RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: FC5
Target: Coedine
Type of nucleic acid: ssRNA
Sequence: 5′GGGACAGGGCUAGCAGUAGGAUUGGGUGAGGGGAUGUGCUGUGGAGGCAAAGCUUCCG3′
Sequence length: 58
GC content: 0.603448275862069
Affinity: Kd: 4.00 ± 0.13 μM
Pool type: 5′-GGGACAGGGCTAGC-N30-GAGGCAAAGCTTCCG-3′
Pool random region: 30
Binding buffer/conditions: 250 mM NaCl, 20 mM Tris–HCl (pH 7.4) and 5 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: Biosensors: " RNA aptamers that bind the opium alkaloid codeine were generated using an iterative in vitro selection process. These aptamers may be used to construct tools, such as synthetic riboswitches that can be employed to redirect flux through an engineered BIA metabolic pathway or in setting up rapid functional screens of pathway variants"
Additional information: SELEX was done with the DNA pool that was transcribed into RNA for selection. The final aptamer is RNA
Reference (2006, Nucleic Acids Res ): Win, M. N., Klein, J. S., & Smolke, C. D. (2006). Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay. Nucleic acids research, 34(19), 5670–5682. https://doi.org/10.1093/nar/gkl718
Aptamer: FC45
Target: Coedine
Type of nucleic acid: ssRNA
Sequence: 5′GGGACAGGGCUAGCUUAGUGCUAUGUGAGAAAAGGGUGUGGGGGGAGGCAAAGCUUCCG3′
Sequence length: 59
GC content: 0.576271186440678
Affinity: Kd: 2.50 ± 0.06 μM
Pool type: 5′-GGGACAGGGCTAGC-N30-GAGGCAAAGCTTCCG-3′
Pool random region: 30
Binding buffer/conditions: 250 mM NaCl, 20 mM Tris–HCl (pH 7.4) and 5 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: Biosensors: " RNA aptamers that bind the opium alkaloid codeine were generated using an iterative in vitro selection process. These aptamers may be used to construct tools, such as synthetic riboswitches that can be employed to redirect flux through an engineered BIA metabolic pathway or in setting up rapid functional screens of pathway variants"
Additional information: SELEX was done with the DNA pool that was transcribed into RNA for selection. The final aptamer is ssDNA
Reference (2006, Nucleic Acids Res ): Win, M. N., Klein, J. S., & Smolke, C. D. (2006). Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay. Nucleic acids research, 34(19), 5670–5682. https://doi.org/10.1093/nar/gkl718
Aptamer: pUC19
Target: S37A-β-catenin, Human
Type of nucleic acid: ssRNA
Sequence: 5'GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC3'
Sequence length: 81
GC content: 0.5679012345679012
Affinity: Kd: ~5.0 nM
Pool type: 5'-GGACGCGCGUGGUACC-N50-GCUUCCGCGGGGAUC-3'
Pool random region: 50
Binding buffer/conditions: 25 mmol/L HEPES (pH 7.5), 150 mmol/L NaCl, 1 mmol/L MgCl2, 2 mmol/L DTT, and 40 units RNase inhibitor
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Activated beta-catenin regulates the transcription of oncogenic target genes and is critical for tumorigenesis. Our results establish that beta-catenin has an important role in both transcription and splicing, and that its action can be modulated by a high-affinity RNA aptamer. The RNA aptamer could be further developed as a specific inhibitor for cancer therapeutics."
Reference (2006, Cancer Res ): Lee, H. K., Choi, Y. S., Park, Y. A., & Jeong, S. (2006). Modulation of oncogenic transcription and alternative splicing by beta-catenin and an RNA aptamer in colon cancer cells. Cancer research, 66(21), 10560–10566. https://doi.org/10.1158/0008-5472.CAN-06-2526
Aptamer: Aptamer #25
Target: Alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) (α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptors
Type of nucleic acid: ssRNA
Sequence: 5′ACCGAGUCCAGAAGCUUGUAGUACUCGGCGAACUACCUAACCCCCCACAAUUGUAUUAUCGCCCGCCUAGAUGGCAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC3′
Sequence length: 107
GC content: 0.4859813084112149
Affinity: Kd: 37 ± 5 nM
Pool type: 5′-ACCGAGTCCAGAAGCTTGTAGTACT-N40-GCCTAGATGGCAGTTGAATTCTCCCTATAGTGAGTCGTATTAC-3′
Pool random region: 40
Binding buffer/conditions: 25 mM HEPES, 145 mM NaCl, 5.3 mM KCl, 1.8 mM CaCl2 and 1.7 mM MgCl2, at pH 7.4
Divalent salt: MgCl/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: Detection: " Present studies clearly establish that the RNA aptamers evolved are competitive antagonists of the AMPA receptors and show significant neuroprotection against OGD mediated injury. These properties of the RNA aptamers coupled to the fact that these are water-soluble ligands make them promising excellent candidates for potential use as neuroprotective drugs."
Reference (2007, Neuropharmacology ): Du, M., Ulrich, H., Zhao, X., Aronowski, J., & Jayaraman, V. (2007). Water soluble RNA based antagonist of AMPA receptors. Neuropharmacology, 53(2), 242–251. https://doi.org/10.1016/j.neuropharm.2007.05.007
Aptamer: aptamer 16
Target: DC-specific intercellular adhesion molecule (ICAM)-3 grabbing non-integrin (DC-SIGN)
Type of nucleic acid: ssDNA
Sequence: 5′CGGGGATCCGGAATTCTCCTCACAGGCGAAAATTTGTGGATATAGAGGGTTACTCGGATGTATGTCGACGAAGCTTGCG3′
Sequence length: 79
GC content: 0.5063291139240507
Affinity: Kd: 21.73 nM
Pool type: 5′-CGGGGATCCGGAATTCTCCTCACA-N35-GTATGTCGACGAAGCTTGCG-3′
Pool random region: 35
Binding buffer/conditions: (SHCMK) containing 20 mmol/l Hepes, pH 7.35, 120 mmol/l KCl, 1 mmol/l CaCl2, and 1 mmol/l MgCl2
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: 44 kd
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic and Detection: "Selected an aptamer with high affinity to DC-SIGN that blocked DC adhesion to ECs with an effectiveness comparable to the antibody. However, further investigation of the construction and function of the aptamer is needed in order to assess its potential in basic research, drug development, and clinical applications."
Reference (2007, Mol Cell Biochem ): Hui, Y., Shan, L., Lin-Fu, Z., & Jian-Hua, Z. (2007). Selection of DNA aptamers against DC-SIGN protein. Molecular and cellular biochemistry, 306(1-2), 71–77. https://doi.org/10.1007/s11010-007-9555-x
Aptamer: ApT4-A
Target: Thyroxine (T4)
Type of nucleic acid: ssRNA
Sequence: 5'GAAUUCGUCGACGGAUCCGCAGUGCGUCUUGGGUUGUGAGCUCCCGGCUCGCAUUGUGAGGUGGAGGGGGACGUGCUGCAGGUCGACGCAUGCGCCG3'
Sequence length: 97
GC content: 0.6494845360824743
Affinity: Kd: 50±10 μM
Pool type: 5′-GAATTCGTCGACGGATCC-N58-CTGCAGGTCGACGCATGCGCCG-3′
Pool random region: 58
Binding buffer/conditions: 10 mM Tris/HCl (pH 7.5), 500 mM NaCl and 1 mM MgCl2
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: " This work provides an original demonstration that RNA species can specifically bind a thyroid hormone. Thyroid hormones are a suitable metabolite with which to search for a potential human riboswitch. Finding equivalent structures within natural mRNAs would most likely lead to a breakthrough in the molecular biology of the thyroid hormones."
Reference (2007, Biochem J ): Lévesque, D., Beaudoin, J. D., Roy, S., & Perreault, J. P. (2007). In vitro selection and characterization of RNA aptamers binding thyroxine hormone. The Biochemical journal, 403(1), 129–138. https://doi.org/10.1042/BJ20061216
Aptamer: Ab1
Target: Abrin toxin, Abrus precatorius (A.precatorius)
Type of nucleic acid: ssDNA
Sequence: 5'CAGCTCAGAAGCTTGATCCTGTGAGCGAAAATCCGGAGTAGAGGAGCAGCTGGGTGCTGACTCGAAGTCGTGCATCTGCA3'
Sequence length: 80
GC content: 0.55
Affinity: Kd: 76 ± 28 nM
Pool type: 5′-CAGCTCAGAAGCTTGATCCTGTG-N35-GACTCGAAGTCGTGCATCTGCA-3
Pool random region: 35
Binding buffer/conditions: SHMCK (20 mM HEPES, pH 7.35, 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: 63 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Abrin toxin as the target protein, belongs to class II ribosome-inactivating proteins family, has high toxicity to eukaryotic cells. Here, we firstly report the DNA aptamers, isolated by in vitro selection, recognize abrin toxin with high affinity and specificity, and have the advantage of no cross-reaction with structure-similar protein ricin toxin over antibodies. This assay can be successfully directly performed not only in physiological buffer but also in more complicated biological matrix, such as diluted serum."
Reference (2007, Biosens Bioelectron ): Tang, J., Yu, T., Guo, L., Xie, J., Shao, N., & He, Z. (2007). In vitro selection of DNA aptamer against abrin toxin and aptamer-based abrin direct detection. Biosensors & bioelectronics, 22(11), 2456–2463. https://doi.org/10.1016/j.bios.2006.09.015
Aptamer: Ab2
Target: Abrin toxin, Abrus precatorius (A.precatorius)
Type of nucleic acid: ssDNA
Sequence: 5′CAGCTCAGAAGCTTGATCCTGTGCAGCCGGGGGACAAGCGCGTTGGCCAGATCATCCGACTCGAAGTCGTGCATCTGCA3'
Sequence length: 79
GC content: 0.5949367088607594
Affinity: Kd: 89 ± 32
Pool type: 5′-CAGCTCAGAAGCTTGATCCTGTG-N35-GACTCGAAGTCGTGCATCTGCA-3
Pool random region: 35
Binding buffer/conditions: SHMCK (20 mM HEPES, pH 7.35, 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: 63 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Abrin toxin as the target protein, belongs to class II ribosome-inactivating proteins family, has high toxicity to eukaryotic cells. Here, we firstly report the DNA aptamers, isolated by in vitro selection, recognize abrin toxin with high affinity and specificity, and have the advantage of no cross-reaction with structure-similar protein ricin toxin over antibodies. This assay can be successfully directly performed not only in physiological buffer but also in more complicated biological matrix, such as diluted serum."
Reference (2007, Biosens Bioelectron ): Tang, J., Yu, T., Guo, L., Xie, J., Shao, N., & He, Z. (2007). In vitro selection of DNA aptamer against abrin toxin and aptamer-based abrin direct detection. Biosensors & bioelectronics, 22(11), 2456–2463. https://doi.org/10.1016/j.bios.2006.09.015
Aptamer: Ab3
Target: Abrin toxin, Abrus precatorius (A.precatorius)
Type of nucleic acid: ssDNA
Sequence: 5′CAGCTCAGAAGCTTGATCCTGTGCGAAAAGGATGCGGGCAGCGGACTCAAGGCCATCTGACTCGAAGTCGTGCATCTGCA3'
Sequence length: 80
GC content: 0.5625
Affinity: Kd: 50 ± 15
Pool type: 5′-CAGCTCAGAAGCTTGATCCTGTG-N35-GACTCGAAGTCGTGCATCTGCA-3
Pool random region: 35
Binding buffer/conditions: SHMCK (20 mM HEPES, pH 7.35, 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: 63 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Abrin toxin as the target protein, belongs to class II ribosome-inactivating proteins family, has high toxicity to eukaryotic cells. Here, we firstly report the DNA aptamers, isolated by in vitro selection, recognize abrin toxin with high affinity and specificity, and have the advantage of no cross-reaction with structure-similar protein ricin toxin over antibodies. This assay can be successfully directly performed not only in physiological buffer but also in more complicated biological matrix, such as diluted serum."
Reference (2007, Biosens Bioelectron ): Tang, J., Yu, T., Guo, L., Xie, J., Shao, N., & He, Z. (2007). In vitro selection of DNA aptamer against abrin toxin and aptamer-based abrin direct detection. Biosensors & bioelectronics, 22(11), 2456–2463. https://doi.org/10.1016/j.bios.2006.09.015
Aptamer: Ab4
Target: Abrin toxin, Abrus precatorius (A.precatorius)
Type of nucleic acid: ssDNA
Sequence: 5′CAGCTCAGAAGCTTGATCCTGTGCGGGGCAAAGAGGTCCGAATTTGAAGGCTCCCCTGGACTCGAAGTCGTGCATCTGCA3'
Sequence length: 80
GC content: 0.5625
Affinity: Kd: 104 ± 47
Pool type: 5′-CAGCTCAGAAGCTTGATCCTGTG-N35-GACTCGAAGTCGTGCATCTGCA-3
Pool random region: 35
Binding buffer/conditions: SHMCK (20 mM HEPES, pH 7.35, 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: 63 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Abrin toxin as the target protein, belongs to class II ribosome-inactivating proteins family, has high toxicity to eukaryotic cells. Here, we firstly report the DNA aptamers, isolated by in vitro selection, recognize abrin toxin with high affinity and specificity, and have the advantage of no cross-reaction with structure-similar protein ricin toxin over antibodies. This assay can be successfully directly performed not only in physiological buffer but also in more complicated biological matrix, such as diluted serum."
Reference (2007, Biosens Bioelectron ): Tang, J., Yu, T., Guo, L., Xie, J., Shao, N., & He, Z. (2007). In vitro selection of DNA aptamer against abrin toxin and aptamer-based abrin direct detection. Biosensors & bioelectronics, 22(11), 2456–2463. https://doi.org/10.1016/j.bios.2006.09.015
Aptamer: Ab6
Target: Abrin toxin, Abrus precatorius (A.precatorius)
Type of nucleic acid: ssDNA
Sequence: 5′CAGCTCAGAAGCTTGATCCTGTGAGGAATGCTCATGCATAGCAAGGGCTAAACACGGCGACTCGAAGTCGTGCATCTGCA3'
Sequence length: 80
GC content: 0.525
Affinity: Kd: 28 ± 9 nM
Pool type: 5′-CAGCTCAGAAGCTTGATCCTGTG-N35-GACTCGAAGTCGTGCATCTGCA-3
Pool random region: 35
Binding buffer/conditions: SHMCK (20 mM HEPES, pH 7.35, 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: 63 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Abrin toxin as the target protein, belongs to class II ribosome-inactivating proteins family, has high toxicity to eukaryotic cells. Here, we firstly report the DNA aptamers, isolated by in vitro selection, recognize abrin toxin with high affinity and specificity, and have the advantage of no cross-reaction with structure-similar protein ricin toxin over antibodies. This assay can be successfully directly performed not only in physiological buffer but also in more complicated biological matrix, such as diluted serum."
Reference (2007, Biosens Bioelectron ): Tang, J., Yu, T., Guo, L., Xie, J., Shao, N., & He, Z. (2007). In vitro selection of DNA aptamer against abrin toxin and aptamer-based abrin direct detection. Biosensors & bioelectronics, 22(11), 2456–2463. https://doi.org/10.1016/j.bios.2006.09.015
Aptamer: Ab7
Target: Abrin toxin, Abrus precatorius (A.precatorius)
Type of nucleic acid: ssDNA
Sequence: 5′CAGCTCAGAAGCTTGATCCTGTGCGATCGAATGAAAGCTGCTGGATTGTCGCTATCCTGACTCGAAGTCGTGCATCTGCA3'
Sequence length: 80
GC content: 0.5125
Affinity: Kd: 67 ± 29
Pool type: 5′-CAGCTCAGAAGCTTGATCCTGTG-N35-GACTCGAAGTCGTGCATCTGCA-3
Pool random region: 35
Binding buffer/conditions: SHMCK (20 mM HEPES, pH 7.35, 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: 63 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Abrin toxin as the target protein, belongs to class II ribosome-inactivating proteins family, has high toxicity to eukaryotic cells. Here, we firstly report the DNA aptamers, isolated by in vitro selection, recognize abrin toxin with high affinity and specificity, and have the advantage of no cross-reaction with structure-similar protein ricin toxin over antibodies. This assay can be successfully directly performed not only in physiological buffer but also in more complicated biological matrix, such as diluted serum."
Reference (2007, Biosens Bioelectron ): Tang, J., Yu, T., Guo, L., Xie, J., Shao, N., & He, Z. (2007). In vitro selection of DNA aptamer against abrin toxin and aptamer-based abrin direct detection. Biosensors & bioelectronics, 22(11), 2456–2463. https://doi.org/10.1016/j.bios.2006.09.015
Aptamer: aptamer-12
Target: Biased conformation(s) of calsenilin
Type of nucleic acid: ssRNA
Sequence: 5′GGGACGCGUGGUACCAAAGAGGCUGCGCGGAAGUGAGGGUGUUGGUUACGAAGGUUGGUGUGUGAAGCUUCCGCGGGGAUC3′
Sequence length: 81
GC content: 0.6049382716049383
Affinity: Kd: 190 nM for Ca2+ bound
Pool type: 5′-CGGAATTCGGGACGCGTGGTACC-N50-AAGCTTCCGCGGGGATCCAA-3′
Pool random region: 50
Binding buffer/conditions: 30 mM Tris (pH 7.5 at 25 °C), 150 mM NaCl, 1 mM MgCl2, 1 mM DTT, 5 mM EGTA, or 1 mM CaCl2
Divalent salt: MgCl/CaCl
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: " We have used SELEX (Systematic Evolution of Ligands by EXponential enrichment) technology to produce aptamers that bind in a conformationally selective manner to calsenilin, which involved in Ca(2+)-mediated apoptotic signaling. Aptamers selected against the two different conformations of calsenilin have different characteristics suggest that aptamers can serve as a plausible tool for recognizing various conformations of proteins, even those caused by interactions with small molecules or ions such as Ca(2+)."
Additional information: Aptamer-12, selected for the active conformation of the protein, binds strongly to the calcium-bound dimeric conformation and not to the calcium-deficient conformation. The paper given fixed region which has less nucleotides than the given pool (5′-Fixed region: GGGACGCGTGGTACC, 3′-fixed region: AGCTTCCGCGGGGAT). The given fixed region is used to construct the aptamer sequence. 
All the thymine converted to Uridine.
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 (2007, Bioorg Med Chem ): Lee, K. H., Jeong, S., Yang, E. G., Park, Y. K., & Yu, J. (2007). An RNA aptamer that recognizes a specific conformation of the protein calsenilin. Bioorganic & medicinal chemistry, 15(24), 7545–7552. https://doi.org/10.1016/j.bmc.2007.09.013
Aptamer: II-1
Target: Release factor 1, Escherichia coli (E. Coli)
Type of nucleic acid: ssRNA
Sequence: 5'GGACCGAGAAGYYACCCAGGAUUGCGUGUUAAGGCGCUCGGCUCGAUAUUUAUGCUGGUCAUGGUGGACGCACAUCGCAGCAAC3'
Sequence length: 82
GC content: 0.5609756097560976
Affinity: Kd: 30 ± 6 nM
Pool type: 5'-GGACCGAGAAGYYACCC-N50-ACGCACATCGCAGCAAC-3'
Pool random region: 50
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " A pool of 84-nt RNAs containing a randomized sequence of 50 nt was selected against gel-immobilized Escherichia coli release factor 1 (RF-1) responsible for translation termination at amber (UAG) stop codon. By binding to and hence inhibiting the action of RF-1 specifically or bio-orthogonally, aptamer class II-1 enhanced the amber suppression efficiency in the presence of an anticodon-adjusted (CUA) suppressor tRNA without practically damaging the protein translation machinery of the cell-free extract of E. coli, as confirmed by the translation of amber-mutated (gfp(amber141) or gfp(amber178)) and wild-type (gfp(wild)) genes of GFP."
Reference (2007, Bioorg Med Chem Lett ): Sando, S., Ogawa, A., Nishi, T., Hayami, M., & Aoyama, Y. (2007). In vitro selection of RNA aptamer against Escherichia coli release factor 1. Bioorganic & medicinal chemistry letters, 17(5), 1216–1220. https://doi.org/10.1016/j.bmcl.2006.12.013
Aptamer: M-2
Target: Amyloid-like fibrils formed in vitro from monomeric beta-2-microglobulin (β2m)
Type of nucleic acid: ssRNA
Sequence: 5'GGGCCAAGCUUGCAUGCCUGCAGUUGGUUACGCGUACAGUGAAACUCGGAAAGUUGAAGGGCCAAAUGGGAACGGUACCGAGCUCAGGUUCCC3'
Sequence length: 93
GC content: 0.5591397849462365
Affinity: Kd: 1.15E-08 M
Pool type: 5'-GGGCCAAGCTTGCATGCCTGCAG-N60-GGTACCGAGCTCAGGTTCCC-3'
Pool random region: 60
Binding buffer/conditions: 25 mm sodium acetate, 25 mm sodium phosphate buffer (Buffer A), pH 3.6, containing 250 mm NaCl
Buffer type: PBS/phosphate buffers
pH: 3.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Whereas the full potential of aptamers as therapeutics or diagnostics has yet to be realized, our results demonstrate the power of RNA aptamers for detection and identification of amyloid and, possibly, other protein misfolding diseases. They also pave the way for future experiments to derive aptamers able to bind tightly and specifically to different amyloid precursors (monomers, oligomers, or other protofibrillar forms), or amyloid fibrils with distinct structural properties that give rise to different disease phenotypes."
Reference (2007, J Biol Chem ): Bunka, D. H., Mantle, B. J., Morten, I. J., Tennent, G. A., Radford, S. E., & Stockley, P. G. (2007). Production and characterization of RNA aptamers specific for amyloid fibril epitopes. The Journal of biological chemistry, 282(47), 34500–34509. https://doi.org/10.1074/jbc.M703679200
Aptamer: WL-2
Target: Amyloid-like fibrils formed in vitro from monomeric beta-2-microglobulin (β2m)
Type of nucleic acid: ssRNA
Sequence: 5'GGGCCAAGCUUGCAUGCCUGCAGAAAAAUAAAGUGUGUACACUAAAUUGCUAGCCCCCGGAAAGAAGGUCAACAAAAGUCAGUGGUACCGAGCUCAGGUUCCC3'
Sequence length: 103
GC content: 0.4951456310679611
Affinity: Kd: 7.48E-09 M
Pool type: 5'-GGGCCAAGCTTGCATGCCTGCAG-N60-GGTACCGAGCTCAGGTTCCC-3'
Pool random region: 60
Binding buffer/conditions: 25 mm sodium acetate, 25 mm sodium phosphate buffer (Buffer A), pH 3.6, containing 250 mm NaCl
Buffer type: PBS/phosphate buffers
pH: 3.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Whereas the full potential of aptamers as therapeutics or diagnostics has yet to be realized, our results demonstrate the power of RNA aptamers for detection and identification of amyloid and, possibly, other protein misfolding diseases. They also pave the way for future experiments to derive aptamers able to bind tightly and specifically to different amyloid precursors (monomers, oligomers, or other protofibrillar forms), or amyloid fibrils with distinct structural properties that give rise to different disease phenotypes."
Reference (2007, J Biol Chem ): Bunka, D. H., Mantle, B. J., Morten, I. J., Tennent, G. A., Radford, S. E., & Stockley, P. G. (2007). Production and characterization of RNA aptamers specific for amyloid fibril epitopes. The Journal of biological chemistry, 282(47), 34500–34509. https://doi.org/10.1074/jbc.M703679200