RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: K
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTACGGCTTCGAAACTAGCCCGGATAGAATTCCCTATAGTGAGTCGTATTAGCTAGTAAGCTTGCCGT3'
Sequence length: 100
GC content: 0.45
Affinity: Kd: 228.4 nM and 7485.3 nM *this Kd was determined with affinity test on entire n round pool
Pool type: 5'-TAATACGACTCACTATAGGGAATTCTATCCGGGTA-N25-GCTAGTAAGCTTGCCGT-3'
Pool random region: 25
Binding buffer/conditions: EMSA binding buffer: 1 pmol BSA, Streptavidin and ANEPIII (5 µL total volume each)
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Current immunoassays detecting MUC1 are sensitive for predicting relapse in breast cancer, but they are not in widespread use in the follow-up of this disease. It has therefore been proposed that aptamers may offer this additional advantage in improving the sensitivity of such immunoassays."
Reference (2008, Arch Pharm Res ): Zhu, J., Wang, J., Su, Z. C., Li, Q., Cheng, M. S., & Zhang, J. H. (2008). Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions. Archives of pharmacal research, 31(9), 1120–1128. https://doi.org/10.1007/s12272-001-1278-2
Aptamer: 4C3
Target: Proteinase K-resistant isoform (PrPSc)
Type of nucleic acid: ssDNA
Sequence: 5'GGTATTGAGGGTCGCATCTGGCTTTCCTTTCTTCTCACTCCCCTGTTCTCTTCGTCTCTTGTTGATGGCTCTAACTCTCCTCT3'
Sequence length: 83
GC content: 0.4939759036144578
Affinity: Kd: 48 nM
Pool type: 5'-GGTATTGAGGGTCGCATC-N45-GATGGCTCTAACTCTCCTCT-3'
Pool random region: 45
Binding buffer/conditions: Selection Buffer: 50 mM NaH2PO4, pH 8.0, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.005% (v/v) Tween-20
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "Aptamers such as those described in the present study offer potentially more sensitive assay formats including rolling circle amplification (Yang et al., 2007), molecular beacon FRET-based signalling (Tombelli et al., 2005) and proximity-dependent DNA ligation, a method capable of detecting zeptomolar concentrations of proteins (Fredriksson et al., 2002). Aptamers may in future also have potential therapeutic application in TSE diseases by inhibiting conversion of PrPC to the pathological PrPSc isoform."
Reference (2008, J Virol Methods ): Bibby, D. F., Gill, A. C., Kirby, L., Farquhar, C. F., Bruce, M. E., & Garson, J. A. (2008). Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. Journal of virological methods, 151(1), 107–115. https://doi.org/10.1016/j.jviromet.2008.03.013
Aptamer: 4C5
Target: Proteinase K-resistant isoform (PrPSc)
Type of nucleic acid: ssDNA
Sequence: 5'GGTATTGAGGGTCGCATCTGGCTTTTCTTTCTTCTCACTCCCCTGTTCTCTTCGTCTCTTGTTGATGGCTCTAACTCTCCTCT3'
Sequence length: 83
GC content: 0.4819277108433735
Affinity: Kd: 30 nM
Pool type: 5'-GGTATTGAGGGTCGCATC-N45-GATGGCTCTAACTCTCCTCT-3'
Pool random region: 45
Binding buffer/conditions: Selection Buffer: 50 mM NaH2PO4, pH 8.0, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.005% (v/v) Tween-21
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "Aptamers such as those described in the present study offer potentially more sensitive assay formats including rolling circle amplification (Yang et al., 2007), molecular beacon FRET-based signalling (Tombelli et al., 2005) and proximity-dependent DNA ligation, a method capable of detecting zeptomolar concentrations of proteins (Fredriksson et al., 2002). Aptamers may in future also have potential therapeutic application in TSE diseases by inhibiting conversion of PrPC to the pathological PrPSc isoform."
Reference (2008, J Virol Methods ): Bibby, D. F., Gill, A. C., Kirby, L., Farquhar, C. F., Bruce, M. E., & Garson, J. A. (2008). Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. Journal of virological methods, 151(1), 107–115. https://doi.org/10.1016/j.jviromet.2008.03.013
Aptamer: 4C6
Target: Proteinase K-resistant isoform (PrPSc)
Type of nucleic acid: ssDNA
Sequence: 5'GGTATTGAGGGTCGCATCGTTTTGTTACAGTTCGTTTCTTTTCCCTGTCTTGTTTTGTTGTCTGATGGCTCTAACTCTCCTCT3'
Sequence length: 83
GC content: 0.4337349397590361
Affinity: Kd: 20 nM
Pool type: 5'-GGTATTGAGGGTCGCATC-N45-GATGGCTCTAACTCTCCTCT-3'
Pool random region: 45
Binding buffer/conditions: Selection Buffer: 50 mM NaH2PO4, pH 8.0, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.005% (v/v) Tween-22
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "Aptamers such as those described in the present study offer potentially more sensitive assay formats including rolling circle amplification (Yang et al., 2007), molecular beacon FRET-based signalling (Tombelli et al., 2005) and proximity-dependent DNA ligation, a method capable of detecting zeptomolar concentrations of proteins (Fredriksson et al., 2002). Aptamers may in future also have potential therapeutic application in TSE diseases by inhibiting conversion of PrPC to the pathological PrPSc isoform."
Reference (2008, J Virol Methods ): Bibby, D. F., Gill, A. C., Kirby, L., Farquhar, C. F., Bruce, M. E., & Garson, J. A. (2008). Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. Journal of virological methods, 151(1), 107–115. https://doi.org/10.1016/j.jviromet.2008.03.013
Aptamer: 4C17
Target: Proteinase K-resistant isoform (PrPSc)
Type of nucleic acid: ssDNA
Sequence: 5'GGTATTGAGGGTCGCATCTCCTTTTGTGTGTTTTTTTTATTGTTTTTTTTTTGTTTTTGATGGCTCTAACTCTCCTCT3'
Sequence length: 78
GC content: 0.3461538461538461
Affinity: Kd: 19 nM
Pool type: 5'-GGTATTGAGGGTCGCATC-N45-GATGGCTCTAACTCTCCTCT-3'
Pool random region: 45
Binding buffer/conditions: Selection Buffer: 50 mM NaH2PO4, pH 8.0, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.005% (v/v) Tween-25
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "Aptamers such as those described in the present study offer potentially more sensitive assay formats including rolling circle amplification (Yang et al., 2007), molecular beacon FRET-based signalling (Tombelli et al., 2005) and proximity-dependent DNA ligation, a method capable of detecting zeptomolar concentrations of proteins (Fredriksson et al., 2002). Aptamers may in future also have potential therapeutic application in TSE diseases by inhibiting conversion of PrPC to the pathological PrPSc isoform."
Reference (2008, J Virol Methods ): Bibby, D. F., Gill, A. C., Kirby, L., Farquhar, C. F., Bruce, M. E., & Garson, J. A. (2008). Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. Journal of virological methods, 151(1), 107–115. https://doi.org/10.1016/j.jviromet.2008.03.013
Aptamer: 4C20
Target: Proteinase K-resistant isoform (PrPSc)
Type of nucleic acid: ssDNA
Sequence: 5'GGTATTGAGGGTCGCATCGTTTCTTCCTTTGGCCTTTCTTCCGTCTTTCTGTTGTTCTTACCTGATGGCTCTAACTCTCCTCT3'
Sequence length: 83
GC content: 0.4698795180722891
Affinity: Kd: 79 nM
Pool type: 5'-GGTATTGAGGGTCGCATC-N45-GATGGCTCTAACTCTCCTCT-3'
Pool random region: 45
Binding buffer/conditions: Selection Buffer: 50 mM NaH2PO4, pH 8.0, 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.005% (v/v) Tween-26
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "Aptamers such as those described in the present study offer potentially more sensitive assay formats including rolling circle amplification (Yang et al., 2007), molecular beacon FRET-based signalling (Tombelli et al., 2005) and proximity-dependent DNA ligation, a method capable of detecting zeptomolar concentrations of proteins (Fredriksson et al., 2002). Aptamers may in future also have potential therapeutic application in TSE diseases by inhibiting conversion of PrPC to the pathological PrPSc isoform."
Reference (2008, J Virol Methods ): Bibby, D. F., Gill, A. C., Kirby, L., Farquhar, C. F., Bruce, M. E., & Garson, J. A. (2008). Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. Journal of virological methods, 151(1), 107–115. https://doi.org/10.1016/j.jviromet.2008.03.013
Aptamer: 10.10v aptamer
Target: Daunomycin
Type of nucleic acid: ssDNA
Sequence: 5'ACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCT3'
Sequence length: 41
GC content: 0.5853658536585366
Affinity: Kd: 272 nM        
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: Truncated sequence 10.10V was obtained by removing primer sequences that were predicted by mfold as not being involved in the secondary structure of the randomized region
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: VEa4
Target: Vascular endothelial growth factor 165 (VEGF165)
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGTCTATTCAATTGGGCGGGGACTGTCGGGATGTGTGTGGGCCAGATAGTATGTGCAATCA3′
Sequence length: 66
GC content: 0.5
Affinity: Kd: 500 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: M7-2
Target: Lipopolysaccharide (LPS)
Type of nucleic acid: ssDNA
Sequence: 5'CCGGATCCGTTGATATAAAATTCTCTGGCTAGGATAGGCAGGAGTTTCATTACTTGTATGTTTTTGATTGTGGTGTTGGCTCCCAAGCTTCGG3'
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"
Additional information: affinities are shown in graph form but accurate numbers are not given
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.
Aptamer: M7-1
Target: Lipopolysaccharide (LPS)
Type of nucleic acid: ssDNA
Sequence: 5'CCGGATCCGTTGATATAAAATTCTCTGGCTAGGATAGGCAGGAGTTTCATTACTTATATGTTTTTGATTGTGGTGTTGGCTCCCAAGCTTCGG3'
Sequence length: 93
GC content: 0.4301075268817204
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.
Aptamer: M7-3/M7-6
Target: Lipopolysaccharide (LPS)
Type of nucleic acid: ssDNA
Sequence: 5'CCGGATCCGTTGATATAAAATTCTCCGGCTAGGATAGGCAGGAGTTTCATTACTTGTATGTTTTTGATTGTGGTGTTGGCTCCCAAGCTTCGG3'
Sequence length: 93
GC content: 0.4516129032258064
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.
Aptamer: M7-13
Target: Lipopolysaccharide (LPS)
Type of nucleic acid: ssDNA
Sequence: 5'CCGGATCCGTTGATATAAAATTCTCTGGCTAGGATAGGCAGGTGTTTCATTACTTGTATGTTTTTGATTGTGGTGTTGGCTCCCAAGCTTCGG3'
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.
Aptamer: ZE5
Target: Hepatitis C virus (HCV) envelope surface glycoprotein E4
Type of nucleic acid: ssDNA
Sequence: 5′GCGGAATTCTAATACGACTCACTATAGGGAACAGTCCGAGCCTCCATTCATGTAACGAACATAGTTTTGGCAGGGTCAATGCGTCATA3′
Sequence length: 88
GC content: 0.4545454545454545
Affinity: Kd 4.29±0.6 nM
Pool type: 5′-GCGGAATTCTAATACGACTCACTATAGGGAACAGTCCGAGCC-N30-GGGTCAATGCGTCATA-3′
Pool random region: 30
Binding buffer/conditions: 25 mM Tris–HCl, 50 mM KCl, 200 mM NaCl, 0.2 mM EDTA, 5% (v/v) glycerol, and 0.5 mM DTT
Buffer type: Tris Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diognostic and Therapeutic: "In this study, we have described the development of an alive cell surface--Systematic Evolution of Ligands by Exponential Enrichment (CS-SELEX) technique and screened the functional ssDNA aptamers that specifically bound to HCV envelope surface glycoprotein E2. Our data demonstrate that the newly selected ssDNA aptamers, especially aptamer ZE2, hold great promise for developing new molecular probes, as an early diagnostic reagent for HCV surface antigen, or a therapeutic drug specifically for HCV."
Reference (2009, PLoS One ): Chen, F., Hu, Y., Li, D., Chen, H., & Zhang, X. L. (2009). CS-SELEX generates high-affinity ssDNA aptamers as molecular probes for hepatitis C virus envelope glycoprotein E2. PloS one, 4(12), e8142. https://doi.org/10.1371/journal.pone.0008142
Aptamer: TV08
Target: Vaccinia virus–infected lung cancer A549 cells
Type of nucleic acid: ssDNA
Sequence: 5′ATCGTCTGCTCCGTCCAATATGATGACACCTGCATAATTTATAGTGAGTCTTGATTCACGCTGCATTTGGTGTGAGGTCGTGC3'
Sequence length: 83
GC content: 0.4578313253012048
Affinity: Kd: 2.7 ± 6.2 nM
Pool type: 5′-ATCGTCTGCTCCGTCCAATA-N45-TTTGGTGTGAGGTCGTGC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose, 5 mmol/L MgCl2 in Dulbecco PBS, yeast tRNA (0.1 g/L; Sigma–Aldrich), FBS (100 mL/L), BSA (1 g/L; 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 Therapeutic: "We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell-SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells."
Reference (2009, Clin Chem ): Tang, Z., Parekh, P., Turner, P., Moyer, R. W., & Tan, W. (2009). Generating aptamers for recognition of virus-infected cells. Clinical chemistry, 55(4), 813–822. https://doi.org/10.1373/clinchem.2008.113515
Aptamer: WT-15
Target: Serine protease inhibitor plasminogen activator inhibitor-1 (PAI-1)
Type of nucleic acid: ssRNA
Sequence: 5′GGGAGGACGAUGCGGAUCAACUCACCGUAGGUCUAGUGAGAACUUCAAGUCUACUCAGACGACUCGCUGAGGAUCC3′
Sequence length: 76
GC content: 0.5394736842105263
Affinity: Kd: 177 pM
Pool type: 5′-GGGAGGACGATGCGG-N40-CAGACGACTCGCTGAGGATCC-3′
Pool random region: 40
Binding buffer/conditions: BSA binding buffer E (20 mM Hepes, pH 7.4, 50 mM NaCl, 2 mM CaCl2, and 0.1% bovine serum albumin [BSA]); CHAPS binding buffer E (20 mM Hepes, pH 7.4, 50 mM NaCl, 2 mM CaCl2, and 0.05% CHAPS); CHAPS binding buffer F (20 mM Hepes, pH 7.4, 150 mM NaCl, 2 mM CaCl2, and 0.05% CHAPS)
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " The serine protease inhibitor plasminogen activator inhibitor-1 (PAI-1) is increased in several cancers, including breast, where it is associated with a poor outcome. Therefore, the PAI-1 aptamer SM-20 demonstrates therapeutic potential as an antimetastatic agent and could possibly be used as an adjuvant to traditional chemotherapy for breast cancer."
Additional information: Different buffers were used during different rounds of selection
Reference (2009, Oligonucleotides ): Blake, C. M., Sullenger, B. A., Lawrence, D. A., & Fortenberry, Y. M. (2009). Antimetastatic potential of PAI-1-specific RNA aptamers. Oligonucleotides, 19(2), 117–128. https://doi.org/10.1089/oli.2008.0177
Aptamer: 13.63
Target: Immunoglobulin E (IgE)-binding epitope of Asp f 1 allergen
Type of nucleic acid: ssDNA
Sequence: 5′TACTAACGGTACAAGCTAGCCCACCAGAACACCCCGTCCCATCGACCTCCCTCCTCATATCCCTGCCCCTCTGCCTCCAACGTTGACCTAGAAGC3'
Sequence length: 95
GC content: 0.5789473684210527
Affinity: Not reported
Pool type: 5′-TACTAACGGTACAAGCTA-N60-AACGTTGACCTAGAAGC-3'
Pool random region: 60
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: 16.8 Kda
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " The objective of the research is to develop a DNA aptamer for the Asp f 1 allergen of the pathogenic fungus Aspergillus fumigatus, using an IgE-binding epitope of the allergen as the target for aptamer selection. Production of this aptamer provides proof-of-principle that allergen measurement methods can be developed to indicate the potent fraction, or allergenicity, of allergens."
Reference (2009, Biochem Biophys Res Commun ): Low, S. Y., Hill, J. E., & Peccia, J. (2009). A DNA aptamer recognizes the Asp f 1 allergen of Aspergillus fumigatus. Biochemical and biophysical research communications, 386(3), 544–548. https://doi.org/10.1016/j.bbrc.2009.06.089
Aptamer: 13.78
Target: Immunoglobulin E (IgE)-binding epitope of Asp f 1 allergen
Type of nucleic acid: ssDNA
Sequence: 5′TACTAACGGTACAAGCTACAAACCCCAACGCACGTACACCTGTCTCCCGCACTAGTTCCCCCTCATGACTGCCCTCCCAACGTTGACCTAGAAGC3'
Sequence length: 95
GC content: 0.5473684210526316
Affinity: Not reported
Pool type: 5′-TACTAACGGTACAAGCTA-N60-AACGTTGACCTAGAAGC-3'
Pool random region: 60
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: 16.8 Kda
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " The objective of the research is to develop a DNA aptamer for the Asp f 1 allergen of the pathogenic fungus Aspergillus fumigatus, using an IgE-binding epitope of the allergen as the target for aptamer selection. Production of this aptamer provides proof-of-principle that allergen measurement methods can be developed to indicate the potent fraction, or allergenicity, of allergens."
Reference (2009, Biochem Biophys Res Commun ): Low, S. Y., Hill, J. E., & Peccia, J. (2009). A DNA aptamer recognizes the Asp f 1 allergen of Aspergillus fumigatus. Biochemical and biophysical research communications, 386(3), 544–548. https://doi.org/10.1016/j.bbrc.2009.06.089