RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: S9
Target: Recombinant truncated human hepatitis B virus (HBV) P protein (miniP)
Type of nucleic acid: ssRNA
Sequence: 5'UGUUCAUGUCCUACUGUUCAAACAAAAAAACUGUGCACAAAAAUAAAUUGGGGCAUGGACA3'
Sequence length: 61
GC content: 0.360655737704918
Affinity: Not reported
Pool type: 5'-UGUUCAUGUCCUACUGUUC-N11-CUGUGC-N12-UGGGGCAUGGACA-3'
Pool random region: 23
Binding buffer/conditions: 0.1 M sodium phosphate, pH 7.4, 150 mM NaCl, 20 mM imidazol, 0.1% (v/v) NP-40, 100 mg/ml yeast tRNA
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 102 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " This study demonstrates the first successful identification of human HBV ε aptamers by an in vitro SELEX approach. Effective suppression of HBV replication by the S9 aptamer provides proof-of-principle for the ability of ε decoy RNAs to interfere with viral P-ε complex formation and suggests that S9-like RNAs may further be developed into useful therapeutics against chronic hepatitis B."
Additional information: Figure 2 pool and the reported pool in main body slightly are different: main body pool (5′-GGTACCTGTCCATGCCCCA-N12-GCACAG-N11-GAACAGTAGGACATGAACAGCCCTATAGTGAGTCGTATTAattc-3)
Reference (2011, PLoS One ): Feng, H., Beck, J., Nassal, M., & Hu, K. H. (2011). A SELEX-screened aptamer of human hepatitis B virus RNA encapsidation signal suppresses viral replication. PloS one, 6(11), e27862. https://doi.org/10.1371/journal.pone.0027862
Aptamer: S6
Target: Recombinant truncated human hepatitis B virus (HBV) P protein (miniP)
Type of nucleic acid: ssRNA
Sequence: 5'UGUUCAUGUCCUACUGUUCACAGAAAAUAGCUGUGCAAAAAAAAAAGAUGGGGCAUGGACA3'
Sequence length: 61
GC content: 0.3934426229508196
Affinity: Not reported
Pool type: 5'-UGUUCAUGUCCUACUGUUC-N11-CUGUGC-N12-UGGGGCAUGGACA-3'
Pool random region: 23
Binding buffer/conditions: 0.1 M sodium phosphate, pH 7.4, 150 mM NaCl, 20 mM imidazol, 0.1% (v/v) NP-40, 100 mg/ml yeast tRNA
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 102 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " This study demonstrates the first successful identification of human HBV ε aptamers by an in vitro SELEX approach. Effective suppression of HBV replication by the S9 aptamer provides proof-of-principle for the ability of ε decoy RNAs to interfere with viral P-ε complex formation and suggests that S9-like RNAs may further be developed into useful therapeutics against chronic hepatitis B."
Reference (2011, PLoS One ): Feng, H., Beck, J., Nassal, M., & Hu, K. H. (2011). A SELEX-screened aptamer of human hepatitis B virus RNA encapsidation signal suppresses viral replication. PloS one, 6(11), e27862. https://doi.org/10.1371/journal.pone.0027862
Aptamer: S18
Target: Acetamiprid
Type of nucleic acid: ssDNA
Sequence: 5'CCTGCCACGCTCCGCAAGCTTTGTAATTTGTCTGCAGCGGTTCTTGATCGCTGACACCATATTATGAAGATAAGCTTGGCACCCGCATCGT3'
Sequence length: 91
GC content: 0.5054945054945055
Affinity: Kd: 4.98 μM
Pool type: 5'-CCTGCCACGCTCCGCAAGCTT-N10-CTGCAGCGATTCTTGATCG-N20-TAAGCTTGGCACCCGCATCGT-3'
Pool random region: 30
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: Detection: " Aptamers have a great potential as analytical tools for pesticide detection. In this work, aptamers targeting acetamiprid were selected by a specific systematic evolution of ligands by exponential enrichment (SELEX) strategy. Further work is ongoing to develop an aptamer-based detection method for field determination of this pesticides in agricultural products and environmental samples."
Additional information: polymerase chain reaction (PCR) amplifications were realized with a biotin-5′-labeled primer P-2 (P-2-B) and a FAM-5′-labeled primer P-3 (F-P-3).
Reference (2011, J Agric Food Chem ): He, J., Liu, Y., Fan, M., & Liu, X. (2011). Isolation and identification of the DNA aptamer target to acetamiprid. Journal of agricultural and food chemistry, 59(5), 1582-1586.https://doi.org/10.1021/jf104189g
Aptamer: 19
Target: Enterotoxigenic Escherichia coli (E. coli) (ETEC) K88 fimbriae protein
Type of nucleic acid: ssDNA
Sequence: 5′CGTACGGTCGACGCTAGCGGCGACCCCCGGGCTACCAGACAATGTACGCAGCAAGAGTGACGGTCGTACCTCGGAGTCCACGTGGAGCTCGGATCC3′
Sequence length: 96
GC content: 0.6458333333333334
Affinity: Kd: 44 ± 7 nM
Pool type: 5′-CGTACGGTCGACGCTAGC-N60-CACGTGGAGCTCGGATCC-3′
Pool random region: 60
Binding buffer/conditions: (SHCMK) containing 20 mmol/L HEPES (N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid), pH 7.35; 1 mmol/L MgCl2; 1 mmol/L CaCl2; and 120 mmol/L KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this study, the first group of single-stranded DNA aptamers that are highly specific to enterotoxigenic Escherichia coli (ETEC) K88 was obtained from an enriched oligonucleotide pool by the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure. Since ETEC K88 is the only type of bacterium that expressed abundant K88 fimbriae, the selected aptamers against the K88 fimbriae protein were able to specifically identify ETEC K88 among other bacteria. This method of detecting ETEC K88 by aptamers can also be applied to bacteria other than ETEC K88."
Reference (2011, Can J Microbiol ): Li, H., Ding, X., Peng, Z., Deng, L., Wang, D., Chen, H., & He, Q. (2011). Aptamer selection for the detection of Escherichia coli K88. Canadian journal of microbiology, 57(6), 453–459. https://doi.org/10.1139/w11-030
Aptamer: 31
Target: Enterotoxigenic Escherichia coli (E. coli) (ETEC) K88 fimbriae protein
Type of nucleic acid: ssDNA
Sequence: 5′CGTACGGTCGACGCTAGCACACTCTTTTGCTCGTGTTTTTGCCTGTTACATAAAATGAATCAGTGGATGTTTCCTTCTCACGTGGAGCTCGGATCC3′
Sequence length: 96
GC content: 0.4791666666666667
Affinity: Kd: 36 ± 8 nM
Pool type: 5′-CGTACGGTCGACGCTAGC-N60-CACGTGGAGCTCGGATCC-3′
Pool random region: 60
Binding buffer/conditions: (SHCMK) containing 20 mmol/L HEPES (N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid), pH 7.35; 1 mmol/L MgCl2; 1 mmol/L CaCl2; and 120 mmol/L KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this study, the first group of single-stranded DNA aptamers that are highly specific to enterotoxigenic Escherichia coli (ETEC) K88 was obtained from an enriched oligonucleotide pool by the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure. Since ETEC K88 is the only type of bacterium that expressed abundant K88 fimbriae, the selected aptamers against the K88 fimbriae protein were able to specifically identify ETEC K88 among other bacteria. This method of detecting ETEC K88 by aptamers can also be applied to bacteria other than ETEC K88."
Reference (2011, Can J Microbiol ): Li, H., Ding, X., Peng, Z., Deng, L., Wang, D., Chen, H., & He, Q. (2011). Aptamer selection for the detection of Escherichia coli K88. Canadian journal of microbiology, 57(6), 453–459. https://doi.org/10.1139/w11-030
Aptamer: 7
Target: Enterotoxigenic Escherichia coli (E. coli) (ETEC) K88 fimbriae protein
Type of nucleic acid: ssDNA
Sequence: 5′CGTACGGTCGACGCTAGCGGCGGCCGTGAAATTTGCCAAATGCCGTCTTGGCTTTCGCCCAATGTATCCTGGGTGTTCCACGTGGAGCTCGGATCC3′
Sequence length: 96
GC content: 0.59375
Affinity: Kd: 43 ± 6 nM
Pool type: 5′-CGTACGGTCGACGCTAGC-N60-CACGTGGAGCTCGGATCC-3′
Pool random region: 60
Binding buffer/conditions: (SHCMK) containing 20 mmol/L HEPES (N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid), pH 7.35; 1 mmol/L MgCl2; 1 mmol/L CaCl2; and 120 mmol/L KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this study, the first group of single-stranded DNA aptamers that are highly specific to enterotoxigenic Escherichia coli (ETEC) K88 was obtained from an enriched oligonucleotide pool by the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure. Since ETEC K88 is the only type of bacterium that expressed abundant K88 fimbriae, the selected aptamers against the K88 fimbriae protein were able to specifically identify ETEC K88 among other bacteria. This method of detecting ETEC K88 by aptamers can also be applied to bacteria other than ETEC K88."
Reference (2011, Can J Microbiol ): Li, H., Ding, X., Peng, Z., Deng, L., Wang, D., Chen, H., & He, Q. (2011). Aptamer selection for the detection of Escherichia coli K88. Canadian journal of microbiology, 57(6), 453–459. https://doi.org/10.1139/w11-030
Aptamer: 37
Target: Enterotoxigenic Escherichia coli (E. coli) (ETEC) K88 fimbriae protein
Type of nucleic acid: ssDNA
Sequence: 5′CGTACGGTCGACGCTAGCGGAGACCGTACCATCTGTTCGTGGAAGCGCTTTGCTCGTCCATTAGCCTTGTGCTCGTGCCACGTGGAGCTCGGATCC3′
Sequence length: 96
GC content: 0.6041666666666666
Affinity: Kd: 25 ± 4 nM
Pool type: 5′-CGTACGGTCGACGCTAGC-N60-CACGTGGAGCTCGGATCC-3′
Pool random region: 60
Binding buffer/conditions: (SHCMK) containing 20 mmol/L HEPES (N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid), pH 7.35; 1 mmol/L MgCl2; 1 mmol/L CaCl2; and 120 mmol/L KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.35
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "In this study, the first group of single-stranded DNA aptamers that are highly specific to enterotoxigenic Escherichia coli (ETEC) K88 was obtained from an enriched oligonucleotide pool by the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure. Since ETEC K88 is the only type of bacterium that expressed abundant K88 fimbriae, the selected aptamers against the K88 fimbriae protein were able to specifically identify ETEC K88 among other bacteria. This method of detecting ETEC K88 by aptamers can also be applied to bacteria other than ETEC K88."
Reference (2011, Can J Microbiol ): Li, H., Ding, X., Peng, Z., Deng, L., Wang, D., Chen, H., & He, Q. (2011). Aptamer selection for the detection of Escherichia coli K88. Canadian journal of microbiology, 57(6), 453–459. https://doi.org/10.1139/w11-030
Aptamer: A3P
Target: Vibrio parahaemolyticus (V. parahaemolyticus)
Type of nucleic acid: ssDNA
Sequence: 5'ATAGGAGTCACGACGACCAGAATCTAAAAATGGGCAAAGAAACAGTGACTCGTTGAGATACTTATGTGCGTCTACCTCTTGACTAAT3′
Sequence length: 87
GC content: 0.4137931034482758
Affinity: Kd: 16.88 ± 1.92 nM
Pool type: 5′-ATAGGAGTCACGACGACCAGAA-N40-TATGTGCGTCTACCTCTTGACTAAT-3′
Pool random region: 40
Binding buffer/conditions: 1× BB, 50 mM Tris-HCl (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: Detection: " In this study, whole-bacterium SELEX was employed to identify DNA aptamer sequences specific to V. parahemolyticus that have the potential to be further developed into a rapid isolation/identification technology to facilitate the detection of V. parahemolyticus in food and environmental samples. Whole-bacterium SELEX is [also] a promising technique for the design of aptamer-based molecular probes for microbial pathogens that does not require the labor-intensive steps of isolating and purifying complex markers or targets."
Reference (2012, J Agric Food Chem ): Duan N, Wu S, Chen X, Huang Y, Wang Z. Selection and identification of a DNA aptamer targeted to Vibrio parahemolyticus. J Agric Food Chem. 2012 Apr 25;60(16):4034-8. doi: 10.1021/jf300395z. Epub 2012 Apr 13. PMID: 22480209.
Aptamer: AraHH001
Target: Primary cultured Mouse tumor endothelial cells (mTECs)
Type of nucleic acid: ssDNA
Sequence: 5'CGTAGAATTCATGAGGACGTTACGTACCGACTTCGTATGCCAACAGCCCTTTATCCACCTCAGCTAAGCTTACCAGTGCGAT3'
Sequence length: 82
GC content: 0.4878048780487805
Affinity: Kd: 43.8±13.7 nM
Pool type: 5′-CGTAGAATTCATGAGGACGTT-N40-AGCTAAGCTTACCAGTGCGAT-3′
Pool random region: 40
Binding buffer/conditions: 50 mM Tris-HCl (pH 7.5), 5 mM KCl, 100 mM NaCl, 1 mM MgCl2, 250 mM sucrose and 0.1% sodium azide
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic and Drug Delivery: "The present study used a spontaneous cell-based SELEX method (Systemic Evolution of Ligands by EXponential Enrichment) to produce DNA aptamers that specifically bind to cell surface proteins or biomarkers produced by primary cultured mouse tumor endothelial cells (mTECs). The development of a specific DNA aptamer that binds to mTECs, as reported here for the first time, holds great promise not only as a therapeutic aptamer but also as a targeted molecular probe that appears to play a major role in angiogenesis, and for the development of a targeted new drug delivery system."
Additional information: Cell-based SELEX, a modification of the usual SELEX technique using live cells
Reference (2012, PLoS One ): Ara, M. N., Hyodo, M., Ohga, N., Hida, K., & Harashima, H. (2012). Development of a novel DNA aptamer ligand targeting to primary cultured tumor endothelial cells by a cell-based SELEX method. PloS one, 7(12), e50174. https://doi.org/10.1371/journal.pone.0050174
Aptamer: AraHH009
Target: Mouse tumor endothelial cells (mTEC)
Type of nucleic acid: ssDNA
Sequence: 5′CGTAGAATTCATGAGGACGTTCGGGTATGGGGTGGTGCTATGTGTATATGAGCTAAGCTTACCAGTGCGAT3′
Sequence length: 71
GC content: 0.4788732394366197
Affinity: Not reported
Pool type: 5′-CGTAGAATTCATGAGGACGTT-N40-AGCTAAGCTTACCAGTGCGAT-3′
Pool random region: 40
Binding buffer/conditions: 50 mM Tris-HCl (pH 7.5), 5 mM KCl, 100 mM NaCl, 1 mM MgCl2, 250 mM sucrose and 0.1% sodium azide.
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic and Drug Delivery: "The present study used a spontaneous cell-based SELEX method (Systemic Evolution of Ligands by EXponential Enrichment) to produce DNA aptamers that specifically bind to cell surface proteins or biomarkers produced by primary cultured mouse tumor endothelial cells (mTECs). The development of a specific DNA aptamer that binds to mTECs, as reported here for the first time, holds great promise not only as a therapeutic aptamer but also as a targeted molecular probe that appears to play a major role in angiogenesis, and for the development of a targeted new drug delivery system."
Reference (2012, PLoS One ): Ara, M. N., Hyodo, M., Ohga, N., Hida, K., & Harashima, H. (2012). Development of a novel DNA aptamer ligand targeting to primary cultured tumor endothelial cells by a cell-based SELEX method. PloS one, 7(12), e50174. https://doi.org/10.1371/journal.pone.0050174
Aptamer: C14B
Target: Anterior gradient homolog 2 (AGR2)
Type of nucleic acid: ssDNA
Sequence: 5′TCTCGGACGCGTGTGGTCGGCGACGCACCGATCGCAGGTTCGGGATTTTCGGGTGGGAGTTGTGGGGGGGGGTGGGAGGGTTCTCGCTGCCTGGCCCTAGAGTG3′
Sequence length: 104
GC content: 0.6730769230769231
Affinity: Kd: 13.1 ± 67.2 nM
Pool type: 5′-TCTCGGACGCGTGTGGTCGG-N45-CTCGCTGCCTGGCCCTAGAGTG-3′
Pool random region: 45
Binding buffer/conditions: 200 µL, 1×PBS buffer containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4 and 2.0 mM KH2PO4, 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: Diagnostic: " Clinical studies have shown that the AGR2 protein is overexpressed in a wide range of human cancers, including carcinomas of the esophagus, pancreas, breast, prostate, and lung, making the protein as a potential cancer biomarke. We have developed new aptamer probes for specific recognition of the AGR2. This aptamer probe has great potential to serve as a useful tool for early diagnosis and prognosis of cancer and for fundamental research to elucidate the biochemical functions of AGR2."
Reference (2012, PLoS One ): Wu, J., Wang, C., Li, X., Song, Y., Wang, W., Li, C., Hu, J., Zhu, Z., Li, J., Zhang, W., Lu, Z., & Yang, C. J. (2012). Identification, characterization and application of a G-quadruplex structured DNA aptamer against cancer biomarker protein anterior gradient homolog 2. PloS one, 7(9), e46393. https://doi.org/10.1371/journal.pone.0046393
Aptamer: C14B1
Target: Anterior gradient homolog 2 (AGR2)
Type of nucleic acid: ssDNA
Sequence: 5'TCTCGGACGCGTGTGGTCGGCGGGTGGGAGTTGTGGGGGGGGGTGGGAGGGTTCTCGCTGCCTGGCCCTAGAGTG3'
Sequence length: 75
GC content: 0.7066666666666667
Affinity: Kd: 19.1 ± 5.1 nM
Pool type: 5′-TCTCGGACGCGTGTGGTCGG-N45-CTCGCTGCCTGGCCCTAGAGTG-3′
Pool random region: 45
Binding buffer/conditions: 200 µL, 1×PBS buffer containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4 and 2.0 mM KH2PO4, 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: Diagnostic: " Clinical studies have shown that the AGR2 protein is overexpressed in a wide range of human cancers, including carcinomas of the esophagus, pancreas, breast, prostate, and lung, making the protein as a potential cancer biomarke. We have developed new aptamer probes for specific recognition of the AGR2. This aptamer probe has great potential to serve as a useful tool for early diagnosis and prognosis of cancer and for fundamental research to elucidate the biochemical functions of AGR2."
Reference (2012, PLoS One ): Wu, J., Wang, C., Li, X., Song, Y., Wang, W., Li, C., Hu, J., Zhu, Z., Li, J., Zhang, W., Lu, Z., & Yang, C. J. (2012). Identification, characterization and application of a G-quadruplex structured DNA aptamer against cancer biomarker protein anterior gradient homolog 2. PloS one, 7(9), e46393. https://doi.org/10.1371/journal.pone.0046393
Aptamer: FKN-S2
Target: Fractalkine (FKN)
Type of nucleic acid: ssDNA
Sequence: 5'GTGCAGTCAAAGACGTCCGGGGTGGGTGGGGGGCACGTGTGGGGGCGGCCAGGGTGCTGACCATGAAGTGCGATTGCC3'
Sequence length: 78
GC content: 0.6794871794871795
Affinity: Kd: 3.4 ± 0.7 nM
Pool type: 5'-GTGCAGTCAAAGACGTCC-N40-GACCATGAAGTGCGATTGCC-3'
Pool random region: 40
Binding buffer/conditions: PBS with 0.5 μg/mL poly dA:dT and 50 μg/mL bovine serum albumin (BSA), 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: Drug Delivery: Fractalkine (FKN) is a unique cell surface protein with potential as a therapeutic target because of its role in inflammatory diseases and cancer. We developed an aptamer, named FKN-S2, with a dissociation constant of 3.4 ± 0.7 nM that is specific to the chemokine domain of fractalkine."
Reference (2012, Chem Commun (Camb) ): Waybrant, B., Pearce, T. R., Wang, P., Sreevatsan, S., & Kokkoli, E. (2012). Development and characterization of an aptamer binding ligand of fractalkine using domain targeted SELEX. Chemical communications (Cambridge, England), 48(80), 10043–10045. https://doi.org/10.1039/c2cc34217k
Aptamer: HA2b
Target: Recombinant HA protein from swine IAV H3 cluster IV
Type of nucleic acid: ssDNA
Sequence: 5'GTGCAGTCAAAGACGTCCTACTCCGTCACTTTAGTGGATATAACAACCTCCCTATGGGGGCAATCGCACTTCATGGTC3'
Sequence length: 78
GC content: 0.5
Affinity: Kd: 3.7 nM
Pool type: 5'GTGCAGTCAAAGACGTCC-N40-GGCAATCGCACTTCATGGTC'6
Pool random region: 40
Binding buffer/conditions: 500 μl of 50 mM NaH2PO4, 300 mM NaCl, and 20 mM imidazole (pH 8.0)
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: Detection: " Triple reassortant influenza A viruses (IAVs) of swine, particularly the North American H3N2 subtype, circulate in swine herds and may reassort and result in the emergence of novel zoonotic strains. Aptamer HA68 was also able to bind and detect H3N2v isolated from recent human cases. We provide subtype-specific aptamers against H3N2 IAVs of swine that can now be used in rapid detection and typing protocols for field applications."
Additional information: Selected aptamer sequences were synthesized and labeled with biotin (5′), while amplicons containing enriched aptamer pool were amplified by pcr with 5′-biotin-labeled forward primer (bio-wp18: biotingtgcagtcaaagacgtcc)
Reference (2012, J Clin Microbiol ): Wongphatcharachai, M., Wang, P., Enomoto, S., Webby, R. J., Gramer, M. R., Amonsin, A., & Sreevatsan, S. (2013). Neutralizing DNA aptamers against swine influenza H3N2 viruses. Journal of clinical microbiology, 51(1), 46–54. https://doi.org/10.1128/JCM.02118-12
Aptamer: Lep3
Target: Leptin protein, Human
Type of nucleic acid: ssDNA
Sequence: 5′CTTCTGCCCGCCTCCTTCCGTTAATGGGGGATCTCGCGGCCGTTCTTGTTGCTTATACAGGAGACGAGATAGGCGGACACT3′
Sequence length: 81
GC content: 0.5679012345679012
Affinity: Kd: 0.32 ± 0.50 μM via NECEEM, Kd: 1.50 ± 0.25 μM via Fluorescence intensity
Pool type: 5′-CTTCTGCCCGCCTCCTTCC-N40-GGAGACGAGATAGGCGGACACT-3′
Pool random region: 40
Binding buffer/conditions: (1× TGK) 25 mM Tris, 192 mM glycine, and 5 mM potassium phosphate (pH 8.3)
Buffer type: Tris Buffers
pH: 8.3
Molecular weight of target: 16 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " In this article, we demonstrate the use of CE–SELEX to select aptamer sequences with high nanomolar binding affinities in free solution against human leptin protein. An aptamer developed against human leptin will have applications in investigating leptin’s role as an inflammatory marker and as a therapeutic affinity probe."
Additional information: 5'-FAM: Fuorescent label modified primers (IDT)
Reference (2012, Anal Biochem ): Ashley J, Li SF. Three-dimensional selection of leptin aptamers using capillary electrophoresis and implications for clone validation. Anal Biochem. 2013;434(1):146-152. doi:10.1016/j.ab.2012.11.024
Aptamer: T9
Target: Rabies virus infected BHK-21 cells
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCAACCGATAACAAGTCTCGTTGTGTTTGCCGGGTGGGTTTTGTTGTTTGGACACGGTGGCTTAGT3'
Sequence length: 81
GC content: 0.5061728395061729
Affinity: Kd: 33 ± 1.2 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N45-TGGACACGGTGGCTTAGT-3'
Pool random region: 45
Binding buffer/conditions: 0.1 g/L yeast tRNA (Invitrogen, NY, USA), 4.5 g/L glucose, 1.0 g/L bovine serum albumin (Solarbio, Beijing, China), and 5 mmol/L MgCl2 in Dullbecco's PBS
Divalent salt: MgCl
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: " In this study, the cell surface-systematic evolution of ligands by exponential enrichment (Cell-SELEX) strategy was used to generate DNA aptamers which targeted to the intact rabies virus-infected live cells. These data show the feasibility of generating functionally effective aptamers against rabies virus-infected cells by the Cell-SELEX iterative procedure. These aptamers may prove clinically useful as therapeutic molecules with specific antiviral potential against RABV infections."
Reference (2012,Int Immunopharmacol): Liang, H. R., Hu, G. Q., Zhang, T., Yang, Y. J., Zhao, L. L., Qi, Y. L., Wang, H. L., Gao, Y. W., Yang, S. T., & Xia, X. Z. (2012). Isolation of ssDNA aptamers that inhibit rabies virus. International immunopharmacology, 14(3), 341–347. https://doi.org/10.1016/j.intimp.2012.06.019