RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: M7-22
Target: Lipopolysaccharide (LPS)
Type of nucleic acid: ssDNA
Sequence: 5'CCGGATCCGTTGATATAAAATTCTCTGGCTAAGATAAACAAGGAGTTTCATTACTTGTATGTTTTTGATTGTGGTGTTGGCTCCCAAGCTTCGG3'
Sequence length: 94
GC content: 0.4042553191489361
Affinity: Not reported
Pool type: 5'-CCGGATCCGTTGATATAAAATTC-N40-TTGATTGTGGTGTTGGCTCCCAAGCTTCGG-3'
Pool random region: 40
Binding buffer/conditions: Phosphate-buffered saline (PBS), 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: Therapeutic: " In Gram-negative bacterial infection, lipopolysaccharide (LPS) readily overwhelms the host innate immune system, which could result in inflammation and sepsis in severe cases Several approaches have been explored to prevent the cascade of LPS-induced events in humans. Therefore, developing anti-LPS molecules would confer an efficient antibacterial strategy. We used SELEX (Systemic Evolution of Ligands by EXponential enrichment) to isolate single-stranded DNA (ssDNA) aptamers"
Reference (2008, J Innate Immun ): Ding JL, Gan ST, Ho B. Single-stranded DNA oligoaptamers: molecular recognition and LPS antagonism are length- and secondary structure-dependent. J Innate Immun. 2009;1(1):46-58. doi: 10.1159/000145542. Epub 2008 Jul 12. PMID: 20375565; PMCID: PMC7312852.
Aptamer: M7-5
Target: Lipopolysaccharide (LPS)
Type of nucleic acid: ssDNA
Sequence: 5'CCGGATCCGTTGATATAAAATTCTAGTCAGGTGAAGTCCGCGGCTAACAATTCAGTAGGTTATTGATTGTGGTGTTGGCTCCCAAGCTTCGG3'
Sequence length: 92
GC content: 0.4673913043478261
Affinity: Not reported
Pool type: 5'-CCGGATCCGTTGATATAAAATTC-N40-TTGATTGTGGTGTTGGCTCCCAAGCTTCGG-3'
Pool random region: 40
Binding buffer/conditions: Phosphate-buffered saline (PBS), 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: Therapeutic: " In Gram-negative bacterial infection, lipopolysaccharide (LPS) readily overwhelms the host innate immune system, which could result in inflammation and sepsis in severe cases Several approaches have been explored to prevent the cascade of LPS-induced events in humans. Therefore, developing anti-LPS molecules would confer an efficient antibacterial strategy. We used SELEX (Systemic Evolution of Ligands by EXponential enrichment) to isolate single-stranded DNA (ssDNA) aptamers"
Reference (2008, J Innate Immun ): Ding JL, Gan ST, Ho B. Single-stranded DNA oligoaptamers: molecular recognition and LPS antagonism are length- and secondary structure-dependent. J Innate Immun. 2009;1(1):46-58. doi: 10.1159/000145542. Epub 2008 Jul 12. PMID: 20375565; PMCID: PMC7312852.
Aptamer: Apt #1
Target: Bovine Prion Protein (bPrP)
Type of nucleic acid: ssRNA
Sequence: 5′GGGAGGUGGAACUGAAGGAGACAAUCCAUUCAUCUCUCGAAUGAGGAAGUAGCCCAAGAGGAGGAGGAGGAUGAGCACUUCGCAAUCGCUCUACGCA3′
Sequence length: 97
GC content: 0.5257731958762887
Affinity: Kd: 82 ± 21 nM
Pool type: 5′-GGGAGGUGGAACUGAAGGAGA-N55-ACUUCGCAAUCGCUCUACGCA-3′
Pool random region: 55
Binding buffer/conditions: 20 mM Tris-HCl (pH 7.5) and 100 mM NaCl
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: Diagnosis: " In order to obtain RNA aptamers against bovine prion protein (bPrP), we carried out in vitro selection from RNA pools containing a 55-nucleotide randomized region to target recombinant bPrP. This minimized form of aptamer #1 may therefore be useful in the detection of bPrP, diagnosis of prion disease, enrichment of bPr and ultimately in gaining a better understanding of prion diseases."
Reference (2008, Prion ): Murakami K, Nishikawa F, Noda K, Yokoyama T, Nishikawa S. Anti-bovine prion protein RNA aptamer containing tandem GGA repeat interacts both with recombinant bovine prion protein and its beta isoform with high affinity. Prion. 2008 Apr-Jun;2(2):73-80. doi: 10.4161/pri.2.2.7024. Epub 2008 Apr 17. PMID: 19098441; PMCID: PMC2634522.
Aptamer: ZE2
Target: Hepatitis C virus (HCV) envelope surface glycoprotein E2
Type of nucleic acid: ssDNA
Sequence: 5′GCGGAATTCTAATACGACTCACTATAGGGAACAGTCCGAGCCGAATGAGGAATAATCTAGCTCCTTCGCTGAGGGTCAATGCGTCATA3′
Sequence length: 88
GC content: 0.4772727272727273
Affinity: Kd 1.05±1 nM
Pool type: 5′-GCGGAATTCTAATACGACTCACTATAGGGAACAGTCCGAGCC-N30-GGGTCAATGCGTCATA-3′
Pool random region: 30
Binding buffer/conditions: 25 mM Tris–HCl, 50 mM KCl, 200 mM NaCl, 0.2 mM EDTA, 5% (v/v) glycerol, and 0.5 mM DTT
Buffer type: Tris Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diognostic and Therapeutic: "In this study, we have described the development of an alive cell surface--Systematic Evolution of Ligands by Exponential Enrichment (CS-SELEX) technique and screened the functional ssDNA aptamers that specifically bound to HCV envelope surface glycoprotein E2. Our data demonstrate that the newly selected ssDNA aptamers, especially aptamer ZE2, hold great promise for developing new molecular probes, as an early diagnostic reagent for HCV surface antigen, or a therapeutic drug specifically for HCV."
Reference (2009, PLoS One ): Chen, F., Hu, Y., Li, D., Chen, H., & Zhang, X. L. (2009). CS-SELEX generates high-affinity ssDNA aptamers as molecular probes for hepatitis C virus envelope glycoprotein E2. PloS one, 4(12), e8142. https://doi.org/10.1371/journal.pone.0008142
Aptamer: ZE3
Target: Hepatitis C virus (HCV) envelope surface glycoprotein E3
Type of nucleic acid: ssDNA
Sequence: 5′GCGGAATTCTAATACGACTCACTATAGGGAACAGTCCGAGCCCGCCGTATTAAGATTGGGAGACCTGGTAGAGGGTCAATGCGTCATA3′
Sequence length: 88
GC content: 0.5
Affinity: Kd 3.22±0.7 nM
Pool type: 5′-GCGGAATTCTAATACGACTCACTATAGGGAACAGTCCGAGCC-N30-GGGTCAATGCGTCATA-3′
Pool random region: 30
Binding buffer/conditions: 25 mM Tris–HCl, 50 mM KCl, 200 mM NaCl, 0.2 mM EDTA, 5% (v/v) glycerol, and 0.5 mM DTT
Buffer type: Tris Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diognostic and Therapeutic: "In this study, we have described the development of an alive cell surface--Systematic Evolution of Ligands by Exponential Enrichment (CS-SELEX) technique and screened the functional ssDNA aptamers that specifically bound to HCV envelope surface glycoprotein E2. Our data demonstrate that the newly selected ssDNA aptamers, especially aptamer ZE2, hold great promise for developing new molecular probes, as an early diagnostic reagent for HCV surface antigen, or a therapeutic drug specifically for HCV."
Reference (2009, PLoS One ): Chen, F., Hu, Y., Li, D., Chen, H., & Zhang, X. L. (2009). CS-SELEX generates high-affinity ssDNA aptamers as molecular probes for hepatitis C virus envelope glycoprotein E2. PloS one, 4(12), e8142. https://doi.org/10.1371/journal.pone.0008142
Aptamer: N2
Target: Amyloid beta-peptide (Aβ)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAUGUUCUAGGCGGUUGAUGAUAGCGUAUGCCACUCUCCUGGGACCCCCCGCCGGAUGGCCACAUCCAGAGUAGCAUAAUUGAUCCGA3'
Sequence length: 90
GC content: 0.5666666666666667
Affinity: Kd: 21.6 μM
Pool type: 5′-GGGATGTTCTAGGCCGGTTGATGA-N40-CATCCAGAGTAGCATAATTTGATCCGA-3′
Pool random region: 40
Binding buffer/conditions: 10 mM Tris·HCl, pH 7.5, containing 150 mM NaCl, 5 mM MgCl2
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: " Aggregation of amyloid beta-peptide (Abeta) is closely related to the pathogenesis of Alzheimer's disease (AD). Using a systematic evolution of ligands using the exponential enrichment (SELEX) procedure, we have constructed RNA aptamers that bind to Abeta1-40 and inhibit aggregation. The selected RNA aptamers may have potential as therapeutic agents for AD pathogenesis."
Reference (2009, Mol Biosyst ): Takahashi, T., Tada, K., & Mihara, H. (2009). RNA aptamers selected against amyloid beta-peptide (Abeta) inhibit the aggregation of Abeta. Molecular bioSystems, 5(9), 986–991. https://doi.org/10.1039/b903391b
Aptamer: TV01
Target: Vaccinia virus–infected lung cancer A549 cells
Type of nucleic acid: ssDNA
Sequence: 5′ATCGTCTGCTCCGTCCAATAGTGCATTGAAACTTCTGCATCCTCGTTTGGTGTGAGGTCGTGC3'
Sequence length: 63
GC content: 0.5079365079365079
Affinity: Kd: 7.3 ± 1.4 nM
Pool type: 5′-ATCGTCTGCTCCGTCCAATA-N45-TTTGGTGTGAGGTCGTGC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose, 5 mmol/L MgCl2 in Dulbecco PBS, yeast tRNA (0.1 g/L; Sigma–Aldrich), FBS (100 mL/L), BSA (1 g/L; Fisher)
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: "We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell-SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells."
Reference (2009, Clin Chem ): Tang, Z., Parekh, P., Turner, P., Moyer, R. W., & Tan, W. (2009). Generating aptamers for recognition of virus-infected cells. Clinical chemistry, 55(4), 813–822. https://doi.org/10.1373/clinchem.2008.113511
Aptamer: TV02
Target: Vaccinia virus–infected lung cancer A549 cells
Type of nucleic acid: ssDNA
Sequence: 5′ATCGTCTGCTCCGTCCAATACCTGCATATACACTTTGCATGTGGTTTGGTGTGAGGTCGTGC3'
Sequence length: 62
GC content: 0.5
Affinity: Kd: 3.6 ± 0.48 nM
Pool type: 5′-ATCGTCTGCTCCGTCCAATA-N45-TTTGGTGTGAGGTCGTGC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose, 5 mmol/L MgCl2 in Dulbecco PBS, yeast tRNA (0.1 g/L; Sigma–Aldrich), FBS (100 mL/L), BSA (1 g/L; Fisher)
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: "We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell-SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells."
Reference (2009, Clin Chem ): Tang, Z., Parekh, P., Turner, P., Moyer, R. W., & Tan, W. (2009). Generating aptamers for recognition of virus-infected cells. Clinical chemistry, 55(4), 813–822. https://doi.org/10.1373/clinchem.2008.113511
Aptamer: TV03
Target: Vaccinia virus–infected lung cancer A549 cells
Type of nucleic acid: ssDNA
Sequence: 5′ATCGTCTGCTCCGTCCAATAGCGTGCATTGGTTTACTGCATCCGTGAAACTGGGCTTTGGTGTGAGGTCGTGC3'
Sequence length: 73
GC content: 0.5342465753424658
Affinity: Kd: 4.1 ± 0.59 nM
Pool type: 5′-ATCGTCTGCTCCGTCCAATA-N45-TTTGGTGTGAGGTCGTGC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose, 5 mmol/L MgCl2 in Dulbecco PBS, yeast tRNA (0.1 g/L; Sigma–Aldrich), FBS (100 mL/L), BSA (1 g/L; Fisher)
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: "We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell-SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells."
Reference (2009, Clin Chem ): Tang, Z., Parekh, P., Turner, P., Moyer, R. W., & Tan, W. (2009). Generating aptamers for recognition of virus-infected cells. Clinical chemistry, 55(4), 813–822. https://doi.org/10.1373/clinchem.2008.113511
Aptamer: TV04
Target: Vaccinia virus–infected lung cancer A549 cells
Type of nucleic acid: ssDNA
Sequence: 5′ATCGTCTGCTCCGTCCAATAAACCTGCATAATTTATAAGTCTAGACTGCTGCATTTGGTGTGAGGTCGTGC3'
Sequence length: 71
GC content: 0.4507042253521127
Affinity: Kd: 6.5 ± 0.94 nM
Pool type: 5′-ATCGTCTGCTCCGTCCAATA-N45-TTTGGTGTGAGGTCGTGC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose, 5 mmol/L MgCl2 in Dulbecco PBS, yeast tRNA (0.1 g/L; Sigma–Aldrich), FBS (100 mL/L), BSA (1 g/L; Fisher)
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: "We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell-SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells."
Reference (2009, Clin Chem ): Tang, Z., Parekh, P., Turner, P., Moyer, R. W., & Tan, W. (2009). Generating aptamers for recognition of virus-infected cells. Clinical chemistry, 55(4), 813–822. https://doi.org/10.1373/clinchem.2008.113511
Aptamer: TV05
Target: Vaccinia virus–infected lung cancer A549 cells
Type of nucleic acid: ssDNA
Sequence: 5′ATCGTCTGCTCCGTCCAATAGCCTCACCCTGCATAATTTATAGACTACACTTAGGAATCGCTGCATTTGGTGTGAGGTCGTGC3'
Sequence length: 83
GC content: 0.4819277108433735
Affinity: Kd: 4.1 ± 0.44 nM
Pool type: 5′-ATCGTCTGCTCCGTCCAATA-N45-TTTGGTGTGAGGTCGTGC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose, 5 mmol/L MgCl2 in Dulbecco PBS, yeast tRNA (0.1 g/L; Sigma–Aldrich), FBS (100 mL/L), BSA (1 g/L; Fisher)
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: "We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell-SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells."
Reference (2009, Clin Chem ): Tang, Z., Parekh, P., Turner, P., Moyer, R. W., & Tan, W. (2009). Generating aptamers for recognition of virus-infected cells. Clinical chemistry, 55(4), 813–822. https://doi.org/10.1373/clinchem.2008.113515
Aptamer: TV06
Target: Vaccinia virus–infected lung cancer A549 cells
Type of nucleic acid: ssDNA
Sequence: 5′ATCGTCTGCTCCGTCCAATAGGACCGATAGGAACCACGGACTGCATGTTTCTGCATTTGACGTGGTTTGGTGTGAGGTCGTGC3'
Sequence length: 83
GC content: 0.5301204819277109
Affinity: Kd: 6.5 ± 1.3 nM
Pool type: 5′-ATCGTCTGCTCCGTCCAATA-N45-TTTGGTGTGAGGTCGTGC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose, 5 mmol/L MgCl2 in Dulbecco PBS, yeast tRNA (0.1 g/L; Sigma–Aldrich), FBS (100 mL/L), BSA (1 g/L; Fisher)
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: "We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell-SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells."
Reference (2009, Clin Chem ): Tang, Z., Parekh, P., Turner, P., Moyer, R. W., & Tan, W. (2009). Generating aptamers for recognition of virus-infected cells. Clinical chemistry, 55(4), 813–822. https://doi.org/10.1373/clinchem.2008.113515
Aptamer: TV07
Target: Vaccinia virus–infected lung cancer A549 cells
Type of nucleic acid: ssDNA
Sequence: 5′ATCGTCTGCTCCGTCCAATATCCGAGCAAGAACTCATATTGCATTATTTATAGCTACGCGCTGCATTTGGTGTGAGGTCGTGC3'
Sequence length: 83
GC content: 0.4698795180722891
Affinity: Kd: 11.7 ± 2.9 nM
Pool type: 5′-ATCGTCTGCTCCGTCCAATA-N45-TTTGGTGTGAGGTCGTGC-3'
Pool random region: 45
Binding buffer/conditions: 4.5 g/L glucose, 5 mmol/L MgCl2 in Dulbecco PBS, yeast tRNA (0.1 g/L; Sigma–Aldrich), FBS (100 mL/L), BSA (1 g/L; Fisher)
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: "We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell-SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells."
Reference (2009, Clin Chem ): Tang, Z., Parekh, P., Turner, P., Moyer, R. W., & Tan, W. (2009). Generating aptamers for recognition of virus-infected cells. Clinical chemistry, 55(4), 813–822. https://doi.org/10.1373/clinchem.2008.113515
Aptamer: E21
Target: Histidine-tagged epidermal growth factor receptor variant III (EGFRvIII) ectodomain
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGAGGACGAUGCGGUACCAAGAUCCCACAACUAGCCGACCACAAUUGCCGGCCACAGACGACUCGCUGAGGAUCCGAGA3'
Sequence length: 80
GC content: 0.6
Affinity: Kd: 33 nM
Pool type: 5'-GGGAGGACGATGCGG-N40-CAGACGACTCGCTGAGGATCCGAGA-3'
Pool random region: 40
Binding buffer/conditions: 20 uM HEPES, pH 7.4; 150 uL NaCl; 2 uM CaCl2; 0.01% bovine serum albumin
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 40 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Epidermal growth factor receptor variant III (EGFRvIII) is a glycoprotein uniquely expressed in glioblastoma, but not in normal brain tissues. To develop targeted therapies for brain tumors, we selected RNA aptamers against the histidine-tagged EGFRvIII ectodomain, using an Escherichia coli system for protein expression and purification. Our work establishes the feasibility of disrupting protein post-translational modifications in situ with aptamers."
Additional information: pyrimidines were 2'-fluoro-modified to improve stability; the article explicitly states the selection of RNA aptamers but only reports the sequence and pool type as DNA. Pool in vitro transcription with 2′-fluoro CTP and UTP, 2′-hydroxy GTP and ATP, and mutant T7 RNA polymerase that efficiently incorporates modified nucleotides
Reference (2009, Biol Chem ): Liu, Y., Kuan, C. T., Mi, J., Zhang, X., Clary, B. M., Bigner, D. D., & Sullenger, B. A. (2009). Aptamers selected against the unglycosylated EGFRvIII ectodomain and delivered intracellularly reduce membrane-bound EGFRvIII and induce apoptosis. Biological chemistry, 390(2), 137–144. https://doi.org/10.1515/BC.2009.022
Aptamer: E17
Target: Histidine-tagged epidermal growth factor receptor variant III (EGFRvIII) ectodomain
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGAGGACGAUGCGGACCAAAAUCAACGCAAAGAGCGCGCCUGCACGUCACCUCACAGACGACUCGCUGAGGAUCCGAGA3'
Sequence length: 80
GC content: 0.6
Affinity: Kd: 50 nM
Pool type: 5'-GGGAGGACGATGCGG-N40-CAGACGACTCGCTGAGGATCCGAGA-3'
Pool random region: 40
Binding buffer/conditions: 20 uM HEPES, pH 7.4; 150 uL NaCl; 2 uM CaCl2; 0.01% bovine serum albumin
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 40 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Epidermal growth factor receptor variant III (EGFRvIII) is a glycoprotein uniquely expressed in glioblastoma, but not in normal brain tissues. To develop targeted therapies for brain tumors, we selected RNA aptamers against the histidine-tagged EGFRvIII ectodomain, using an Escherichia coli system for protein expression and purification. Our work establishes the feasibility of disrupting protein post-translational modifications in situ with aptamers."
Additional information: pyrimidines were 2'-fluoro-modified to improve stability; the article explicitly states the selection of RNA aptamers but only reports the sequence and pool type as DNA. Pool in vitro transcription with 2′-fluoro CTP and UTP, 2′-hydroxy GTP and ATP, and mutant T7 RNA polymerase that efficiently incorporates modified nucleotides
Reference (2009, Biol Chem ): Liu, Y., Kuan, C. T., Mi, J., Zhang, X., Clary, B. M., Bigner, D. D., & Sullenger, B. A. (2009). Aptamers selected against the unglycosylated EGFRvIII ectodomain and delivered intracellularly reduce membrane-bound EGFRvIII and induce apoptosis. Biological chemistry, 390(2), 137–144. https://doi.org/10.1515/BC.2009.022
Aptamer: KH1C12
Target: Acute myeloid leukemia cells (HL60)
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCATGCCCTAGTTACTACTACTCTTTTTAGCAAACGCCCTCGCTTTGGACACGGTGGCTTAGT3'
Sequence length: 78
GC content: 0.5
Affinity: Kd: 4.5± 1.6 nM
Pool type: 5′-FITC- ATCCAGAGTGACGCAGCA-N45-TGGACACGGTGGCTTAGT-3′
Pool random region: 45
Binding buffer/conditions: 4.5 g/liter glucose, 5 mM MgCl2, 0.1 mg/ml tRNA and 1mg/ml BSA, all dissolved in Dulbecco's PBS with magnesium chloride and calcium chloride
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: "Cell surface proteins can play important roles in cancer pathogenesis. Selected aptamers can be used as a molecular tool for further understanding surface protein expression patterns on tumor cells and thus providing a foundation for effective molecular analysis of leukemia and its subcategories; tumor diagnosis, classification and therapy"
Reference (2009, Leukemia ): Sefah, K., Tang, Z. W., Shangguan, D. H., Chen, H., Lopez-Colon, D., Li, Y., Parekh, P., Martin, J., Meng, L., Phillips, J. A., Kim, Y. M., & Tan, W. H. (2009). Molecular recognition of acute myeloid leukemia using aptamers. Leukemia, 23(2), 235–244. https://doi.org/10.1038/leu.2008.335