types of cellular RNAs. The goal of this work was to obtain novel ligands to RNAP which would target different epitopes of the enzyme and serve as specific probes to study the mechanism of transcription and conformational flexibility of RNAP. We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme."
Reference (2004, Eur J Biochem ): Kulbachinskiy, A., Feklistov, A., Krasheninnikov, I., Goldfarb, A., & Nikiforov, V. (2004). Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. European journal of biochemistry, 271(23-24), 4921–4931. https://doi.org/10.1111/j.1432-1033.2004.04461.x
Aptamer: E6
Target: Escherichia coli (E. coli) core bacterial RNA polymerase (RNAP)
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGCTCAGAATAAACGCTCAACTTCCGACGATGTAAGTCACCACCCGGCTCAGTTCGACATGAGGCCCGGATC3'
Sequence length: 75
GC content: 0.56
Affinity: Kd: 1.62 nM
Pool type: 5'-GGGAGCTCAGAATAAACGCTCAA-N32-TTCGACATGAGGCCCGGATC-3'
Pool random region: 32
Binding buffer/conditions: 20 mM Tris/HCl pH 7.9, 10 mM MgCl2, 300 mM NaCl, 30 mM KCl; in subsequent rounds NaCl and KCl concentrations were increased to 400 and 40 mM, respectively
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.9
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Bacterial RNA polymerase (RNAP) is the central enzyme of gene expression that is responsible for the synthesis of all types of cellular RNAs. The goal of this work was to obtain novel ligands to RNAP which would target different epitopes of the enzyme and serve as specific probes to study the mechanism of transcription and conformational flexibility of RNAP. We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme."
Reference (2004, Eur J Biochem ): Kulbachinskiy, A., Feklistov, A., Krasheninnikov, I., Goldfarb, A., & Nikiforov, V. (2004). Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. European journal of biochemistry, 271(23-24), 4921–4931. https://doi.org/10.1111/j.1432-1033.2004.04461.x