RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: T15
Target: Tetracycline (TET), oxytetracycline (OTC), doxycycline (DOX)
Type of nucleic acid: ssDNA
Sequence: 5'CGTACGGAATTCGCTAGCGGAGGAACGGGTTCCAGTGTGGGGTCTATCGGGGCgtgcGGGATCCGAGCTCCACGTG3'
Sequence length: 76
GC content: 0.6447368421052632
Affinity: Kd: 197 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.
Aptamer: T19
Target: Tetracycline (TET), oxytetracycline (OTC), doxycycline (DOX)
Type of nucleic acid: ssDNA
Sequence: 5'CGTACGGAATTCGCTAGCCGGGAGGGCGGGGTGTGGTATGTATTGAGCGTGGTCCGTGGGATCCGAGCTCCACGTG3'
Sequence length: 76
GC content: 0.631578947368421
Affinity: Kd: 424.8 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
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.
Aptamer: T20
Target: Tetracycline (TET), oxytetracycline (OTC), doxycycline (DOX)
Type of nucleic acid: ssDNA
Sequence: 5'CGTACGGAATTCGCTAGCCCCCCGGCAGGCCACGGCTTGGGTTGGTCCCACTGCGCGTGGATCCGAGCTCCACGTG3'
Sequence length: 76
GC content: 0.6842105263157895
Affinity: Kd: 63.6 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
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.
Aptamer: T22
Target: Tetracycline (TET), oxytetracycline (OTC), doxycycline (DOX)
Type of nucleic acid: ssDNA
Sequence: 5'CGTACGGAATTCGCTAGCGGGCGGACGCTAGGTGGTGATGCTgtgcTACACGTGTTGTGGATCCGAGCTCCACGTG3'
Sequence length: 76
GC content: 0.6052631578947368
Affinity: Kd: 483.5 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.
Aptamer: T23
Target: Tetracycline (TET), oxytetracycline (OTC), doxycycline (DOX)
Type of nucleic acid: ssDNA
Sequence: 5'CGTACGGAATTCGCTAGCGGGGGCACACATGTAGgtgcTGTCCAGGTGTGGTTGTGGTGGATCCGAGCTCCACGTG3'
Sequence length: 76
GC content: 0.6052631578947368
Affinity: Kd: 100.6 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.
Aptamer: T24
Target: Tetracycline (TET), oxytetracycline (OTC), doxycycline (DOX)
Type of nucleic acid: ssDNA
Sequence: 5'CGTACGGAATTCGCTAGCGGGCGGGGgtgcTGGGGGAATGGAgtgcTGCgtgcTGCGGGGATCCGAGCTCCACGTG3'
Sequence length: 76
GC content: 0.6842105263157895
Affinity: Kd: 70.7 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.
Aptamer: aptamer 6
Target: (1→3)-β-D-glucans
Type of nucleic acid: ssDNA
Sequence: 5′CGACTGACGCCTCCAAGCCACACGTGTGAGAAGGGTGTTATCATGTATTTCGTGTTCCTTTCGTCATTCCTTTGTCTGCATGCATCGCTACGTG3'
Sequence length: 94
GC content: 0.5
Affinity: Kd: 0.303 ± 0.067 μM
Pool type: 5′-CGACTGACGCCTCCAAGC-N60-GCATGCATCGCTACGTG-3'
Pool random region: 60
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: 53 to 2000 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "We describe the development of aptamers that could bind with high affinity and specificity to the biotoxin, (1→3)-β-D glucans. These represent the first aptamers developed for common indoor contaminants. The use of these aptamers in sensors or detection assays should lead to increased accuracy and decreased expense in exposure monitoring and epidemiological investigations for environmental respiratory diseases."
Reference (2008, Biochem Biophys Res Commun ): Low, S. Y., Hill, J. E., & Peccia, J. (2009). DNA aptamers bind specifically and selectively to (1-->3)-beta-D-glucans. Biochemical and biophysical research communications, 378(4), 701–705. https://doi.org/10.1016/j.bbrc.2008.11.087
Aptamer: aptamer 30
Target: (1→3)-β-D-glucans
Type of nucleic acid: ssDNA
Sequence: 5′CGACTGACGCCTCCAAGCACATAGACAGCCTATCCTCGATTAGTTGTTGTTATGGTCCTATTCTCTCCATTCCGCTGTGCATGCATCGCTACGTG3'
Sequence length: 95
GC content: 0.5052631578947369
Affinity: Kd: 0.326 ± 0.089 μM
Pool type: 5′-CGACTGACGCCTCCAAGC-N60-GCATGCATCGCTACGTG-3'
Pool random region: 60
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: 53 to 2000 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "We describe the development of aptamers that could bind with high affinity and specificity to the biotoxin, (1→3)-β-D glucans. These represent the first aptamers developed for common indoor contaminants. The use of these aptamers in sensors or detection assays should lead to increased accuracy and decreased expense in exposure monitoring and epidemiological investigations for environmental respiratory diseases."
Reference (2008, Biochem Biophys Res Commun ): Low, S. Y., Hill, J. E., & Peccia, J. (2009). DNA aptamers bind specifically and selectively to (1-->3)-beta-D-glucans. Biochemical and biophysical research communications, 378(4), 701–705. https://doi.org/10.1016/j.bbrc.2008.11.087
Aptamer: VEa5
Target: Vascular endothelial growth factor 165 (VEGF165)
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGTCTATTCAATTGGGCCCGTCCGTATGGTGGGTGTGCTGGCCAGATAGTATGTGCAATCA3′
Sequence length: 66
GC content: 0.5
Affinity: Kd: 130 nM
Pool type: 5′-ATACCAGTCTATTCAATT-N30-AGATAGTATGTGCAATCA-3′
Pool random region: 30
Binding buffer/conditions: TBSE (10 mM Tris/HCl, pH 7.0, 100 mM NaCl, 0.05 mM EDTA)
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Two DNA aptamers against a tumor marker protein, human vascular endothelial growth factor (VEGF(165)) were identified. This selection method enabled us to efficiently select the specific aptamers against the target protein.These specific aptamers would be useful sensor elements for cancer diagnosis."
Additional information: ssDNA library was labeled with FITC at the 5' end.
Reference (2008, Biotechnol Lett ): Hasegawa, H., Sode, K. & Ikebukuro, K. Selection of DNA aptamers against VEGF165 using a protein competitor and the aptamer blotting method. Biotechnol Lett 30, 829–834 (2008). https://doi.org/10.1007/s10529-007-9629-6
Aptamer: FMD 1F
Target: VP1 structural polypeptide of O-serotype FMD
Type of nucleic acid: ssDNA
Sequence: 5′ATACGGGAGCCAACACCATTCTATCGTTCCGGACGCTTATGCCTTGCCATCTACAGAGCAGGTGTGACGGAT3′
Sequence length: 72
GC content: 0.5277777777777778
Affinity: Not reported
Pool type: 5′-ATCCGTCACACCTGCTCT-N36-TGGTGTTGGCTCCCGTAT-3′
Pool random region: 36
Binding buffer/conditions: 1XBB: 0.5M NaCl, 20 mM Tris HCl, and 2 mM MgCl2, pH 7.2–7.4
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " We sought to develop a novel competitive fluorescence resonance energy transfer (FRET)-aptamer-based strategy for detection of foot-and-mouth (FMD) disease within minutes. We are currently working on a high-throughput means to accomplish FRET screening much more rapidly, thereby facilitating the search for an optimal competitive FRET–aptamer sequence."
Reference (2008, J Biomol Tech ): Bruno, J. G., Carrillo, M. P., & Phillips, T. (2008). Development of DNA aptamers to a foot-and-mouth disease peptide for competitive FRET-based detection. Journal of biomolecular techniques : JBT, 19(2), 109–115.
Aptamer: FMD 1R
Target: VP1 structural polypeptide of O-serotype FMD
Type of nucleic acid: ssDNA
Sequence: 5′ATCCGTCACTCCTGCTCTGTAGATGGCAAGGCATAAGCGTCCGGAACGATAGAATGGTGTTGGCTCCCGTAT3′
Sequence length: 72
GC content: 0.5277777777777778
Affinity: Not reported
Pool type: 5′-ATCCGTCACACCTGCTCT-N36-TGGTGTTGGCTCCCGTAT-3′
Pool random region: 36
Binding buffer/conditions: 1XBB: 0.5M NaCl, 20 mM Tris HCl, and 2 mM MgCl2, pH 7.2–7.4
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " We sought to develop a novel competitive fluorescence resonance energy transfer (FRET)-aptamer-based strategy for detection of foot-and-mouth (FMD) disease within minutes. We are currently working on a high-throughput means to accomplish FRET screening much more rapidly, thereby facilitating the search for an optimal competitive FRET–aptamer sequence."
Reference (2008, J Biomol Tech ): Bruno, J. G., Carrillo, M. P., & Phillips, T. (2008). Development of DNA aptamers to a foot-and-mouth disease peptide for competitive FRET-based detection. Journal of biomolecular techniques : JBT, 19(2), 109–115.
Aptamer: FMD 10F
Target: VP1 structural polypeptide of O-serotype FMD
Type of nucleic acid: ssDNA
Sequence: 5′ATACGGGAGCCAACACCATGAATATCTCTTCTACCTCCTCTCCTCCCTTTACTTAGAGCAGGTGTGACGGAT3′
Sequence length: 72
GC content: 0.4861111111111111
Affinity: Not reported
Pool type: 5′-ATCCGTCACACCTGCTCT-N36-TGGTGTTGGCTCCCGTAT-3′
Pool random region: 36
Binding buffer/conditions: 1XBB: 0.5M NaCl, 20 mM Tris HCl, and 2 mM MgCl2, pH 7.2–7.4
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " We sought to develop a novel competitive fluorescence resonance energy transfer (FRET)-aptamer-based strategy for detection of foot-and-mouth (FMD) disease within minutes. We are currently working on a high-throughput means to accomplish FRET screening much more rapidly, thereby facilitating the search for an optimal competitive FRET–aptamer sequence."
Reference (2008, J Biomol Tech ): Bruno, J. G., Carrillo, M. P., & Phillips, T. (2008). Development of DNA aptamers to a foot-and-mouth disease peptide for competitive FRET-based detection. Journal of biomolecular techniques : JBT, 19(2), 109–115.
Aptamer: ACh 6R
Target: Acetylcholine
Type of nucleic acid: ssDNA
Sequence: 5′ATCCGTCACACCTGCTCTAGGGGATCAAAGCTATGCGACCATGCGAGTGGATACTGGTGTTGGCTCCCGTAT3′
Sequence length: 72
GC content: 0.5416666666666666
Affinity: Not reported
Pool type: 5′-ATCCGTCACACCTGCTCT-N36-TGGTGTTGGCTCCCGTAT-3′
Pool random region: 36
Binding buffer/conditions: 0.5 M NaCl, 10 mM Tris HCl, and 1 mM MgCl2 in sterile deionized nuclease-free water (NFW) at pH 7.2–7.4
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " The present work establishes the specific feasibility of aptamers to detect ACh in situ. We have described relatively high affinity aptamers from five to eight rounds of SELEX that were useful in both aptamer-peroxidase and fluorescence-based staining protocols."
Reference (2008, In Vitro Cell Dev Biol Anim ): Bruno, J. G., Carrillo, M. P., Phillips, T., & King, B. (2008). Development of DNA aptamers for cytochemical detection of acetylcholine. In vitro cellular & developmental biology. Animal, 44(3-4), 63–72. https://doi.org/10.1007/s11626-008-9086-0
Aptamer: A05
Target: Recombinant HA1 proteins of the H5N1 influenza virus
Type of nucleic acid: ssDNA
Sequence: 5'GAATTCAGTCGGACAGCGGGGGGGAATTCTAGCAGTACACCTCGAGAATTATAGCCAGGATGGACGAATATCGTCTCCC3'
Sequence length: 79
GC content: 0.5189873417721519
Affinity: Not reported
Pool type: 5′-GAATTCAGTCGGACAGCG-N40-GATGGACGAATATCGTCTCCC-3′
Pool random region: 40
Binding buffer/conditions: 50 mM Tris–Cl, pH 7.4, 5 mM KCl, 100 mM NaCl, and 1 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " New therapeutics are urgently needed for the treatment of pandemic influenza caused by H5N1 influenza virus mutants. Among them, aptamer 10 had the strongest binding to the HA1 protein, and had an inhibitory effect on H5N1 influenza virus, as shown by the hemagglutinin and MTT assays. These results should aid the development of new drugs for the prevention and control of influenza virus infections."
Reference (2008, Biochem Biophys Res Commun ): Cheng, C., Dong, J., Yao, L., Chen, A., Jia, R., Huan, L., Guo, J., Shu, Y., & Zhang, Z. (2008). Potent inhibition of human influenza H5N1 virus by oligonucleotides derived by SELEX. Biochemical and biophysical research communications, 366(3), 670–674. https://doi.org/10.1016/j.bbrc.2007.11.183
Aptamer: A10
Target: Recombinant HA1 proteins of the H5N1 influenza virus
Type of nucleic acid: ssDNA
Sequence: 5'GAATTCAGTCGGACAGCGGGTTCCCATGCGGATGTTATAAAGCAGTCGCTTATAAGGGATGGACGAATATCGTCTCCC3'
Sequence length: 78
GC content: 0.5
Affinity: Not reported
Pool type: 5′-GAATTCAGTCGGACAGCG-N40-GATGGACGAATATCGTCTCCC-3′
Pool random region: 40
Binding buffer/conditions: 50 mM Tris–Cl, pH 7.4, 5 mM KCl, 100 mM NaCl, and 1 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " New therapeutics are urgently needed for the treatment of pandemic influenza caused by H5N1 influenza virus mutants. Among them, aptamer 10 had the strongest binding to the HA1 protein, and had an inhibitory effect on H5N1 influenza virus, as shown by the hemagglutinin and MTT assays. These results should aid the development of new drugs for the prevention and control of influenza virus infections."
Additional information: highest affinity aptamer
Reference (2008, Biochem Biophys Res Commun ): Cheng, C., Dong, J., Yao, L., Chen, A., Jia, R., Huan, L., Guo, J., Shu, Y., & Zhang, Z. (2008). Potent inhibition of human influenza H5N1 virus by oligonucleotides derived by SELEX. Biochemical and biophysical research communications, 366(3), 670–674. https://doi.org/10.1016/j.bbrc.2007.11.183
Aptamer: RNA 20
Target: Drosophila muscleblind protein (Mbl)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAAUGGAUCCACAUCUACGAAUUCACCGUAGAUGAUGGAUGUGCGGUAGAGUCUUUCACUGCAGACUUGACGAAGCUU3'
Sequence length: 80
GC content: 0.475
Affinity: Kd: 0.23 nM ± 0.09
Pool type: 5′-GGGAATGGATCCACATCTACGAATTC-N30-TTCACTGCAGACTTGACGAAGCTT-3′
Pool random region: 30
Binding buffer/conditions: 20 mM Tris (pH 7.5), 5 mM MgCl2, and 100 mM NaCl
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: Detection: " Members of the muscleblind family of RNA binding proteins found in Drosophila and mammals are key players in both the human disease myotonic dystrophy and the regulation of alternative splicing. It was also found that Mbl specifically bound a human MBNL1 RNA target, demonstrating the conservation of the muscleblind proteins in recognizing RNA targets."
Reference (2008, Biochemistry ): Goers, E. S., Voelker, R. B., Gates, D. P., & Berglund, J. A. (2008). RNA binding specificity of Drosophila muscleblind. Biochemistry, 47(27), 7284–7294. https://doi.org/10.1021/bi702252d
Aptamer: M7-14
Target: Lipopolysaccharide (LPS)
Type of nucleic acid: ssDNA
Sequence: 5'CCGGATCCGTTGATATAAAATTCTCTGGCTAGGATAGGCAGGAGCTTCATTATTTGTATGTTTTTGATTGTGGTGTTGGCTCCCAAGCTTCGG3'
Sequence length: 93
GC content: 0.4408602150537634
Affinity: Not reported
Pool type: 5'-CCGGATCCGTTGATATAAAATTC-N40-TTGATTGTGGTGTTGGCTCCCAAGCTTCGG-3'
Pool random region: 40
Binding buffer/conditions: Phosphate-buffered saline (PBS), pH 7.4
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: Therapeutic: " In Gram-negative bacterial infection, lipopolysaccharide (LPS) readily overwhelms the host innate immune system, which could result in inflammation and sepsis in severe cases Several approaches have been explored to prevent the cascade of LPS-induced events in humans. Therefore, developing anti-LPS molecules would confer an efficient antibacterial strategy. We used SELEX (Systemic Evolution of Ligands by EXponential enrichment) to isolate single-stranded DNA (ssDNA) aptamers"
Reference (2008, J Innate Immun ): Ding JL, Gan ST, Ho B. Single-stranded DNA oligoaptamers: molecular recognition and LPS antagonism are length- and secondary structure-dependent. J Innate Immun. 2009;1(1):46-58. doi: 10.1159/000145542. Epub 2008 Jul 12. PMID: 20375565; PMCID: PMC7312852.