RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: Apt-50
Target: Liver X receptors beta (LXRbeta, LXRβ)
Type of nucleic acid: ssDNA
Sequence: 5′ATGACCATGACCCTCCACACACCCTACGCGTGTCAGACTGTGGCAGGGAAAC3′
Sequence length: 52
GC content: 0.5769230769230769
Affinity: Kd: 1.11 pM
Pool type: 5′-ATGACCATGACCCTCCACAC-N12-TCAGACTGTGGCAGGGAAAC-3′
Pool random region: 12
Binding buffer/conditions: 21 mM Tris, 5 mM MgCl2, and 150 mM NaCl at pH 7.5
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: " Selection and use of small ssDNAs as alternative binders for HDL proteins. An essential function of HDL is linked with reverse cholesterol transport (RCT). Two sterol-responsive transcription factors, LXRa and LXRb, are directly involved in RCT. Crossreactivity studies show that the aptamer sequences, analyzed in this paper, would be more suitable as binders for LXRb"
Reference (2005, Biochem Biophys Res Commun ): Surugiu-Wärnmark, I., Wärnmark, A., Toresson, G., Gustafsson, J. A., & Bülow, L. (2005). Selection of DNA aptamers against rat liver X receptors. Biochemical and biophysical research communications, 332(2), 512–517. https://doi.org/10.1016/j.bbrc.2005.04.147
Aptamer: Apt- 11.4
Target: Ethanolamine
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTTGAGGCGGGTGGGTGGGTTGAATACGCTGATCACCCCATCGGAGAACGTTAAGGCGCTTTAGATAGTAAGTGCAATCT3′
Sequence length: 96
GC content: 0.46875
Affinity: Kd: 9 ± 5 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N60-AGATAGTAAGTGCAATCT-3′
Pool random region: 60
Binding buffer/conditions: 100 mmol L−1 NaCl/20 mmol L−1 Tris/HCl, pH 7.6/2 mmol L−1 MgCl2/5 mmol L−1 KCl/1 mmol L−1 CaCl2/0.02% Tween 20
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: Detection: " The aim of the development of ethanolamine aptamers is their use for the detection of this substance in clinical and environmental analysis. Ethanolamine is associated with several diseases. Moreover, ethanolamine and its derivatives di- and tri-ethanolamine are used in chemical and cosmetic industries. The use of biosensors with ethanolamine aptamer as new molecular recognition element could be an innovative method for an easy and fast detection of ethanolamine"
Reference (2005, Biochem Biophys Res Commun ): Mann, D., Reinemann, C., Stoltenburg, R., & Strehlitz, B. (2005). In vitro selection of DNA aptamers binding ethanolamine. Biochemical and biophysical research communications, 338(4), 1928–1934. https://doi.org/10.1016/j.bbrc.2005.10.172
Aptamer: I-26
Target: Streptavidin
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGATGCAGCCACCTACATTGCAGGTTTTATAATACAACTACGCGCCGTTCGCAGGCTAGTTAGATAGTAAGTGCAATCT3′
Sequence length: 96
GC content: 0.4166666666666667
Affinity: Kd: 85.2 ± 5.3 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N60-AGATAGTAAGTGCAATCT-3′
Pool random region: 60
Binding buffer/conditions: 100 mmol L−1 NaCl, 20 mmol L−1 Tris-HCl pH 7.6, 2 mmol L−1 MgCl2, 5 mmol L−1 KCl, 1 mmol L−1 CaCl2, 0.02% Tween 20)
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: Detection: " With FluMag-SELEX we have provided a methodological background for our objective of being able to select DNA aptamers for targets with very different properties and size. These aptamers will be applied as new biosensor receptors. In this work selection of streptavidin-specific aptamers by FluMag-SELEX is described. The streptavidin-specific aptamers will be used to check the surface occupancy of streptavidin-coated magnetic beads with biotinylated molecules after immobilization procedures."
Reference (2005, Anal Bioanal Chem ): Stoltenburg, R., Reinemann, C., & Strehlitz, B. (2005). FluMag-SELEX as an advantageous method for DNA aptamer selection. Analytical and bioanalytical chemistry, 383(1), 83–91. https://doi.org/10.1007/s00216-005-3388-9
Aptamer: II-31
Target: Streptavidin
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTCTATACTCCACTTTGCTATTTCTCGGTTCCTTCACGCGCCCATCGCAGGCTGATGAATTGAGATAGTAAGTGCAATCT3′
Sequence length: 96
GC content: 0.4270833333333333
Affinity: Kd: 56.7 ± 8.2 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N60-AGATAGTAAGTGCAATCT-3′
Pool random region: 60
Binding buffer/conditions: 100 mmol L−1 NaCl, 20 mmol L−1 Tris-HCl pH 7.6, 2 mmol L−1 MgCl2, 5 mmol L−1 KCl, 1 mmol L−1 CaCl2, 0.02% Tween 20
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: Detection: " With FluMag-SELEX we have provided a methodological background for our objective of being able to select DNA aptamers for targets with very different properties and size. These aptamers will be applied as new biosensor receptors. In this work selection of streptavidin-specific aptamers by FluMag-SELEX is described. The streptavidin-specific aptamers will be used to check the surface occupancy of streptavidin-coated magnetic beads with biotinylated molecules after immobilization procedures."
Reference (2005, Anal Bioanal Chem ): Stoltenburg, R., Reinemann, C., & Strehlitz, B. (2005). FluMag-SELEX as an advantageous method for DNA aptamer selection. Analytical and bioanalytical chemistry, 383(1), 83–91. https://doi.org/10.1007/s00216-005-3388-9
Aptamer: V-2
Target: Streptavidin
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTTCGCGTGATTTGGTCACAAATTGTATGATCCGGTGTCCTGCAAGTGTTGGTGTTCTCTCAAGATAGTAAGTGCAATCT3′
Sequence length: 96
GC content: 0.40625
Affinity: Not reported
Pool type: 5′-ATACCAGCTTATTCAATT-N60-AGATAGTAAGTGCAATCT-3′
Pool random region: 60
Binding buffer/conditions: 100 mmol L−1 NaCl, 20 mmol L−1 Tris-HCl pH 7.6, 2 mmol L−1 MgCl2, 5 mmol L−1 KCl, 1 mmol L−1 CaCl2, 0.02% Tween 20
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: Detection: " With FluMag-SELEX we have provided a methodological background for our objective of being able to select DNA aptamers for targets with very different properties and size. These aptamers will be applied as new biosensor receptors. In this work selection of streptavidin-specific aptamers by FluMag-SELEX is described. The streptavidin-specific aptamers will be used to check the surface occupancy of streptavidin-coated magnetic beads with biotinylated molecules after immobilization procedures."
Reference (2005, Anal Bioanal Chem ): Stoltenburg, R., Reinemann, C., & Strehlitz, B. (2005). FluMag-SELEX as an advantageous method for DNA aptamer selection. Analytical and bioanalytical chemistry, 383(1), 83–91. https://doi.org/10.1007/s00216-005-3388-9
Aptamer: Ab8
Target: Abrin toxin
Type of nucleic acid: ssDNA
Sequence: 5'CAGCTCAGAAGCTTGATCCTGTGCGGGCGGCAAGGCCCTGACAGAGATACTGGCTCGGGACTCGAAGTCGTGCATCTGCA3'
Sequence length: 80
GC content: 0.6
Affinity: Kd: 130 ± 54 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 MgCl4
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: 65 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " In this assay, three truncated aptamers against abrin toxin were chosen and evaluated, in which aptamer TA6 has been shown as the best signaling performance. The signaling aptamers with luminescence switching complexes were further proved to be a series of powerful reagents for aptamer-based target detection, even in a quite complicated biological matrix, such as diluted serum, and without further signal amplifications."
Reference (2006, 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: SSAP1-9
Target: Recombinant human (rhu) cellular prlon protein (Prpc)
Type of nucleic acid: ssDNA
Sequence: 5'TTTGGTCCTTGTCTTATGTCCAGAATGCGGCTACAGGCATTTCTCCTACTGGGATAGGTGGATTAT3'
Sequence length: 66
GC content: 0.4545454545454545
Affinity: Not reported
Pool type: 5'-TTTGGTCCTTGTCTTATGTCCAGAATGC-N40 -ATTTCTCCTACTGGGATAGGTGGATTAT-3'
Pool random region: 40
Binding buffer/conditions: 1% bovine serum albumin (BSA) in phosphate-buffered saline (PBS) containing 0.05% Tween-20 (PBST)
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: "The Prpcspecific aptamers seem to recognize a conformationand could be used in competitive or double-ligand assayformats to differentiateprion isoforms, aiding in the diagnostics of TSEs. The Prpc-specific aptamers could also be applied as therapeutic tools to deter the progression of TSEs, and some aptamers developed in these studies mayfind application in the future to the decontamination of blood, body fluids, foods, pharmaceuticals, and cosmetics in an automated fashion during manufacture."
Reference (2006, Exp Biol Med (Maywood) ): Takemura, K., Wang, P., Vorberg, I., Surewicz, W., Priola, S. A., Kanthasamy, A., Pottathil, R., Chen, S. G., & Sreevatsan, S. (2006). DNA aptamers that bind to PrP(C) and not PrP(Sc) show sequence and structure specificity. Experimental biology and medicine (Maywood, N.J.), 231(2), 204–214. https://doi.org/10.1177/153537020623100211
Aptamer: Ab5
Target: Abrin toxin, Abrus precatorius (A.precatorius)
Type of nucleic acid: ssDNA
Sequence: 5′CAGCTCAGAAGCTTGATCCTGTGAAGGGCTGATGAGGGGCGTAGCGGCTTGTTCGTAAGACTCGAAGTCGTGCATCTGCA3'
Sequence length: 80
GC content: 0.55
Affinity: Kd: 81 ± 26
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: Ab8
Target: Abrin toxin, Abrus precatorius (A.precatorius)
Type of nucleic acid: ssDNA
Sequence: 5′CAGCTCAGAAGCTTGATCCTGTGCGGGCGGCAAGGCCCTGACAGAGATACTGGCTCGGGACTCGAAGTCGTGCATCTGCA3'
Sequence length: 80
GC content: 0.6
Affinity: Kd: 130 ± 54
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: Clone 4-9
Target: Prion protein (PrP), Mouse
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGTCTATTCAATTGGGCCCTTTTCTGTGTCTTTCTGTGCCCTTAGATAGTATGTGCAATCA3′
Sequence length: 66
GC content: 0.4090909090909091
Affinity: Kd: 1.13 × 10−7 M
Pool type: 5′-ATACCAGTCTATTCAATT-30N-AGATAGTATGTGCAATCA-3′
Pool random region: 30
Binding buffer/conditions: 4% skim milk in PBS containing 0.5% Tween 20 (PBS-T) buffer
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: " Prion disease is a neurodegenerative disorder, in which the normal prion protein (PrP) changes structurally into an abnormal form and accumulates in the brain. The investigation by aptamer blotting and Western blotting showed that clone 4-9 was specifically able to recognize both alpha-PrP and beta-PrP. Moreover, it was indicated that clone 4-9 could recognize the flexible region of the N-terminal domain of PrP. These characteristics suggest that clone 4-9 might be a useful tool in prion-disease diagnosis and research."
Reference (2007, Prion ): Ogasawara, D., Hasegawa, H., Kaneko, K., Sode, K., & Ikebukuro, K. (2007). Screening of DNA aptamer against mouse prion protein by competitive selection. Prion, 1(4), 248–254. https://doi.org/10.4161/pri.1.4.5803
Aptamer: #9
Target: Advanced glycation end products (AGE), Human serum albumin
Type of nucleic acid: ssDNA
Sequence: 5′AGCTCAGAATGGATCCAAACGCTCATAACTCACTCCATACTCACTTGCTGATTCGCCAACAACACACCCTTAAACAGTCCCTTCGACATGAGAATTCGGCCGGATC3′
Sequence length: 106
GC content: 0.4811320754716981
Affinity: Kd: 1 μM
Pool type: 5′-AGCTCAGAATGGATCCAAACGCTCA-N56-TTCGACATGAGAATTCGGCCGGATC-3′
Pool random region: 56
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: " We have previously shown that advanced glycation end products (AGE) not only inhibit DNA synthesis but also induce apoptosis in cultured retinal pericytes, thereby being involved in pericyte loss, the earliest histopathological hallmark of diabetic retinopathy. Among the selected aptamers, the clone 9 aptamer completely blocked the toxic effects of AGE, and its dissociation constant was 1 micromol/L. These results indicate that DNA aptamers are a useful tool for inhibiting the cytotoxic effects of AGE on cultured retinal pericytes. Our study suggests that blockade of the AGE effects by DNA aptamers may lead to a novel therapeutic strategy for the treatment of diabetic retinopathy."
Reference (2007, Microvasc Res ): Higashimoto, Y., Yamagishi, S., Nakamura, K., Matsui, T., Takeuchi, M., Noguchi, M., & Inoue, H. (2007). In vitro selection of DNA aptamers that block toxic effects of AGE on cultured retinal pericytes. Microvascular research, 74(1), 65–69. https://doi.org/10.1016/j.mvr.2007.04.001
Aptamer: 9-14
Target: Hepatitis C virus (HCV)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGCCGUUCGAACACGAGCAUGUUGUCUACGUUGUAGAAGCUGUUAUGGUAGGUACUUCCACGAGGUAUCAACGGAGUUGGUGGACAGUACUCAGGUCAUCCUAGG3'
Sequence length: 106
GC content: 0.5094339622641509
Affinity: Kd: 142 nM via format protein chip assay (Biacore)
Pool type: 5'-GGGCCGTTCGAACACGAGCATG-N60-GGACAGTACTCAGGTCATCCTAGG-3'
Pool random region: 60
Binding buffer/conditions: Binding Buffer for Binding Assay: 0.01 M Hepes, pH 7.4, 0.15 M NaCl, 3 mM EDTA, and 0.005% (v/v) surfactant P20
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Using the same sol–gel materials as those used for the protein chips [22], we immobilized the 2′-F modified (for protection of aptamers against RNases) aptamers (2′F-9-14 , 2′F-9-15, and 2′F-9-19) along with the core and NS5 proteins as diagnostic controls
Application as quoted in the referenced paper: Diagnostic: " The selected aptamers specifically bound to the core antigen, but not to another HCV antigen, NS5, in a protein chip-based assay. Using these aptamers, we developed an aptamer-based biosensor for HCV diagnosis and detected the core antigen from HCV infected patients’ sera with good specificity. This novel aptamer-based antigen detection sensor could be applied to the early diagnosis of HCV infection."
Additional information: Protein info: A fusion protein including the N-terminal amino acids 2–114 of the core antigen with the C-terminal His tag was bacterially expressed, and the resulting core(2-114)-His6 proteins were purified using Ni-NTA affinity chromatography
Reference (2007, Biochem Biophys Res Commun ): Lee, S., Kim, Y. S., Jo, M., Jin, M., Lee, D. K., & Kim, S. (2007). Chip-based detection of hepatitis C virus using RNA aptamers that specifically bind to HCV core antigen. Biochemical and biophysical research communications, 358(1), 47–52. https://doi.org/10.1016/j.bbrc.2007.04.057
Aptamer: AN58
Target: Recombinant GluR2Qflip AMPA receptor transiently expressed in HEK-293 (human embryonic kidney) cells
Type of nucleic acid: ssRNA
Sequence: 5'GGGCGAAUUCAACUGCCAUCUAGGCAGUAACCAGGAGUUAGUAGGACAAGUUUCGUCC3'
Sequence length: 58
GC content: 0.5
Affinity: Kd: 0.419 ± 0.221 nM & IC50: 121 ± 7 nM
Pool type: 5'-GGGCGAAUUCAACUGCCAUCUAGGC-N50-AGUACUACAAGCUUCUGGACUCGGU-3'
Pool random region: 50
Binding buffer/conditions: 150 NaCl, 3 KCl, 1 CaCl2, 1 MgCl2, 10 HEPES (pH 7.4)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: An1444 was reduced to a 58 nt long, functional aptamer (an58) (the original 99 nt an1444 was truncated from both 5‘ and 3‘ directions)
Application as quoted in the referenced paper: Therapeutic: " The excessive activation of AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors, a subtype of glutamate ion channels, has been implicated in various neurological diseases such as cerebral ischemeia and amyotrophic lateral sclerosis. herefore, AN58 serves as a unique lead compound for developing water-soluble inhibitors with a nanomolar affinity for GluR2 AMPA receptors."
Reference (2007, Biochemistry ): Huang, Z., Pei, W., Jayaseelan, S., Shi, H., & Niu, L. (2007). RNA aptamers selected against the GluR2 glutamate receptor channel. Biochemistry, 46(44), 12648–12655. https://doi.org/10.1021/bi701036p
Aptamer: A38
Target: Vaccinia virus (VACV) as a model for orthopoxviruses (OPV)
Type of nucleic acid: ssDNA
Sequence: 5'TACGACTCACTATAGGGATCCTGTATATATTTTGCAACTAATTGAATTCCCTTTAGTGAGGGTT3'
Sequence length: 64
GC content: 0.359375
Affinity: IC50: 0.59 μM
Pool type: 5'-TACGACTCACTATAGGGATCC-N7-A-N7-A-N6-GAATTCCCTTTAGTGAGGGTT-3'
Pool random region: 20
Binding buffer/conditions: Binding Buffer not required for MonoLEX selection.
Buffer type: Other Buffers
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Biosensor: " The in vitro replication of several OPV could significantly be inhibited in the presence of A38 in a concentration-dependent manner, with IC50 values of 0.59 μM, a concentration that is in agreement with previously published aptamers specific for other viruses. Further studies have to evaluate the mechanism of inhibition and the potential to inhibit OPV replication in animal models."
Additional information: utilizled MonoLEX selection
Wash Buffer: Tris buffer (pH 7.3, 0.1% TWEEN-20), DMEM (0.1% TWEEN-20) and phosphate buffer (pH 7.5, 0.1% TWEEN-20)
Reference (2007, BMC Biotechnol ): Nitsche, A., Kurth, A., Dunkhorst, A., Pänke, O., Sielaff, H., Junge, W., Muth, D., Scheller, F., Stöcklein, W., Dahmen, C., Pauli, G., & Kage, A. (2007). One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX. BMC biotechnology, 7, 48. https://doi.org/10.1186/1472-6750-7-48
Aptamer: 1.12
Target: Ochratoxin A (OTA)
Type of nucleic acid: ssDNA
Sequence: 5'TGGTGGCTGTAGGTCAGCATCTGATCGGGTGTGGGTGGCGTAAAGGGAGCATCGGACAACG3'
Sequence length: 61
GC content: 0.5901639344262295
Affinity: Kd: 0.36
Pool type: 5'TGGTGGCTGTAGGTCA-N30-CGTTGTCCGATGCTC
Pool random region: 30
Binding buffer/conditions: Selection buffer (SB), composed of 10 mM HEPES, pH 7.0, 120 mM NaCl, 5 mM KCl, and 5 mM MgCl2; binding buffer (BB): (10 mM TRIS, pH 8.5,120 mM NaCl, 5 mM KCl, and 20 mM CaCl2)
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research and Detection: "This work describes the identification of an aptamer that binds with high affinity and specificity to ochratoxin A (OTA), a mycotoxin that occurs in wheat and other foodstuffs, and a quantitative detection method for OTA based on the use of this aptamer. Further work is ongoing to broaden the application demonstrated here with the development of sensors, affinity columns, and other analytical systems for field and laboratory determination of this toxin in food and agricultural products."
Additional information: The library was designed with 30 random nucleotides, flanked with two constant regions for primer annealing. The primers were as follows: reverse, Biotin_x0002_CGTTGTCCGATGCTC; and forward, Cy3-TGGTGGCTGTAGGTCA
Reference (2008, J Agric Food Chem ): Cruz-Aguado, J. A., & Penner, G. (2008). Determination of ochratoxin a with a DNA aptamer. Journal of agricultural and food chemistry, 56(22), 10456–10461. https://doi.org/10.1021/jf801957h
Aptamer: J
Target: Anti-neuroexcitation peptide III (ANEPIII)
Type of nucleic acid: ssDNA
Sequence: 5'TAATACGACTCACTATAGGGAATTCTATCCGGGTAAAGCTGACTACCTATCTACTGGTCTTCTGGGTCCCTGCTAGTAAGCTTGCCGT3'
Sequence length: 88
GC content: 0.4659090909090909
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