RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: B30
Target: Salmonella typhimurium (S. typhimurium)
Type of nucleic acid: ssDNA
Sequence: 5'AATCGCTGAATGAAATCCACGTGGGAAGTGTGTGGGTGACCAGAGGTGTGGTGATGGGATTGTCGTACCTCGCGAATCTGTCCTGGACTG3'
Sequence length: 90
GC content: 0.5333333333333333
Affinity: Kd: 51.02 nM
Pool type: 5'-AATCGCTGAATGAAATCCACGTG-N45-CCTCGCGAATCTGTCCTGGACTG-3'
Pool random region: 45
Binding buffer/conditions: 52 mM Tris-HCl, pH 7.5, 25 mM NaCl, 5 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: 5′-amino modification and a six carbon spacer. Then amino-modified aptamer was immobilized on the electrode surface for label-free detection of S. typhimurium.
Application as quoted in the referenced paper: Diagnostic and Detection: " In this study, quartz crystal microbalance (QCM) was used to select aptamers against Salmonella typhimurium. A QCM-based aptasensor was developed to detect S. typhimurium. This aptasensor was able to detect 103CFU/mL of S. typhimurium with less than 1h. This study demonstrated QCM-based selection could be more effective selection of aptamers and QCM-based aptasensor could be more sensitive in detecting S. typhimurium."
Reference (2016, Food Chem ): Wang, L., Wang, R., Chen, F., Jiang, T., Wang, H., Slavik, M., Wei, H., & Li, Y. (2017). QCM-based aptamer selection and detection of Salmonella typhimurium. Food chemistry, 221, 776–782. https://doi.org/10.1016/j.foodchem.2016.11.104
Aptamer: UCH37‐1
Target: Proteasome‐associated deubiquitylating enzyme UCH37
Type of nucleic acid: ssRNA
Sequence: 5′GGGUUCACUGCAGACUUGACGAAGCUUGGAGGGCAUGCUUCGGGCAAACCUGUAGGGGUGCGGCUCUAAUGGAUCCACAUCUACGAAUUC3′
Sequence length: 90
GC content: 0.5444444444444444
Affinity: Not reported
Pool type: 5'-GGGUUCACUGCAGACUUGACGAAGCUU-N40-AAUGGAUCCACAUCUACGAAUUC-3'
Pool random region: 40
Binding buffer/conditions: Tris⋅ HCl (30 mm , pH 7.5), NaCl (150 mm) , MgCl2 (1.5 mm) , DTT (2 mm) , and BSA (1 %, w /v )
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: " Deubiquitylating (DUB) enzymes antagonize ubiquitin-dependent protein degradation both before and after the substrates are engaged with proteasomes. Here, we report the identification of specific RNA aptamers for UCH37 through in vitro selection, and we describe their inhibitory effects on the DUB activity of UCH37. The UCH37 aptamers efficiently facilitated the hydrolysis of peptide-based reporter substrates of proteasomes. Thus, the UCH37 aptamers might offer a possible strategy for removing toxic cellular proteins through enhancing proteasome activity."
Reference (2016, Chembiochem ): Lee, J. H., & Lee, M. J. (2017). Isolation and Characterization of RNA Aptamers against a Proteasome-Associated Deubiquitylating Enzyme UCH37. Chembiochem : a European journal of chemical biology, 18(2), 171–175. https://doi.org/10.1002/cbic.201600515
Aptamer: Aptamer 2
Target: Rhesus (Rh) D antigen
Type of nucleic acid: ssDNA
Sequence: 5'AGAGACGGACACAGGATGAGCGGTGCAGGGGGGGCGGAGAAGAGGTTGAGGGGAGCGGGTCCTTCCCCAAGACAGCATCCA3'
Sequence length: 81
GC content: 0.6419753086419753
Affinity: Kd: 51.46 ±14.90 nM
Pool type: 5'-AGAGACGGACACAGGATGAGC-N40-CCTTCCCCAAGACAGCATCCA-3'
Pool random region: 40
Binding buffer/conditions: 20 mM HEPES, 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2 and 0.02% Tween 20, 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: Therapeutic: " Rhesus (Rh) D antigen is the most important antigen in the Rh blood group system because of its strong immunogenicity. Inhibition of the binding of anti-D antibody with RhD antigens on the surface of red blood cells may effectively prevent immune haemolytic diseases. In this study, single-stranded (ss) DNA aptamers, specifically binding to anti-D antibodies, were selected via systematic evolution of ligands by exponential enrichment (SELEX) technology. Our results demonstrate that ssDNA aptamers may be a novel, promising strategy for the treatment of delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn."
Reference (2016, Blood Transfus ): Zhang, Y., Wu, F., Wang, M., Zhuang, N., Zhou, H., & Xu, H. (2018). Single-stranded DNA aptamer targeting and neutralization of anti-D alloantibody: a potential therapeutic strategy for haemolytic diseases caused by Rhesus alloantibody. Blood transfusion = Trasfusione del sangue, 16(2), 184–192. https://doi.org/10.2450/2016.0123-16
Aptamer: Aptamer 8
Target: Rhesus (Rh) D antigen
Type of nucleic acid: ssDNA
Sequence: 5'AGAGACGGACACAGGATGAGCGCAGGGGGGGCGGAGAAGAGGTTGAGGGGAGCGGGTCCTTCCCCAAGACAGCATCCA3'
Sequence length: 78
GC content: 0.6410256410256411
Affinity: Kd: 403.70 ± 71.47 nM 
Pool type: 5'-AGAGACGGACACAGGATGAGC-N40-CCTTCCCCAAGACAGCATCCA-3'
Pool random region: 40
Binding buffer/conditions: 21 mM HEPES, 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2 and 0.02% Tween 20, 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: Therapeutic: " Rhesus (Rh) D antigen is the most important antigen in the Rh blood group system because of its strong immunogenicity. Inhibition of the binding of anti-D antibody with RhD antigens on the surface of red blood cells may effectively prevent immune haemolytic diseases. In this study, single-stranded (ss) DNA aptamers, specifically binding to anti-D antibodies, were selected via systematic evolution of ligands by exponential enrichment (SELEX) technology. Our results demonstrate that ssDNA aptamers may be a novel, promising strategy for the treatment of delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn."
Reference (2016, Blood Transfus ): Zhang, Y., Wu, F., Wang, M., Zhuang, N., Zhou, H., & Xu, H. (2018). Single-stranded DNA aptamer targeting and neutralization of anti-D alloantibody: a potential therapeutic strategy for haemolytic diseases caused by Rhesus alloantibody. Blood transfusion = Trasfusione del sangue, 16(2), 184–192. https://doi.org/10.2450/2016.0123-16
Aptamer: Aptamer 7
Target: Rhesus (Rh) D antigen
Type of nucleic acid: ssDNA
Sequence: 5'AGAGACGGACACAGGATGAGCGGCGCAGGGGGGGCGGAGAAGAGGTTGAGGGGAGCGGGTCCTTCCCCAAGACAGCATCCA3'
Sequence length: 81
GC content: 0.654320987654321
Affinity: Kd: 543.30 ± 92.59 nM
Pool type: 5'-AGAGACGGACACAGGATGAGC-N40-CCTTCCCCAAGACAGCATCCA-3'
Pool random region: 40
Binding buffer/conditions: 21 mM HEPES, 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2 and 0.02% Tween 20, 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: Therapeutic: " Rhesus (Rh) D antigen is the most important antigen in the Rh blood group system because of its strong immunogenicity. Inhibition of the binding of anti-D antibody with RhD antigens on the surface of red blood cells may effectively prevent immune haemolytic diseases. In this study, single-stranded (ss) DNA aptamers, specifically binding to anti-D antibodies, were selected via systematic evolution of ligands by exponential enrichment (SELEX) technology. Our results demonstrate that ssDNA aptamers may be a novel, promising strategy for the treatment of delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn."
Reference (2016, Blood Transfus ): Zhang, Y., Wu, F., Wang, M., Zhuang, N., Zhou, H., & Xu, H. (2018). Single-stranded DNA aptamer targeting and neutralization of anti-D alloantibody: a potential therapeutic strategy for haemolytic diseases caused by Rhesus alloantibody. Blood transfusion = Trasfusione del sangue, 16(2), 184–192. https://doi.org/10.2450/2016.0123-16
Aptamer: Aptamer 1
Target: Pancreatic cancer cell line HPAC (CRL2119, human pancreatic adenocarcinoma)
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATATCCGTTCGTACTCGCAAGCTGATCCGCGGCGCGACTTGTGACAATTAGGGTGTGTCGTCGTGGT3'
Sequence length: 84
GC content: 0.5714285714285714
Affinity: Kd: 22.62 ± 8.25 nM
Pool type: 5′‐AAGGAGCAGCGTGGAGGATA‐N45‐TTAGGGTGTGTCGTCGTGGT‐3′
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2, in Phosphate‐buffered saline (PBS) with yeast tRNA (0.1 mg/mL) and bovine serum albumin (BSA; 1 mg/mL)
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: " Pancreatic cancer remains one of the most common and lethal cancers. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). Here, we investigated pancreatic CSC-associated aptamers as a novel tool for diagnosis and therapeutic agents. In the present study, these 2 pancreatic CSC-associated aptamers may be potential candidates for novel diagnostic markers, CSC-targeting drug delivery, or circulating tumor cell detection."
Reference (2016, J Mol Recognit ): Kim, Y. J., Lee, H. S., Jung, D. E., Kim, J. M., & Song, S. Y. (2017). The DNA aptamer binds stemness-enriched cancer cells in pancreatic cancer. Journal of molecular recognition : JMR, 30(4), 10.1002/jmr.2591. https://doi.org/10.1002/jmr.2591
Aptamer: Aptamer 146
Target: Pancreatic cancer cell line HPAC (CRL2119, human pancreatic adenocarcinoma)
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATAACCACTAGTCTAAAAGACAGCCGTAGAGCCGGGACCGGTGCCACTTAGGGTGTGTCGTCGTGGT3'
Sequence length: 84
GC content: 0.5714285714285714
Affinity: Kd: 22.18 ± 9.6 nM
Pool type: 5′‐AAGGAGCAGCGTGGAGGATA‐N45‐TTAGGGTGTGTCGTCGTGGT‐3′
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2, in Phosphate‐buffered saline (PBS) with yeast tRNA (0.1 mg/mL) and bovine serum albumin (BSA; 1 mg/mL)
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: " Pancreatic cancer remains one of the most common and lethal cancers. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). Here, we investigated pancreatic CSC-associated aptamers as a novel tool for diagnosis and therapeutic agents. In the present study, these 2 pancreatic CSC-associated aptamers may be potential candidates for novel diagnostic markers, CSC-targeting drug delivery, or circulating tumor cell detection."
Reference (2016, J Mol Recognit ): Kim, Y. J., Lee, H. S., Jung, D. E., Kim, J. M., & Song, S. Y. (2017). The DNA aptamer binds stemness-enriched cancer cells in pancreatic cancer. Journal of molecular recognition : JMR, 30(4), 10.1002/jmr.2591. https://doi.org/10.1002/jmr.2591
Aptamer: Aptamer 25
Target: Pancreatic cancer cell line HPAC (CRL2119, human pancreatic adenocarcinoma)
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATAACCATTAGTTTAAAAGACAGCCGTAGAGCCGGGACCGGTGCCACTTAGGGTGTGTCGTCGTGGT3'
Sequence length: 84
GC content: 0.5476190476190477
Affinity: Kd: 65.79 ± 23.83
Pool type: 5′‐AAGGAGCAGCGTGGAGGATA‐N45‐TTAGGGTGTGTCGTCGTGGT‐3′
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2, in Phosphate‐buffered saline (PBS) with yeast tRNA (0.1 mg/mL) and bovine serum albumin (BSA; 1 mg/mL)
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: " Pancreatic cancer remains one of the most common and lethal cancers. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). Here, we investigated pancreatic CSC-associated aptamers as a novel tool for diagnosis and therapeutic agents. In the present study, these 2 pancreatic CSC-associated aptamers may be potential candidates for novel diagnostic markers, CSC-targeting drug delivery, or circulating tumor cell detection."
Reference (2016, J Mol Recognit ): Kim, Y. J., Lee, H. S., Jung, D. E., Kim, J. M., & Song, S. Y. (2017). The DNA aptamer binds stemness-enriched cancer cells in pancreatic cancer. Journal of molecular recognition : JMR, 30(4), 10.1002/jmr.2591. https://doi.org/10.1002/jmr.2591
Aptamer: Aptamer 40
Target: Pancreatic cancer cell line HPAC (CRL2119, human pancreatic adenocarcinoma)
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATAGCGCTCCCAACGGCCACATACCAGTACACGCGGGACCGCGGCCTGTTAGGGTGTGTCGTCGTGGT3'
Sequence length: 85
GC content: 0.6352941176470588
Affinity: Kd: 54.28 ± 36.47
Pool type: 5′‐AAGGAGCAGCGTGGAGGATA‐N45‐TTAGGGTGTGTCGTCGTGGT‐3′
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2, in Phosphate‐buffered saline (PBS) with yeast tRNA (0.1 mg/mL) and bovine serum albumin (BSA; 1 mg/mL)
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: " Pancreatic cancer remains one of the most common and lethal cancers. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). Here, we investigated pancreatic CSC-associated aptamers as a novel tool for diagnosis and therapeutic agents. In the present study, these 2 pancreatic CSC-associated aptamers may be potential candidates for novel diagnostic markers, CSC-targeting drug delivery, or circulating tumor cell detection."
Reference (2016, J Mol Recognit ): Kim, Y. J., Lee, H. S., Jung, D. E., Kim, J. M., & Song, S. Y. (2017). The DNA aptamer binds stemness-enriched cancer cells in pancreatic cancer. Journal of molecular recognition : JMR, 30(4), 10.1002/jmr.2591. https://doi.org/10.1002/jmr.2591
Aptamer: Aptamer 23
Target: Pancreatic cancer cell line HPAC (CRL2119, human pancreatic adenocarcinoma)
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATATCCATTAGTCTAAAACACAGCCTTAGAGCCGGGACCGGAGCCGCTTAGGGTGTGTCTGCTTGGT3'
Sequence length: 84
GC content: 0.5476190476190477
Affinity: Kd: 49.69 ± 24.98
Pool type: 5′‐AAGGAGCAGCGTGGAGGATA‐N45‐TTAGGGTGTGTCGTCGTGGT‐3′
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2, in Phosphate‐buffered saline (PBS) with yeast tRNA (0.1 mg/mL) and bovine serum albumin (BSA; 1 mg/mL)
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: " Pancreatic cancer remains one of the most common and lethal cancers. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). Here, we investigated pancreatic CSC-associated aptamers as a novel tool for diagnosis and therapeutic agents. In the present study, these 2 pancreatic CSC-associated aptamers may be potential candidates for novel diagnostic markers, CSC-targeting drug delivery, or circulating tumor cell detection."
Reference (2016, J Mol Recognit ): Kim, Y. J., Lee, H. S., Jung, D. E., Kim, J. M., & Song, S. Y. (2017). The DNA aptamer binds stemness-enriched cancer cells in pancreatic cancer. Journal of molecular recognition : JMR, 30(4), 10.1002/jmr.2591. https://doi.org/10.1002/jmr.2591
Aptamer: Aptamer 15
Target: Pancreatic cancer cell line HPAC (CRL2119, human pancreatic adenocarcinoma)
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATACCGATGCCAGACACAATTGTTATCCCGCGCATGCCACCATCCGTCTTAGGGTGTGTCGTCGTGGT3'
Sequence length: 85
GC content: 0.5647058823529412
Affinity: Kd: 45.18 ± 13.39
Pool type: 5′‐AAGGAGCAGCGTGGAGGATA‐N45‐TTAGGGTGTGTCGTCGTGGT‐3′
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2, in Phosphate‐buffered saline (PBS) with yeast tRNA (0.1 mg/mL) and bovine serum albumin (BSA; 1 mg/mL)
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: " Pancreatic cancer remains one of the most common and lethal cancers. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). Here, we investigated pancreatic CSC-associated aptamers as a novel tool for diagnosis and therapeutic agents. In the present study, these 2 pancreatic CSC-associated aptamers may be potential candidates for novel diagnostic markers, CSC-targeting drug delivery, or circulating tumor cell detection."
Reference (2016, J Mol Recognit ): Kim, Y. J., Lee, H. S., Jung, D. E., Kim, J. M., & Song, S. Y. (2017). The DNA aptamer binds stemness-enriched cancer cells in pancreatic cancer. Journal of molecular recognition : JMR, 30(4), 10.1002/jmr.2591. https://doi.org/10.1002/jmr.2591
Aptamer: Aptamer 108
Target: Pancreatic cancer cell line HPAC (CRL2119, human pancreatic adenocarcinoma)
Type of nucleic acid: ssDNA
Sequence: 5'AAGGAGCAGCGTGGAGGATAGGGGATAGCGGGTGTATATTTAAGCTTTACGGCTGTGTGGTCTGTTAGGGTGTGTCGTCGTGGT3'
Sequence length: 84
GC content: 0.5238095238095238
Affinity: Kd: 62.8 ± 31.84
Pool type: 5′‐AAGGAGCAGCGTGGAGGATA‐N45‐TTAGGGTGTGTCGTCGTGGT‐3′
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose and 5 mM MgCl2, in Phosphate‐buffered saline (PBS) with yeast tRNA (0.1 mg/mL) and bovine serum albumin (BSA; 1 mg/mL)
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: " Pancreatic cancer remains one of the most common and lethal cancers. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). Here, we investigated pancreatic CSC-associated aptamers as a novel tool for diagnosis and therapeutic agents. In the present study, these 2 pancreatic CSC-associated aptamers may be potential candidates for novel diagnostic markers, CSC-targeting drug delivery, or circulating tumor cell detection."
Reference (2016, J Mol Recognit ): Kim, Y. J., Lee, H. S., Jung, D. E., Kim, J. M., & Song, S. Y. (2017). The DNA aptamer binds stemness-enriched cancer cells in pancreatic cancer. Journal of molecular recognition : JMR, 30(4), 10.1002/jmr.2591. https://doi.org/10.1002/jmr.2591
Aptamer: P37
Target: Penicillin G
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGGACGAAGCGGAACTTAGTGCGCTTGAGGCTCGATCAGGAGATCTGGAGTCGTGGGCACTCACAACGATACGTGGTCAGAAGACACGCCCGAC3'
Sequence length: 97
GC content: 0.5876288659793815
Affinity: Not reported
Pool type: 5'-GGGAGGACGAAGCGGAAC-N10-TGAGGCTCGATC-N40-CAGAAGACACGCCCGACA-3'
Pool random region: 50
Binding buffer/conditions: Phosphate buffer 0.1 M pH 7 containing 5 mM of MgCl3
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diognostic: " This paper describes for the first time the selection of aptamers selective to penicillin. The selectivity of the developed sensor was also studied, showing that the sensor was also able to bind other beta-lactam antibiotics, although with a weaker affinity. Finally the sensor was used for detection of penicillin G in milk. It was shown that a simple sample treatment with isopropanol followed by filtration was sufficient to eliminate matrix effects, allowing the determination of penicillin in milk at concentrations compatible with legislation requirements."
Reference (2016, Talanta ): Paniel, N., Istamboulié, G., Triki, A., Lozano, C., Barthelmebs, L., & Noguer, T. (2017). Selection of DNA aptamers against penicillin G using Capture-SELEX for the development of an impedimetric sensor. Talanta, 162, 232–240. https://doi-org.ezproxy.lib.utexas.edu/10.1016/j.talanta.2016.09.058
Aptamer: AP1153
Target: G-protein-coupled cholecystokinin B receptor (CCKBR)
Type of nucleic acid: ssDNA
Sequence: 5'CGCTCTAGAGTCGAATCACATGGTGCAGGTGTGGCTGGGATTCATTTGCCGGTGCTGGTGCGTCCGCGGCCGCTAATCCTGTTCGCGGCCGCTAATCCTGTT3'
Sequence length: 102
GC content: 0.5980392156862745
Affinity: Kd: 0.0155 nM
Pool type: 5′-CGCTCTAGAGTCGAATCA-N45-GCGGCCGCTAATCCTGTT-3′
Pool random region: 45
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: " Pancreatic ductal adenocarcinomas (PDACs) constitutively express the G-protein-coupled cholecystokinin B receptor (CCKBR). In this study, we identified DNA aptamers (APs) that bind to the CCKBR and describe their characterization and targeting efficacy. Bioconjugation of AP1153 to the surface of fluorescent NPs greatly facilitated delivery of NPs to PDAC tumors in vivo. The selectivity of this AP-targeted NP delivery system holds promise for enhanced early detection of PDAC lesions as well as improved chemotherapeutic treatments for PDAC patients."
Additional information: SELEX binding conditions: cycle I of selection used 1 nmole library and 3 nmoles PA63 and 150 pmoles ssDNA and 800 pmoles PA63 for all other cycles. Incubated at 30 min at room temperature. Buffer not reported
Reference (2016, Nucleic Acid Ther ): Clawson, G. A., Abraham, T., Pan, W., Tang, X., Linton, S. S., McGovern, C. O., Loc, W. S., Smith, J. P., Butler, P. J., Kester, M., Adair, J. H., & Matters, G. L. (2017). A Cholecystokinin B Receptor-Specific DNA Aptamer for Targeting Pancreatic Ductal Adenocarcinoma. Nucleic acid therapeutics, 27(1), 23–35. https://doi.org/10.1089/nat.2016.0621
Aptamer: PA1T4PPZZ
Target: Protective antigen (PA) PA63
Type of nucleic acid: ssDNA
Sequence: 5'CGTGTPPACCATGGPGTGAGTGPGTAGGTGTZZTGAGGAGGT3'
Sequence length: 36
GC content: 0.5555555555555556
Affinity: Kd: 35 nM
Pool type: 5′-AGAGAGCGTCGTGTGGA-N25-TGAGGAGGTGCGCAAGT-3′
Pool random region: 25
Binding buffer/conditions: Assay Binding buffer: Phosphate-buffered saline (PBS)
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Replacing aegis p with standard nucleotides, individually replacing the p's by a in the optimally truncated aptamer. Replacing two adjacent g:c pairs in stem ii by two stronger p:z pairs (aptamer pa1t4ppzz).
Application as quoted in the referenced paper: Research and Therapeutic: " This experiment delivers the first example of an AEGIS aptamer that binds to an isolated protein target, the first whose structural contact with its target has been outlined and the first to inhibit biologically important activities of its target, the protective antigen from Bacillus anthracis. These results illustrate the value of AEGIS-LIVE for those seeking to obtain receptors and ligands without the complexities of medicinal chemistry, and also challenge the biophysical community to develop new tools to analyze the spectroscopic signatures of new DNA folds that will emerge in synthetic genetic systems replacing standard DNA and RNA as platforms for LIVE."
Reference (2016, Nucleic Acids Res ): Biondi, E., Lane, J. D., Das, D., Dasgupta, S., Piccirilli, J. A., Hoshika, S., Bradley, K. M., Krantz, B. A., & Benner, S. A. (2016). Laboratory evolution of artificially expanded DNA gives redesignable aptamers that target the toxic form of anthrax protective antigen. Nucleic acids research, 44(20), 9565–9577. https://doi.org/10.1093/nar/gkw890