RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: CD133-A15
Target: CD133-positive on cell line HT-29
Type of nucleic acid: ssRNA
Sequence: 5'CCCUCCUACAUAGGG'3
Sequence length: 15
GC content: 0.6
Affinity: Kd: 83.2 ± 82.9 nM
Pool type: 5′-GGAGACAAGAATAAACGCTCAA-N40-TTCGACAGGAGGCTCACAACAGGC-3' 
Pool random region: 40
Binding buffer/conditions: 100 μl Dulbecco's PBS (2.5 mM MgCl2)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.39999999999999
Molecular weight of target: Not reported
Post-SELEX modifications: Cd133-a aptamer was truncated to 15 nucleotides
Application as quoted in the referenced paper: Therapeutic: " The monoclonal antibody against the AC133 epitope of CD133 has been widely used as a cell surface marker of cancer stem cells in several different cancer types. Here, we describe the isolation and characterisation of two RNA aptamers, including the smallest described 15 nucleotide RNA aptamer, which specifically recognise the AC133 epitope and the CD133 protein with high sensitivity. These novel CD133 aptamers will aid future development of cancer stem cell targeted therapeutics and molecular imaging."
Reference (2013, Cancer Lett ): Shigdar, S., Qiao, L., Zhou, S. F., Xiang, D., Wang, T., Li, Y., Lim, L. Y., Kong, L., Li, L., & Duan, W. (2013). RNA aptamers targeting cancer stem cell marker CD133. Cancer letters, 330(1), 84–95. https://doi.org/10.1016/j.canlet.2012.11.032
Aptamer: CD133-A15
Target: CD133-positive on cell line Hep3B
Type of nucleic acid: ssRNA
Sequence: 5'CCCUCCUACAUAGGG'3
Sequence length: 15
GC content: 0.6
Affinity: Kd: 33.9 ± 12.5 nM
Pool type: 5′-GGAGACAAGAATAAACGCTCAA-N40-TTCGACAGGAGGCTCACAACAGGC-3' 
Pool random region: 40
Binding buffer/conditions: 100 μl Dulbecco's PBS (2.5 mM MgCl2)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.39999999999999
Molecular weight of target: Not reported
Post-SELEX modifications: Cd133-a aptamer was truncated to 15 nucleotides
Application as quoted in the referenced paper: Therapeutic: " The monoclonal antibody against the AC133 epitope of CD133 has been widely used as a cell surface marker of cancer stem cells in several different cancer types. Here, we describe the isolation and characterisation of two RNA aptamers, including the smallest described 15 nucleotide RNA aptamer, which specifically recognise the AC133 epitope and the CD133 protein with high sensitivity. These novel CD133 aptamers will aid future development of cancer stem cell targeted therapeutics and molecular imaging."
Reference (2013, Cancer Lett ): Shigdar, S., Qiao, L., Zhou, S. F., Xiang, D., Wang, T., Li, Y., Lim, L. Y., Kong, L., Li, L., & Duan, W. (2013). RNA aptamers targeting cancer stem cell marker CD133. Cancer letters, 330(1), 84–95. https://doi.org/10.1016/j.canlet.2012.11.032
Aptamer: CD133-B19
Target: CD133-positive on cell line HT-29
Type of nucleic acid: ssRNA
Sequence: 5′CAGAACGUAUACUAUUCUG3'
Sequence length: 19
GC content: 0.3684210526315789
Affinity: Kd: 145.1 ± 75.4
Pool type: 5′-GGAGACAAGAATAAACGCTCAA-N40-TTCGACAGGAGGCTCACAACAGGC-3' 
Pool random region: 40
Binding buffer/conditions: 100 μl Dulbecco's PBS (2.5 mM MgCl2)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.39999999999999
Molecular weight of target: Not reported
Post-SELEX modifications: Cd133-b aptamer was truncated to 19 nucleotides
Application as quoted in the referenced paper: Therapeutic: " The monoclonal antibody against the AC133 epitope of CD133 has been widely used as a cell surface marker of cancer stem cells in several different cancer types. Here, we describe the isolation and characterisation of two RNA aptamers, including the smallest described 15 nucleotide RNA aptamer, which specifically recognise the AC133 epitope and the CD133 protein with high sensitivity. These novel CD133 aptamers will aid future development of cancer stem cell targeted therapeutics and molecular imaging."
Reference (2013, Cancer Lett ): Shigdar, S., Qiao, L., Zhou, S. F., Xiang, D., Wang, T., Li, Y., Lim, L. Y., Kong, L., Li, L., & Duan, W. (2013). RNA aptamers targeting cancer stem cell marker CD133. Cancer letters, 330(1), 84–95. https://doi.org/10.1016/j.canlet.2012.11.032
Aptamer: CD133-B19
Target: CD133-positive on cell line Hep3B
Type of nucleic acid: ssRNA
Sequence: 5′CAGAACGUAUACUAUUCUG3'
Sequence length: 19
GC content: 0.3684210526315789
Affinity: Kd: 52.3 ± 15.8 nM
Pool type: 5′-GGAGACAAGAATAAACGCTCAA-N40-TTCGACAGGAGGCTCACAACAGGC-3' 
Pool random region: 40
Binding buffer/conditions: 100 μl Dulbecco's PBS (2.5 mM MgCl2)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.39999999999999
Molecular weight of target: Not reported
Post-SELEX modifications: Cd133-b aptamer was truncated to 19 nucleotides
Application as quoted in the referenced paper: Therapeutic: " The monoclonal antibody against the AC133 epitope of CD133 has been widely used as a cell surface marker of cancer stem cells in several different cancer types. Here, we describe the isolation and characterisation of two RNA aptamers, including the smallest described 15 nucleotide RNA aptamer, which specifically recognise the AC133 epitope and the CD133 protein with high sensitivity. These novel CD133 aptamers will aid future development of cancer stem cell targeted therapeutics and molecular imaging."
Reference (2013, Cancer Lett ): Shigdar, S., Qiao, L., Zhou, S. F., Xiang, D., Wang, T., Li, Y., Lim, L. Y., Kong, L., Li, L., & Duan, W. (2013). RNA aptamers targeting cancer stem cell marker CD133. Cancer letters, 330(1), 84–95. https://doi.org/10.1016/j.canlet.2012.11.032
Aptamer: C2
Target: CD30
Type of nucleic acid: ssDNA
Sequence: 5'TACCAGTGCGATGCTCAGACTGGGCGAAACAAGTCTATTGACTATGAGCCTGACGCATTCGGTTGAC3'
Sequence length: 67
GC content: 0.5074626865671642
Affinity: Not reported
Pool type: 5'-TACCAGTGCGATGCTCAG-N30-CTGACGCATTCGGTTGAC-3
Pool random region: 30
Binding buffer/conditions: 4.5 g/l glucose and 5 mM MgCl2 in Dulbecco's PBS (Sigma, St. Louis, MO). One mg/mL BSA (Fisher, Waltham, MA), 0.1 mg/mL t-RNA
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: " CD30 is highly expressed on Hodgkins lymphoma and anaplastic large cell lymphoma, making it an attractive target for therapy. We describe the generation of serum-stabilized ssDNA aptamers that bind CD30 via a hybrid SELEX methodology. Immunotherapy using aptamer-based co-stimulation provides an alternative to antibodies, and has potential to transform cancer treatment."
Reference (2013, Biomaterials ): Parekh, P., Kamble, S., Zhao, N., Zeng, Z., Portier, B. P., & Zu, Y. (2013). Immunotherapy of CD30-expressing lymphoma using a highly stable ssDNA aptamer. Biomaterials, 34(35), 8909–8917. https://doi.org/10.1016/j.biomaterials.2013.07.099
Aptamer: C2NP
Target: CD30
Type of nucleic acid: ssDNA
Sequence: 5'ACTGGGCGAAACAAGTCTATTGACTATGGC3'
Sequence length: 30
GC content: 0.4666666666666667
Affinity: Not reported
Pool type: 5'-TACCAGTGCGATGCTCAG-N30-CTGACGCATTCGGTTGAC-3
Pool random region: 30
Binding buffer/conditions: 4.5 g/l glucose and 5 mM MgCl2 in Dulbecco's PBS (Sigma, St. Louis, MO). One mg/mL BSA (Fisher, Waltham, MA), 0.1 mg/mL t-RNA
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated version of c2 aptamer
Application as quoted in the referenced paper: Diagnostic and Therapeutic: " CD30 is highly expressed on Hodgkins lymphoma and anaplastic large cell lymphoma, making it an attractive target for therapy. We describe the generation of serum-stabilized ssDNA aptamers that bind CD30 via a hybrid SELEX methodology. Immunotherapy using aptamer-based co-stimulation provides an alternative to antibodies, and has potential to transform cancer treatment."
Reference (2013, Biomaterials ): Parekh, P., Kamble, S., Zhao, N., Zeng, Z., Portier, B. P., & Zu, Y. (2013). Immunotherapy of CD30-expressing lymphoma using a highly stable ssDNA aptamer. Biomaterials, 34(35), 8909–8917. https://doi.org/10.1016/j.biomaterials.2013.07.099
Aptamer: Apt1
Target: Cell-surface Glycoprotein CD44
Type of nucleic acid: ssRNA
Sequence: 5'GGGAUGGAUCCAAGCUUACUGGCAUCUGGAUUUGCGCGUGCCAGAAUAAAGAGUAUAACGUGUGAAUGGGAAGCUUCGAUAGGAAUUCGG3'
Sequence length: 90
GC content: 0.4777777777777778
Affinity: Kd: 81.3 ± 30.6 nM
Pool type: 5′-GGGATGGATCCAAGCTTACTGG-N45-GGGAAGCTTCGATAGGAATTCGG-3′
Pool random region: 45
Binding buffer/conditions: 4.2 mM Na2HPO4, 2 mM K2HPO4, 140 mM NaCl, 10 mM KCl, 2.5 mM MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic and Drug Delivery: " Cancer stem cells are thought to be resistant to conventional chemotherapy, which makes them potential targets for cancer research and drug development; CD44 is a cell-surface glycoprotein expressed on lymphocytes, monocytes, and granulocytes, which have been identified as a stem cell marker in some solid tumors, including breast and head and neck cancers"
Reference (2013, Nucleic Acid Ther ): Ababneh N, Alshaer W, Allozi O, et al. In vitro selection of modified RNA aptamers against CD44 cancer stem cell marker. Nucleic Acid Ther. 2013;23(6):401-407. doi:10.1089/nat.2013.0423
Aptamer: DTMRSA1
Target: Methicillin-resistant Staphylococcus aureus (MRSA)
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCAATCCAGACGTGACGCAGCATGCGGTTGGTTGCGGTTGGGCATGATGTATTTCTGTGTGGACACGGTGGCTTAGTATGGACACGGTGGCTTAGT3'
Sequence length: 111
GC content: 0.5405405405405406
Affinity: kD: 160 ± 50 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N40-TGGACACGGTGGCTTAGT-3'
Pool random region: 40
Binding buffer/conditions: 4.5 g/L glucose, 5 mL MgCl2, 1.0 g/L bovine serum albumin and 100 mg/L tRNA
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: " The Cell-Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology was used to run the selection against MRSA bacteria and develop target-specific aptamers. The development of MRSA aptamer would present a great tool to new therapeutic approaches to eradicate the MRSA superbug, either without the use of antibiotics or with a strain-specific antibiotic."
Reference (2013, World J Transl Med ): Turek, D., Van Simaeys, D., Johnson, J., Ocsoy, I., & Tan, W. (2013). Molecular recognition of live methicillin-resistant staphylococcus aureus cells using DNA aptamers. World journal of translational medicine, 2(3), 67–74. https://doi.org/10.5528/wjtm.v2.i3.67
Aptamer: Apt22
Target: Salmonella Paratyphi A
Type of nucleic acid: ssDNA
Sequence: 5'GAATTCAGTCGGACAGCGATGGACGAATATCGTCTCCCAGTGAATTCAGTCGGACAGCGGATGGACGAATATCGTCTCCC3'
Sequence length: 80
GC content: 0.525
Affinity: Kd: 47 ± 3 nM
Pool type: 5′-GAATTCAGTCGGACAGCG-N40-GATGGACGAATATCGTCTCCC-3′
Pool random region: 40
Binding buffer/conditions: 50 mM Tris-HCl (pH 7.4), 100 mM NaCl, 5 mM KCl, 1 mM MgCl2, and 0.1% NaN3
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 paper, a panel of single-stranded DNA aptamers with high affinity and specificity against Salmonella Paratyphi A was selected from an enriched oligonucleotide pool by a whole-cell-Systematic Evolution of Ligands by Exponential Enrichment (SELEX) procedure. This study demonstrated the applicability of Salmonella specific aptamers and their potential for use in the detection of Salmonella in food, clinical and environmental samples."
Additional information: Unclear if the primer/static-regions are part of the aptamer. This UTexas Aptamer DB includes them as part of the aptamer, but the Apta-Index does not.

The FITC-labeled forward primer (5'-C12-FITC-GAATTCAGTCGGACAGCG-3') and biotin-labeled reverse primer (5'-Bio-GGGAGACGATATTCGTCCATC-3') were used in PCR to get the double-labeled DNA and measure the concentration of the ssDNA in fluorescence analysis.
Reference (2013, Sensors (Basel) ): Yang, M., Peng, Z., Ning, Y., Chen, Y., Zhou, Q., & Deng, L. (2013). Highly specific and cost-efficient detection of Salmonella Paratyphi A combining aptamers with single-walled carbon nanotubes. Sensors (Basel, Switzerland), 13(5), 6865–6881. https://doi.org/10.3390/s130506865
Aptamer: Apt 1
Target: Eukaryotic translation initiation factor 4E (eIF4e)
Type of nucleic acid: ssDNA
Sequence: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCTTGAGTAGTCAGGGATCAGTGCGGTTCGTGATGGAGATCGGAAGAGCTC3'
Sequence length: 81
GC content: 0.5308641975308642
Affinity: Not reported
Pool type: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-N33-AGATCGGAAGAGCTC-3′
Pool random region: 33
Binding buffer/conditions: Tris/Triton buffer (50 mmol/l Tris pH 8.0, 2 mmol/l EDTA, 100 mmol/l NaCL, 0.5% Triton X-100)
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e. We show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest."
Additional information: dominates early on in selection, peaking at rounds 3–6
Reference (2014, Mol Ther Nucleic Acids ): Guo, W. M., Kong, K. W., Brown, C. J., Quah, S. T., Yeo, H. L., Hoon, S., & Seow, Y. (2014). Identification and Characterization of an eIF4e DNA Aptamer That Inhibits Proliferation With High Throughput Sequencing. Molecular therapy. Nucleic acids, 3(12), e217. https://doi.org/10.1038/mtna.2014.70
Aptamer: Apt 2
Target: Eukaryotic translation initiation factor 4E (eIF4e)
Type of nucleic acid: ssDNA
Sequence: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCTAATGAGATTCGGCAAGACCCGTCTTATTACAACAGATCGGAAGAGCTC3'
Sequence length: 81
GC content: 0.4814814814814814
Affinity: Not reported
Pool type: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-N33-AGATCGGAAGAGCTC-3′
Pool random region: 33
Binding buffer/conditions: Tris/Triton buffer (50 mmol/l Tris pH 8.0, 2 mmol/l EDTA, 100 mmol/l NaCL, 0.5% Triton X-100)
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e. We show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest."
Additional information: begins displacing the first class after round 7
Reference (2014, Mol Ther Nucleic Acids ): Guo, W. M., Kong, K. W., Brown, C. J., Quah, S. T., Yeo, H. L., Hoon, S., & Seow, Y. (2014). Identification and Characterization of an eIF4e DNA Aptamer That Inhibits Proliferation With High Throughput Sequencing. Molecular therapy. Nucleic acids, 3(12), e217. https://doi.org/10.1038/mtna.2014.70
Aptamer: Apt 3
Target: Eukaryotic translation initiation factor 4E (eIF4e)
Type of nucleic acid: ssDNA
Sequence: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCTATGCGTTTGAAGTTGCCCCGGAAGTAGGTTTTCAGATCGGAAGAGCTC3'
Sequence length: 81
GC content: 0.5061728395061729
Affinity: Not reported
Pool type: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-N33-AGATCGGAAGAGCTC-3′
Pool random region: 33
Binding buffer/conditions: Tris/Triton buffer (50 mmol/l Tris pH 8.0, 2 mmol/l EDTA, 100 mmol/l NaCL, 0.5% Triton X-100)
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e. We show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest."
Additional information: dominates early on in selection, peaking at rounds 3–6
Reference (2014, Mol Ther Nucleic Acids ): Guo, W. M., Kong, K. W., Brown, C. J., Quah, S. T., Yeo, H. L., Hoon, S., & Seow, Y. (2014). Identification and Characterization of an eIF4e DNA Aptamer That Inhibits Proliferation With High Throughput Sequencing. Molecular therapy. Nucleic acids, 3(12), e217. https://doi.org/10.1038/mtna.2014.70
Aptamer: Apt 4
Target: Eukaryotic translation initiation factor 4E (eIF4e)
Type of nucleic acid: ssDNA
Sequence: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCTAATGGGATGGAATTATTGTGTATTGATGACGATAGATCGGAAGAGCTC3'
Sequence length: 81
GC content: 0.4444444444444444
Affinity: Not reported
Pool type: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-N33-AGATCGGAAGAGCTC-3′
Pool random region: 33
Binding buffer/conditions: Tris/Triton buffer (50 mmol/l Tris pH 8.0, 2 mmol/l EDTA, 100 mmol/l NaCL, 0.5% Triton X-100)
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e. We show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest."
Additional information: dominates early on in selection, peaking at rounds 3–6
Reference (2014, Mol Ther Nucleic Acids ): Guo, W. M., Kong, K. W., Brown, C. J., Quah, S. T., Yeo, H. L., Hoon, S., & Seow, Y. (2014). Identification and Characterization of an eIF4e DNA Aptamer That Inhibits Proliferation With High Throughput Sequencing. Molecular therapy. Nucleic acids, 3(12), e217. https://doi.org/10.1038/mtna.2014.70
Aptamer: Apt 5
Target: Eukaryotic translation initiation factor 4E (eIF4e)
Type of nucleic acid: ssDNA
Sequence: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCTTGTGGAGGTGGTTGGGGGTTCGGTGGGGGGGGGAGATCGGAAGAGCTC3'
Sequence length: 81
GC content: 0.6049382716049383
Affinity: Not reported
Pool type: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-N33-AGATCGGAAGAGCTC-3′
Pool random region: 33
Binding buffer/conditions: Tris/Triton buffer (50 mmol/l Tris pH 8.0, 2 mmol/l EDTA, 100 mmol/l NaCL, 0.5% Triton X-100)
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e. We show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest."
Additional information: begins displacing the first class after round 7
Reference (2014, Mol Ther Nucleic Acids ): Guo, W. M., Kong, K. W., Brown, C. J., Quah, S. T., Yeo, H. L., Hoon, S., & Seow, Y. (2014). Identification and Characterization of an eIF4e DNA Aptamer That Inhibits Proliferation With High Throughput Sequencing. Molecular therapy. Nucleic acids, 3(12), e217. https://doi.org/10.1038/mtna.2014.70
Aptamer: Apt 6
Target: Eukaryotic translation initiation factor 4E (eIF4e)
Type of nucleic acid: ssDNA
Sequence: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGGTGGGAGGGTGGGGGTGGGAATGGGGGTTCAAGATCGGAAGAGCTC3'
Sequence length: 81
GC content: 0.5802469135802469
Affinity: Not reported
Pool type: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-N33-AGATCGGAAGAGCTC-3′
Pool random region: 33
Binding buffer/conditions: Tris/Triton buffer (50 mmol/l Tris pH 8.0, 2 mmol/l EDTA, 100 mmol/l NaCL, 0.5% Triton X-100)
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e. We show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest."
Additional information: begins displacing the first class after round 7
Reference (2014, Mol Ther Nucleic Acids ): Guo, W. M., Kong, K. W., Brown, C. J., Quah, S. T., Yeo, H. L., Hoon, S., & Seow, Y. (2014). Identification and Characterization of an eIF4e DNA Aptamer That Inhibits Proliferation With High Throughput Sequencing. Molecular therapy. Nucleic acids, 3(12), e217. https://doi.org/10.1038/mtna.2014.70
Aptamer: Apt 7
Target: Eukaryotic translation initiation factor 4E (eIF4e)
Type of nucleic acid: ssDNA
Sequence: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCTTATCGCAAGGCTATGGATCGCAATTCAGTGGCAGATCGGAAGAGCTC3'
Sequence length: 80
GC content: 0.5125
Affinity: Not reported
Pool type: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-N33-AGATCGGAAGAGCTC-3′
Pool random region: 33
Binding buffer/conditions: Tris/Triton buffer (50 mmol/l Tris pH 8.0, 2 mmol/l EDTA, 100 mmol/l NaCL, 0.5% Triton X-100)
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 25 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e. We show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest."
Additional information: dominates early on in selection, peaking at rounds 3–6
Reference (2014, Mol Ther Nucleic Acids ): Guo, W. M., Kong, K. W., Brown, C. J., Quah, S. T., Yeo, H. L., Hoon, S., & Seow, Y. (2014). Identification and Characterization of an eIF4e DNA Aptamer That Inhibits Proliferation With High Throughput Sequencing. Molecular therapy. Nucleic acids, 3(12), e217. https://doi.org/10.1038/mtna.2014.70