RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: M9-5
Target: Cyclophilin B (CypB)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAGGACGAUGCGGGGACCUAUGCAGUAGCCAGUGUGGACUGGGCUGCCCCCCCCAGACGACUCGCCCGA3'
Sequence length: 71
GC content: 0.6901408450704225
Affinity: Kd: 1.5 ± 0.02 nM
Pool type: 5'-GGGAGGACGAUGCGG-N40-CAGACGACUCGCCCGA-3'
Pool random region: 40
Binding buffer/conditions: 20 mM HEPES pH 7.5; 150 mM NaCl; 2 mM CaCl2 and 3 mM MgCl2
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: 50 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic " and Therapeutic: In order to identify biomarkers for pancreatic cancer, we devised an in vitro positive/negative selection strategy to identify RNA ligands (aptamers) that could detect structural differences between the secretomes of pancreatic cancer and non-cancerous cells. We suggest that the aptamer we identified has the potential to serve as a tool for the early detection of pancreatic cancer."
Reference (2012, J Clin Invest ): Ray P, Rialon-Guevara KL, Veras E, Sullenger BA, White RR. Comparing human pancreatic cell secretomes by in vitro aptamer selection identifies cyclophilin B as a candidate pancreatic cancer biomarker. J Clin Invest. 2012;122(5):1734-1741. doi:10.1172/JCI62385
Aptamer: Aptamer 14
Target: Human papillomavirus (HPV)-transformed HeLa cervical carcinoma cells
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGGGCGGGGAGTAGGGAGAGGGGTTTCCATCGGCGACAGAGGAGTTATGTGTGTAGATAGTAAGTGCAATCT3′
Sequence length: 89
GC content: 0.4831460674157303
Affinity: Kd: 7.1±0.4 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N52-AGATAGTAAGTGCAATCT-3′
Pool random region: 52
Binding buffer/conditions: 1% BSA in PBS with salts
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: Dectection: " Using AC-SELEX we have generated several aptamers that have high affinity and specificity to the nontumorigenic, revertant of HPV-transformed cervical cancer cells. These aptamers can be used to identify new biomarkers that are related to carcinogenesis. Panels of aptamers, such as these may be useful in predicting the tumorigenic potential and properties of cancer biopsies and aid in the effective management of pathological conditions (diagnosis, predicted outcome, and treatment options)."
Reference (2012, PLoS One ): Graham, J. C., & Zarbl, H. (2012). Use of cell-SELEX to generate DNA aptamers as molecular probes of HPV-associated cervical cancer cells. PloS one, 7(4), e36103. https://doi.org/10.1371/journal.pone.0036103
Aptamer: Aptamer 28
Target: Human papillomavirus (HPV)-transformed HeLa cervical carcinoma cells
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGGGGGACACGGAGGTGGTGGAAAGGCTAAGATTTGATGATGAGTAGTGTGGTAGATAGTAAGTGCAATCT3′
Sequence length: 88
GC content: 0.4318181818181818
Affinity: Kd: 6.9±0.2 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N52-AGATAGTAAGTGCAATCT-3′
Pool random region: 52
Binding buffer/conditions: 1% BSA in PBS with salts
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: Dectection: " Using AC-SELEX we have generated several aptamers that have high affinity and specificity to the nontumorigenic, revertant of HPV-transformed cervical cancer cells. These aptamers can be used to identify new biomarkers that are related to carcinogenesis. Panels of aptamers, such as these may be useful in predicting the tumorigenic potential and properties of cancer biopsies and aid in the effective management of pathological conditions (diagnosis, predicted outcome, and treatment options)."
Reference (2012, PLoS One ): Graham, J. C., & Zarbl, H. (2012). Use of cell-SELEX to generate DNA aptamers as molecular probes of HPV-associated cervical cancer cells. PloS one, 7(4), e36103. https://doi.org/10.1371/journal.pone.0036103
Aptamer: MA3
Target: MUC1 protein
Type of nucleic acid: ssDNA
Sequence: 5′AACCGCCCAAATCCCTAAGAGTCGGACTGCAACCTATGCTATCGTTGATGTCTGTCCAAGCAACACAGACACACTACACACGCACA3′
Sequence length: 86
GC content: 0.5
Affinity: Kd: 38.3 nM
Pool type: 5′-AACCGCCCAAATCCCTAAGAGTC-N40-CACAGACACACTACACACGCACA-3′
Pool random region: 40
Binding buffer/conditions: Hanks buffer with 0.1 mg/ml salmon sperm DNA and 1 mg/ml of BSA
Buffer type: Other Buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not appilcable
Application as quoted in the referenced paper: Therapeutic " and Drug Delivery: Targeted drug delivery may reduce the non-specific toxicity of chemotherapy by selectively directing anticancer drugs to tumor cells. MUC1 protein is an attractive target for tumor-specific drug delivery owning to its overexpression in most adenocarcinomas. The results suggest that the MUC1 aptamer may have potential utility as a targeting ligand for selective delivery of cytotoxic agent to MUC1-expressing tumors."
Reference (2012, PLoS One ): Hu, Y., Duan, J., Zhan, Q., Wang, F., Lu, X., & Yang, X. D. (2012). Novel MUC1 aptamer selectively delivers cytotoxic agent to cancer cells in vitro. PloS one, 7(2), e31970. https://doi.org/10.1371/journal.pone.0031970
Aptamer: OTC3
Target: Oxytetracycline (OTC)
Type of nucleic acid: ssDNA
Sequence: 5′CGTACGGAATTCGCTAGCCGACGCACAGTCGCTGGTGCGTACCTGGTTGCCGTTGTGTGGATCCGAGCTCCACGTG3′
Sequence length: 76
GC content: 0.618421052631579
Affinity: Kd: 4.7 nM
Pool type: 5′-CGTACGGAATTCGCTAGC-N40-GGATCCGAGCTCCACGTG-3′
Pool random region: 40
Binding buffer/conditions: 20 mM Tris–HCl, 50 mM NaCl, 5 mM KCl, 1 mM MgCl2, pH 7.2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: "Oxytetracycline (OTC) is a common antibacterial agent used for the control of animal diseases. OTC abuse can seriously affect human health; therefore, we developed a biosensor using single-stranded DNA (ssDNA) aptamers for the detection of OTC. This biosensor method with high sensitivity and specificity based on indirect competitive ELAA can be applied to OTC detection in food products on-site because of the simplicity of detection."
Reference (2013, Biosens Bioelectron ): Kim, C. H., Lee, L. P., Min, J. R., Lim, M. W., & Jeong, S. H. (2014). An indirect competitive assay-based aptasensor for detection of oxytetracycline in milk. Biosensors & bioelectronics, 51, 426–430. https://doi.org/10.1016/j.bios.2013.08.003
Aptamer: NS1 aptamer
Target: Influenza virus non-structural protein 1 (NS1) protein
Type of nucleic acid: ssDNA
Sequence: 5'GCAATGGTACGGTACTTCCGCGGTCCGGGGTGGGTGGGTGGTGGGGGGTGCGGGGGGGCGGCCGCAAAAGTGCACGCTACTTTGCTAA3'
Sequence length: 88
GC content: 0.6704545454545454
Affinity: Kd: 18.91 ± 3.95 nM
Pool type: 5'-GCAATGGTACGGTACTTCC-N45-CAAAAGTGCACGCTACTTTGCTAA-3'
Pool random region: 45
Binding buffer/conditions: 50 mM Tris/Cl (pH 8.0), 150 mM NaCl, 1.5 mM MgCl2, 2 mM DTT and 1% (w/v) BSA
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Blocking NS1 activity can be a potential strategy in the development of antiviral agents against IAV infection. In the present study, we selected a single-stranded DNA aptamer specific to the IAV NS1 protein. We also found that the selected aptamer was able to inhibit the viral replication without affecting cell viability. These results indicate that the selected ssDNA aptamer has strong potential to be further developed as a therapeutic agent against IAV."
Reference (2013, Antiviral Res ): Woo, H. M., Kim, K. S., Lee, J. M., Shim, H. S., Cho, S. J., Lee, W. K., Ko, H. W., Keum, Y. S., Kim, S. Y., Pathinayake, P., Kim, C. J., & Jeong, Y. J. (2013). Single-stranded DNA aptamer that specifically binds to the influenza virus NS1 protein suppresses interferon antagonism. Antiviral research, 100(2), 337–345. https://doi.org/10.1016/j.antiviral.2013.09.004
Aptamer: F2
Target: Saxitoxin (STX)
Type of nucleic acid: ssDNA
Sequence: 5'CATCTGCAGTGTGGCACCATGTCACCGGTTCGCGGTATGTGGTCGCAGGATGGTGTTCACGTGCTGAGCGTGAATTCGC3'
Sequence length: 79
GC content: 0.5822784810126582
Affinity: Not reported
Pool type: 5′-CATCTGCAGTGTGGCACCATG-N40-CGTGCTGAGCGTGAATTCGC-3′
Pool random region: 40
Binding buffer/conditions: 20 mM PB, pH 7.35, 120 mM KCl, 1 mM CaCl2, and 1 mM MgCl2
Divalent salt: MgCl/CaCl
pH: 7.35
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In this article, high-affinity single-stranded DNA (ssDNA) aptamer-targeting F(ab')₂ fragments of saxitoxin (STX) antibodies were selected from a random ssDNA library by the SELEX strategy. We successfully obtained an aptamer that mimics STX in antibody binding, and a substitute for STX in aptamer form has been developed. Further work is in progress aimed at using this aptamer substitute to replace the STX standard in an antibody-based, nontoxic detection method for field determination of STX in seafood products."
Reference (2013, J Agric Food Chem ): Hu, P., Liu, Z., Tian, R., Ren, H., Wang, X., Lin, C., Gong, S., Meng, X., Wang, G., Zhou, Y., & Lu, S. (2013). Selection and identification of a DNA aptamer that mimics saxitoxin in antibody binding. Journal of agricultural and food chemistry, 61(14), 3533–3541. https://doi.org/10.1021/jf400880r
Aptamer: F3
Target: Saxitoxin (STX)
Type of nucleic acid: ssDNA
Sequence: 5'CATCTGCAGTGTGGCACCATGGAATACGACATTGTTGGCTGTTCTTGGTTATGCGGTTTTTCGTGCTGAGCGTGAATTCGC3'
Sequence length: 81
GC content: 0.4938271604938271
Affinity: Kd: 96.37 nM
Pool type: 5′-CATCTGCAGTGTGGCACCATG-N40-CGTGCTGAGCGTGAATTCGC-3′
Pool random region: 40
Binding buffer/conditions: 20 mM PB, pH 7.35, 120 mM KCl, 1 mM CaCl2, and 1 mM MgCl2
Divalent salt: MgCl/CaCl
pH: 7.35
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In this article, high-affinity single-stranded DNA (ssDNA) aptamer-targeting F(ab')₂ fragments of saxitoxin (STX) antibodies were selected from a random ssDNA library by the SELEX strategy. We successfully obtained an aptamer that mimics STX in antibody binding, and a substitute for STX in aptamer form has been developed. Further work is in progress aimed at using this aptamer substitute to replace the STX standard in an antibody-based, nontoxic detection method for field determination of STX in seafood products."
Reference (2013, J Agric Food Chem ): Hu, P., Liu, Z., Tian, R., Ren, H., Wang, X., Lin, C., Gong, S., Meng, X., Wang, G., Zhou, Y., & Lu, S. (2013). Selection and identification of a DNA aptamer that mimics saxitoxin in antibody binding. Journal of agricultural and food chemistry, 61(14), 3533–3541. https://doi.org/10.1021/jf400880r
Aptamer: F19
Target: Saxitoxin (STX)
Type of nucleic acid: ssDNA
Sequence: 5'CATCTGCAGTGTGGCACCATGGCGGGAAAGGGTCCGGTTGTGATGTTGTTTCTGTTTTGGTCGTGCTGAGCGTGAATTCGC3'
Sequence length: 81
GC content: 0.5432098765432098
Affinity: Not reported
Pool type: 5′-CATCTGCAGTGTGGCACCATG-N40-CGTGCTGAGCGTGAATTCGC-3′
Pool random region: 40
Binding buffer/conditions: 20 mM PB, pH 7.35, 120 mM KCl, 1 mM CaCl2, and 1 mM MgCl2
Divalent salt: MgCl/CaCl
pH: 7.35
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In this article, high-affinity single-stranded DNA (ssDNA) aptamer-targeting F(ab')₂ fragments of saxitoxin (STX) antibodies were selected from a random ssDNA library by the SELEX strategy. We successfully obtained an aptamer that mimics STX in antibody binding, and a substitute for STX in aptamer form has been developed. Further work is in progress aimed at using this aptamer substitute to replace the STX standard in an antibody-based, nontoxic detection method for field determination of STX in seafood products."
Reference (2013, J Agric Food Chem ): Hu, P., Liu, Z., Tian, R., Ren, H., Wang, X., Lin, C., Gong, S., Meng, X., Wang, G., Zhou, Y., & Lu, S. (2013). Selection and identification of a DNA aptamer that mimics saxitoxin in antibody binding. Journal of agricultural and food chemistry, 61(14), 3533–3541. https://doi.org/10.1021/jf400880r
Aptamer: R3
Target: Prostate-specific antigen (PSA)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'AGCUCCAGAAGAUAAAUUACAGGUCCAGGCGCGUUAGCAAAACCGCGGAUCAAACUUAGUUGACAACUAGGAUACUAUGACCC3'
Sequence length: 83
GC content: 0.4578313253012048
Affinity: Kd: 8.7 nM
Pool type: 5′-AGCTCCAGAAGATAAATTACAGG–N53–CAACTAGGATACTATGACCCC-3′
Pool random region: 53
Binding buffer/conditions: PBS buffer containing 3 mM MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 33 kDa
Application as quoted in the referenced paper: Therapeutic and Detection: "Prostate-specific antigen (PSA) is considered to be the most sensitive marker available for prostate cancer detection and for monitoring of disease progression. The potential use of the selected aptamers in therapeutics was demonstrated with the 2'F-modified aptamers being highly stable in human serum and having the ability to moderate the activity of PSA, which will be explored for the treatment of prostate cancer."
Additional information: 2′F-modified RNA pool, 2'F-modified CTP and UTP
Reference (2013, Anal Bioanal Chem ): Svobodova, M., Bunka, D. H., Nadal, P., Stockley, P. G., & O'Sullivan, C. K. (2013). Selection of 2'F-modified RNA aptamers against prostate-specific antigen and their evaluation for diagnostic and therapeutic applications. Analytical and bioanalytical chemistry, 405(28), 9149–9157. https://doi.org/10.1007/s00216-013-7350-y
Aptamer: S2
Target: Prostate-specific antigen (PSA)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'AGCUCCAGAAGAUAAAUUACAGGUACGGUUCACGCCUGUCUCAUGCUGACUAAGAAAGUUUAGCAACUAGGAUACUAUGACCC3'
Sequence length: 83
GC content: 0.4337349397590361
Affinity: Kd: 6.3 nM
Pool type: 5′-AGCTCCAGAAGATAAATTACAGG–N53–CAACTAGGATACTATGACCCC-3′
Pool random region: 53
Binding buffer/conditions: PBS buffer containing 3 mM MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 33 kDa
Application as quoted in the referenced paper: Therapeutic and Detection: "Prostate-specific antigen (PSA) is considered to be the most sensitive marker available for prostate cancer detection and for monitoring of disease progression. The potential use of the selected aptamers in therapeutics was demonstrated with the 2'F-modified aptamers being highly stable in human serum and having the ability to moderate the activity of PSA, which will be explored for the treatment of prostate cancer."
Additional information: 2′F-modified RNA pool, 2'F-modified CTP and UTP
Reference (2013, Anal Bioanal Chem ): Svobodova, M., Bunka, D. H., Nadal, P., Stockley, P. G., & O'Sullivan, C. K. (2013). Selection of 2'F-modified RNA aptamers against prostate-specific antigen and their evaluation for diagnostic and therapeutic applications. Analytical and bioanalytical chemistry, 405(28), 9149–9157. https://doi.org/10.1007/s00216-013-7350-y
Aptamer: HA09
Target: Human-derived hepatoma cell line HepG2
Type of nucleic acid: ssDNA
Sequence: 5'ACGCTCGGATGCCACTACAGGACAGGGCACCACCATAGTACCTGTACTACCCAGCCGAGGCTCATGGACGTGCTGGTGAC3'
Sequence length: 80
GC content: 0.6
Affinity: Kd: 103.61 ± 35.05 nM
Pool type: 5′-ACGCTCGGATGCCACTACAG-N40-CTCATGGACGTGCTGGTGAC-3′
Pool random region: 40
Binding buffer/conditions: 0.2 mg/ml yeast tRNA and 2 mg/ml bovine serum albumin in washing buffer (4.5 g/l glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline (PBS))
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: "Hepatocellular carcinoma (HCC) is one of the most malignant cancers in the world. Molecular probes that can recognize biomarkers specific for HCC are urgently needed to improve the sensitivity and specificity of early diagnosis. Using human-derived hepatoma cell line HepG2 as positive target cell line and normal hepatocyte cell line HL-7702 as negative one, we obtained an aptamer HA09 that could specifically bind to human liver cancer cells. This aptamer may facilitate the discovery of novel biomarkers and serve as an ideal molecular probe for intracellular delivery with both diagnostic and therapeutic implications."
Reference (2013, Acta Biochim Biophys Sin (Shanghai) ): Lu, B., Wang, J., Zhang, J., Zhang, X., Yang, D., Wu, L., Luo, Z., Ma, Y., Zhang, Q., Ma, Y., Pei, X., Yu, H., & Liu, J. (2014). Screening and verification of ssDNA aptamers targeting human hepatocellular carcinoma. Acta biochimica et biophysica Sinica, 46(2), 128–135. https://doi.org/10.1093/abbs/gmt130
Aptamer: HA05
Target: Human-derived hepatoma cell line HepG3
Type of nucleic acid: ssDNA
Sequence: 5'ACGCTCGGATGCCACTACAGGCCCCAACTAGGTTAAAAGTATCACATTCGAGGTGCTATGCTCATGGACGTGCTGGTGAC3'
Sequence length: 80
GC content: 0.525
Affinity: Not reported
Pool type: 5′-ACGCTCGGATGCCACTACAG-N40-CTCATGGACGTGCTGGTGAC-3′
Pool random region: 40
Binding buffer/conditions: 0.2 mg/ml yeast tRNA and 2 mg/ml bovine serum albumin in washing buffer (4.5 g/l glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline (PBS))
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: " Hepatocellular carcinoma (HCC) is one of the most malignant cancers in the world. Molecular probes that can recognize biomarkers specific for HCC are urgently needed to improve the sensitivity and specificity of early diagnosis. Using human-derived hepatoma cell line HepG2 as positive target cell line and normal hepatocyte cell line HL-7702 as negative one, we obtained an aptamer HA09 that could specifically bind to human liver cancer cells. This aptamer may facilitate the discovery of novel biomarkers and serve as an ideal molecular probe for intracellular delivery with both diagnostic and therapeutic implications."
Reference (2013, Acta Biochim Biophys Sin (Shanghai) ): Lu, B., Wang, J., Zhang, J., Zhang, X., Yang, D., Wu, L., Luo, Z., Ma, Y., Zhang, Q., Ma, Y., Pei, X., Yu, H., & Liu, J. (2014). Screening and verification of ssDNA aptamers targeting human hepatocellular carcinoma. Acta biochimica et biophysica Sinica, 46(2), 128–135. https://doi.org/10.1093/abbs/gmt130
Aptamer: HA15
Target: Human-derived hepatoma cell line HepG4
Type of nucleic acid: ssDNA
Sequence: 5'ACGCTCGGATGCCACTACAGCTGGGCACCATGCAGGTTTGTCACGTTTATCGCGTAATGGCTCATGGACGTGCTGGTGAC3'
Sequence length: 80
GC content: 0.5625
Affinity: Not reported
Pool type: 5′-ACGCTCGGATGCCACTACAG-N40-CTCATGGACGTGCTGGTGAC-3′
Pool random region: 40
Binding buffer/conditions: 0.2 mg/ml yeast tRNA and 2 mg/ml bovine serum albumin in washing buffer (4.5 g/l glucose and 5 mM MgCl2 in Dulbecco's phosphate-buffered saline (PBS))
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: " Hepatocellular carcinoma (HCC) is one of the most malignant cancers in the world. Molecular probes that can recognize biomarkers specific for HCC are urgently needed to improve the sensitivity and specificity of early diagnosis. Using human-derived hepatoma cell line HepG2 as positive target cell line and normal hepatocyte cell line HL-7702 as negative one, we obtained an aptamer HA09 that could specifically bind to human liver cancer cells. This aptamer may facilitate the discovery of novel biomarkers and serve as an ideal molecular probe for intracellular delivery with both diagnostic and therapeutic implications."
Reference (2013, Acta Biochim Biophys Sin (Shanghai) ): Lu, B., Wang, J., Zhang, J., Zhang, X., Yang, D., Wu, L., Luo, Z., Ma, Y., Zhang, Q., Ma, Y., Pei, X., Yu, H., & Liu, J. (2014). Screening and verification of ssDNA aptamers targeting human hepatocellular carcinoma. Acta biochimica et biophysica Sinica, 46(2), 128–135. https://doi.org/10.1093/abbs/gmt130
Aptamer: 2′,4′-BNA/LNA (A#17)
Target: Thrombin, Human
Type of nucleic acid: 2',4'-BNA/LNA-DNA
Sequence: 5′TCGCCTTGCCGGATCGCAGACtCttAACAGGACAAGtGAAACAAACCCGCTGGTCCGTGAGCCTGACACC3′
Sequence length: 70
GC content: 0.5714285714285714
Affinity: Kd: 23nM
Pool type: 5′-TCGCCTTGCCGGATCGCAGA-N30-TGGTCCGTGAGCCTGACACC-3′
Pool random region: 30
Binding buffer/conditions: 20 mM Tris-HCl buffer (pH 7.40), MgCl2 (1 mM) and NaCl (10 mM)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic and Diagnostic: " Biostability is a critical property of medicinal and biological agents, and 2′,4′-BNA/LNA analogs are well known to have superior nuclease resistance than other types of sugar-modified nucleotides. Therefore, to create nucleic acid aptamers that are extremely stable under physiological conditions, attempts to use 2′,4′-BNA/LNA in SELEX experiments have been made."
Additional information: DNA library contained B/L thymidines (t's) instead of the natural thymidines in the non-primer region and 8 B/L nucleotides placed at intervals of two residues in the primer region. 2′,4′-BNA/LNA library was enzymatically prepared from 70-mer oligodeoxyribonucleotides (ODNs) comprising the variable region (30 bases) flanked by the forward and reverse primer regions (20 bases each) 2′,4′-BNA/LNA -->2'-O,4'-C-methylene bridged/locked nucleic acid
Reference (2013, Bioorg Med Chem Lett ): Kasahara, Y., Irisawa, Y., Ozaki, H., Obika, S., & Kuwahara, M. (2013). 2',4'-BNA/LNA aptamers: CE-SELEX using a DNA-based library of full-length 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides. Bioorganic & medicinal chemistry letters, 23(5), 1288–1292. https://doi.org/10.1016/j.bmcl.2012.12.093
Aptamer: 2′,4′-BNA/LNA (A#18)
Target: Thrombin, Human
Type of nucleic acid: 2',4'-BNA/LNA-DNA
Sequence: 5′TCGCCTTGCCGGATCGCAGACtCttGACAGGACtCAtGCACGGGGGGGCtTGGTCCGTGAGCCTGACACC3′
Sequence length: 70
GC content: 0.6428571428571429
Affinity: Kd: 27nM
Pool type: 5′-TCGCCTTGCCGGATCGCAGA-N30-TGGTCCGTGAGCCTGACACC-3′
Pool random region: 30
Binding buffer/conditions: 20 mM Tris-HCl buffer (pH 7.40), MgCl2 (1 mM) and NaCl (10 mM)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic and Diagnostic: " Biostability is a critical property of medicinal and biological agents, and 2′,4′-BNA/LNA analogs are well known to have superior nuclease resistance than other types of sugar-modified nucleotides. Therefore, to create nucleic acid aptamers that are extremely stable under physiological conditions, attempts to use 2′,4′-BNA/LNA in SELEX experiments have been made."
Additional information: DNA library contained B/L thymidines (t's) instead of the natural thymidines in the non-primer region and 8 B/L nucleotides placed at intervals of two residues in the primer region. 2′,4′-BNA/LNA library was enzymatically prepared from 70-mer oligodeoxyribonucleotides (ODNs) comprising the variable region (30 bases) flanked by the forward and reverse primer regions (20 bases each) 2′,4′-BNA/LNA -->2'-O,4'-C-methylene bridged/locked nucleic acid
Reference (2013, Bioorg Med Chem Lett ): Kasahara, Y., Irisawa, Y., Ozaki, H., Obika, S., & Kuwahara, M. (2013). 2',4'-BNA/LNA aptamers: CE-SELEX using a DNA-based library of full-length 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides. Bioorganic & medicinal chemistry letters, 23(5), 1288–1292. https://doi.org/10.1016/j.bmcl.2012.12.093