RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: d12
Target: Plasmodium falciparum (P. falciparum) erythrocyte membrane protein 1 (PfEMP1)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′CGACUGCAGAGCUUGCUACGAACAAUACGACUACACCAUCAAAAGUAUUAUCUUGCAUCGAAGGUUGGCAGGUACCGAGCUCGAAUUCCC3′
Sequence length: 90
GC content: 0.4777777777777778
Affinity: Not reported
Pool type: 5′-CGACTGCAGAGCTTGCTACG-N50-GGTACCGAGCTCGAATTCCC-3′
Pool random region: 50
Binding buffer/conditions: PBSM (PBS, 1 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: " The var-gene encoding Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is known to play a major role in the pathogenicity of the P. falciparum parasite. The protein enables the parasite to adhere to the endothelial linings of small blood vessels (cytoadherence) as well as to non-infected erythrocytes (rosetting), thus preventing clearance from the bloodstream. The described results show that RNA aptamers are promising candidates for adjunct therapy in severe malaria."
Additional information: DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection.
The DNA library was generated using oligo B (5′-CGACTGCAGAGCTTGCTACG (N)50 GGTACCGAGCTCGAATTCCC-3′) and oligo A (5′-GCGTAATACGACTCACTATAGGGAATTCGAGCTCGGTACC-3′), sequence for T7 promoter underlined.
2′F-modified library (ATP, GTP, 2′F-dCTP, 2′F-dUTP)
Reference (2009, Parasitol Res ): Barfod, A., Persson, T., & Lindh, J. (2009). In vitro selection of RNA aptamers against a conserved region of the Plasmodium falciparum erythrocyte membrane protein 1. Parasitology research, 105(6), 1557–1566. https://doi.org/10.1007/s00436-009-1583-x
Aptamer: D16
Target: Diclofenac (DCF)
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGCCCGGCAACAGGTTGTGACATGCCAGTGCGAGACCGCCCGAGATAGTAAGTGCAATCT3′
Sequence length: 77
GC content: 0.5064935064935064
Affinity: Kd: 148.73 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl pH 7.6, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% Tween 20
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Drug Delivery and Detection: "A series of 56 ssDNA aptamer variants that bind to diclofenac (DCF) were selected from an initial pool of 2.4x10^(14) ssDNA molecules by Flu-Mag SELEX process. DCF aptamers selected can be potential candidates for drug-delivery systems, specific detection of DCF and its derivatives in pharmaceutical preparations and contaminants"
Reference (2009, Bioorg Med Chem ): Joeng, C. B., Niazi, J. H., Lee, S. J., & Gu, M. B. (2009). ssDNA aptamers that recognize diclofenac and 2-anilinophenylacetic acid. Bioorganic & medicinal chemistry, 17(15), 5380–5387. https://doi.org/10.1016/j.bmc.2009.06.044
Aptamer: Aptamer 29
Target: Streptavidin
Type of nucleic acid: ssDNA
Sequence: 5′TAATACGACTCACTATAGCAATGGTACGGTACTTCCAGATACGCtCGTGTTGCTCGATAGCCAAAAGTGCACGCTACTTTG3′
Sequence length: 81
GC content: 0.4567901234567901
Affinity: Kd: 94.228 ± 5.443 nM
Pool type: 5′-TAATACGACTCACTATAGCAATGGTACGGTACTTCC-N25-CAAAAGTGCACGCTACTTTG-3′
Pool random region: 25
Binding buffer/conditions: 5 mM of MgCl2 in 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: Detection: " The streptavidin-specific aptamers obtained in this work can be used as tools for characterization of the occupancy of streptavidin-modified surfaces with biotinylated target molecules. The method described in the study is also generally applicable to target molecules other than streptavidin."
Reference (2009, Acta Biochim Biophys Sin (Shanghai) ): Wang, C., Yang, G., Luo, Z., & Ding, H. (2009). In vitro selection of high-affinity DNA aptamers for streptavidin. Acta biochimica et biophysica Sinica, 41(4), 335–340. https://doi.org/10.1093/abbs/gmp022
Aptamer: Aptamer 30
Target: Streptavidin
Type of nucleic acid: ssDNA
Sequence: 5′TAATACGACTCACTATAGCAATGGTACGGTACTTCCCGACGCACCGATCGCAGGTTCGGGACAAAAGTGCACGCTACTTTG3′
Sequence length: 81
GC content: 0.5061728395061729
Affinity: Kd: 104.265 ± 5.688 nM
Pool type: 5′-TAATACGACTCACTATAGCAATGGTACGGTACTTCC-N25-CAAAAGTGCACGCTACTTTG-3′
Pool random region: 25
Binding buffer/conditions: 5 mM of MgCl2 in 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: Detection: " The streptavidin-specific aptamers obtained in this work can be used as tools for characterization of the occupancy of streptavidin-modified surfaces with biotinylated target molecules. The method described in the study is also generally applicable to target molecules other than streptavidin."
Reference (2009, Acta Biochim Biophys Sin (Shanghai) ): Wang, C., Yang, G., Luo, Z., & Ding, H. (2009). In vitro selection of high-affinity DNA aptamers for streptavidin. Acta biochimica et biophysica Sinica, 41(4), 335–340. https://doi.org/10.1093/abbs/gmp022
Aptamer: Apta 13A
Target: 17 beta-Estradiol (17β-Estradiol) (E2）
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGTTCTTATGTCGAACTAAATTTGGCCTGACCAAGCCGAATTTGACCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.475
Affinity: Kd: 63 μM
Pool type: 5′-AGCAGCACAGAGGTCAGTTC-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 10 mM HEPES, pH 7.4
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: Detection: " Aptamers targeting different functional groups of 17β-estradiol.The selected aptamers with affinities for different functional groups of E2 can potentially be applied to develop a cross-reactive aptasensor. This aptasensor introduces a promising tool for the future of in-field real-time monitoring of a wide range of steroid hormones."
Reference (2010, J Steroid Biochem Mol Biol ): Vanschoenbeek K, Vanbrabant J, Hosseinkhani B, Vermeeren V, Michiels L. Aptamers targeting different functional groups of 17β-estradiol. J Steroid Biochem Mol Biol. 2015 Mar;147:10-6. doi: 10.1016/j.jsbmb.2014.10.013. Epub 2014 Oct 22. PMID: 25465478.
Aptamer: Apta 1B
Target: 17 beta-Estradiol (17β-Estradiol) (E2）
Type of nucleic acid: ssDNA
Sequence: 5'TGTGTGTGAGACTTCGTTCCGGCGATGGGGTAGGGGGTGTGGAGGGGCCGGACGGAGGGGCAGCAAGGCATCAGAGGTAT3'
Sequence length: 80
GC content: 0.6375
Affinity: Kd: 0.9 μM
Pool type: 5'-TGTGTGTGAGACTTCGTTCC-N40-CAGCAAGGCATCAGAGGTAT-3'
Pool random region: 40
Binding buffer/conditions: PBS with 10% ethanol, 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: Detection: " Aptamers targeting different functional groups of 17β-estradiol.The selected aptamers with affinities for different functional groups of E2 can potentially be applied to develop a cross-reactive aptasensor. This aptasensor introduces a promising tool for the future of in-field real-time monitoring of a wide range of steroid hormones."
Reference (2010, J Steroid Biochem Mol Biol ): Vanschoenbeek K, Vanbrabant J, Hosseinkhani B, Vermeeren V, Michiels L. Aptamers targeting different functional groups of 17β-estradiol. J Steroid Biochem Mol Biol. 2015 Mar;147:10-6. doi: 10.1016/j.jsbmb.2014.10.013. Epub 2014 Oct 22. PMID: 25465478.
Aptamer: selected aptamer
Target: Immunoglobulin G (IgG) Fc fragment, Mouse
Type of nucleic acid: ssDNA
Sequence: 5′CCACTCCTCCACCTTTGACATGTGTCTGCGGCGTTTTATCATTGGCTACAGCAACAGGGTTAATACGACTCACTATAGCAATGGTACGGTACTTCCAAGCTAACCCTCATCTGCGCGCTCCCAAAAGTGCACGCTACTTTGCTAA3′
Sequence length: 145
GC content: 0.4896551724137931
Affinity: Reported through qualitiative analysis
Pool type: 5′-TAATACGACTCACTATAGCAATGGTACGGTACTTCC-N25-CAAAAGTGCACGCTACTTTG-3′
Pool random region: 25
Binding buffer/conditions: 10 mM HEPES (pH 7.6), 1 mM EDTA, 2 mM dithiothreitol, 50 mM KCl, 0.05% Triton X-100, and 5% glycerol
Buffer type: Other Buffers
pH: 7.6
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Biosensor and Research: "To explore an aptamer-based approach for target sensing and detection with higher sensitivity and specificity, instead of directly labeling aptamer with fluorophores, we proposed a new strategy by attaching a polymerase chain reaction (PCR) template to an oligonucleotide aptamer selected by systematic evolution of ligands by exponential enrichment (SELEX). This new approach also has potential applications in multiple parallel target detection and analysis in a wide range of research fields."
Additional information: The first 61 nucleotides are part of a double-strand fragment which serves as PCR template and the remaining sequence is the loop-stem fragment and functions as aptamer moiety. Used a Taqman Probe during the PCR process: FAM-TGTGTCTGCGGCGTTTTATCA-TAMRA; FAM-TGTGTCTGATAGTAAGTGCCA-TAMRA; FAM-TGCACGCAGGTCAAGATCAGA-TAMRA Using dsDNA templates tethered Aptamers
Reference (2010,Bioconjug Chem): Liao S, Liu Y, Zeng J, Li X, Shao N, Mao A, Wang L, Ma J, Cen H, Wang Y, Zhang X, Zhang R, Wei Z, Wang X. Aptamer-Based Sensitive Detection of Target Molecules via RT-PCR Signal Amplification. Bioconjug Chem. 2010 Dec 15;21(12):2183-9. doi: 10.1021/bc100032v. Epub 2010 Nov 10. PMID: 21067135.
Aptamer: m009
Target: Sphingosylphosphorylcholine (SPC)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAUCCACAUCUACGAAUUCUACCGUUAUUGGUGUCACCGAAGAUGUUAUUCC3'
Sequence length: 54
GC content: 0.4444444444444444
Affinity: Kd: 186 ± 5.05 nM
Pool type: 5'-GGGAAUGGAUCCACAUCUACGAAUUC-N30-UUCACUGCAGACUUGACGAAGC-3′
Pool random region: 30
Binding buffer/conditions: SB: 20 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 5 mM KCl
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Tructated aptamer derived from c1 and c2
Application as quoted in the referenced paper: Diagnostic: " Sphingosylphosphorylcholine (SPC) is a lysosphingolipid that exerts multiple functions, including acting as a spasmogen, as a mitogenic factor for various types of cells, and sometimes as an inflammatory mediator. This is the first case of the Systematic Evolution of Ligands by EXponential enrichment (SELEX) process being performed with a lysosphingolipid. The SPC aptamers would be valuable tools for the development of aptamer-based medical diagnosis and for elucidating the biological role of SPC."
Reference (2010, Molecules ): Horii, K., Omi, K., Yoshida, Y., Imai, Y., Sakai, N., Oka, A., Masuda, H., Furuichi, M., Tanimoto, T., & Waga, I. (2010). Development of a sphingosylphosphorylcholine detection system using RNA aptamers. Molecules (Basel, Switzerland), 15(8), 5742–5755. https://doi.org/10.3390/molecules15085742
Aptamer: S132B-C11
Target: Light chain of type A botulinum neurotoxin (BoNT/A) (LCA)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′GGGAGGAGGAGAGAUGUGAACUUAUUCGGGCCCAGGAACCAACUAUAUAAAUGUCCCGAAUGCUUCGACGAGAAACUCUACACUGGACUGGCG3′
Sequence length: 93
GC content: 0.5053763440860215
Affinity: Kd: 186 ± 18 nM
Pool type: 5′-GGGAGGAGGAGAGATGTGAACTT-N47-AGAAACTCTACACTGGACTGGCG-3′
Pool random region: 47
Binding buffer/conditions: PBS pH 7.4, 300 mM NaCl, 3 mM MgCl2, 5 mM DTT 1 mg/ml BSA, 0.2% Tween, 1 mg/ml heparin
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 150 kDa
Application as quoted in the referenced paper: Therapeutic: " The category A agent, botulinum neurotoxin (BoNT), is the most toxic molecule known to mankind. The endopeptidase activity of light chain domain of BoNT is the cause for the inhibition of the neurotransmitter release and the flaccid paralysis that leads to lethality in botulism. These data on K(I) and IC(50) strongly suggest that the aptamers have strong potential as antidotes that can reverse the symptom caused by BoNT/A."
Additional information: 2′-fluoro-pyrimidin modified nucleic acid (2′-F-CTP and 2′-F-UTP) during in vitro transcription step to generate 2′-F-modified RNA
Reference (2010, Biochem Biophys Res Commun ): Chang, T. W., Blank, M., Janardhanan, P., Singh, B. R., Mello, C., Blind, M., & Cai, S. (2010). In vitro selection of RNA aptamers that inhibit the activity of type A botulinum neurotoxin. Biochemical and biophysical research communications, 396(4), 854–860. https://doi.org/10.1016/j.bbrc.2010.05.006
Aptamer: Vap7
Target: Receptor-binding domain (RBD) of vascular endothelial growth factor 121 (VEGF121)
Type of nucleic acid: ssDNA
Sequence: 5'ATACCAGTCTATTCAATTGCACTCTGTGGGGGTGGACGGGCCGGGTAGATAGTATGTGCAATCA3'
Sequence length: 64
GC content: 0.5
Affinity: Kd: 1.0 nM
Pool type: 5'-ATACCAGTCTATTCAATT-N30-AGATAGTATGTGCAATCA-3'
Pool random region: 30
Binding buffer/conditions: TBSE (10 mM Tris/HCl, 100 mM NaCl, and 0.05 mM EDTA; pH 7.0)
Buffer type: Other Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensors: " With the aim of creating a more effective tool for the diagnosis of cancer, we considered vascular endothelial growth factor A (VEGF-A) as a target marker protein. We also produced an aptamer heterodimer consisting of our previously derived aptamer (del5-1), which binds to the heparin-binding domain of VEGF, linked to V7t1. The resulting heterodimer bound strongly to VEGF(165) with a K(D) value of 4.7 x 10(2) pM."
Reference (2010, Molecules ): Nonaka Y, Sode K, Ikebukuro K. Screening and improvement of an anti-VEGF DNA aptamer. Molecules. 2010 Jan 7;15(1):215-25. doi: 10.3390/molecules15010215. PMID: 20110884; PMCID: PMC6256979.
Aptamer: Vap7
Target: Receptor-binding domain (RBD) of vascular endothelial growth factor 165 (VEGF165)
Type of nucleic acid: ssDNA
Sequence: 5'ATACCAGTCTATTCAATTGCACTCTGTGGGGGTGGACGGGCCGGGTAGATAGTATGTGCAATCA3'
Sequence length: 64
GC content: 0.5
Affinity: Kd: 20 nM
Pool type: 5'-ATACCAGTCTATTCAATT-N30-AGATAGTATGTGCAATCA-3'
Pool random region: 30
Binding buffer/conditions: TBSE (10 mM Tris/HCl, 100 mM NaCl, and 0.05 mM EDTA; pH 7.0)
Buffer type: Other Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensors: " With the aim of creating a more effective tool for the diagnosis of cancer, we considered vascular endothelial growth factor A (VEGF-A) as a target marker protein. We also produced an aptamer heterodimer consisting of our previously derived aptamer (del5-1), which binds to the heparin-binding domain of VEGF, linked to V7t1. The resulting heterodimer bound strongly to VEGF(165) with a K(D) value of 4.7 x 10(2) pM."
Reference (2010, Molecules ): Nonaka Y, Sode K, Ikebukuro K. Screening and improvement of an anti-VEGF DNA aptamer. Molecules. 2010 Jan 7;15(1):215-25. doi: 10.3390/molecules15010215. PMID: 20110884; PMCID: PMC6256979.
Aptamer: PSap4#5
Target: Prostate specific antigen (PSA)
Type of nucleic acid: ssDNA
Sequence: 5′CATGCTTACCTATAGTGAACTTTATTAGCCTCCCGGAAGAGCACCTCTTTCATGCTTACCTATAGTGAAC3'
Sequence length: 70
GC content: 0.4285714285714285
Affinity: Kd: "several tens of nM"
Pool type: 5′-CATGCTTACCTATAGTGAACttt-N24-tttCTTTGAGAACTGACTCATAC-3′
Pool random region: 24
Binding buffer/conditions: TBS buffer (10 mM Tris/HCl, 150 mM NaCl, 5 mM KCl, 5 mM MgCl2, pH 7.4)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: 33–34kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensors: " With the aim of creating a more effective tool for the diagnosis of cancer, we considered vascular endothelial growth factor A (VEGF-A) as a target marker protein. We also produced an aptamer heterodimer consisting of our previously derived aptamer (del5-1), which binds to the heparin-binding domain of VEGF, linked to V7t1. The resulting heterodimer bound strongly to VEGF(165) with a K(D) value of 4.7 x 10(2) pM."
Additional information: An FITC-labeled single-stranded DNA library containing a 24mer randomized region linked to 20mer primer-binding sequences at both ends through 3mer thymine- (T3-) linker (5′-CATGCTTACCTATAGTGAACttt(N24)tttCTTTGAGAACTGACTCATAC-3′) was used.
Reference (2010, Biosens Bioelectron ): Savory, N., Abe, K., Sode, K., & Ikebukuro, K. (2010). Selection of DNA aptamer against prostate specific antigen using a genetic algorithm and application to sensing. Biosensors & bioelectronics, 26(4), 1386–1391. https://doi-org.ezproxy.lib.utexas.edu/10.1016/j.bios.2010.07.057
Aptamer: PSap#4-4
Target: Prostate specific antigen (PSA)
Type of nucleic acid: ssDNA
Sequence: 5′CATGCTTACCTATAGTGAACtttCTGGTGTTTATTGTTTACTGTCCCtttCATGCTTACCTATAGTGAAC3′
Sequence length: 70
GC content: 0.3714285714285714
Affinity: Kd: "several tens of nM"
Pool type: 5′-CATGCTTACCTATAGTGAACttt-N24-tttCTTTGAGAACTGACTCATAC-3′
Pool random region: 24
Binding buffer/conditions: TBS buffer (10 mM Tris/HCl, 150 mM NaCl, 5 mM KCl, 5 mM MgCl2, pH 7.4)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: 33–34kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Although PSMA is one of novel biomarkers currently being investigated for the diagnosis of prostate cancer, PSMA has not been used in clinical practice yet. Thus, we focused on PSA in this study as a target protein of aptamer selection for its practical use as a molecular recognition element in biosensors."
Additional information: Post-selex screening of aptamers using genetic algorithms for improvement of affinity. An FITC-labeled single-stranded DNA library containing a 24mer randomized region linked to 20mer primer-binding sequences at both ends through 3mer thymine- (T3-) linker (5′-CATGCTTACCTATAGTGAACttt(N24)tttCTTTGAGAACTGACTCATAC-3′) was used.
Reference (2010, Biosens Bioelectron ): Savory, N., Abe, K., Sode, K., & Ikebukuro, K. (2010). Selection of DNA aptamer against prostate specific antigen using a genetic algorithm and application to sensing. Biosensors & bioelectronics, 26(4), 1386–1391. https://doi-org.ezproxy.lib.utexas.edu/10.1016/j.bios.2010.07.057
Aptamer: IBA 8
Target: (R)-ibuprofen
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGCGAACGACTTCATAAAATGCTATAAGGTTGCCCTCTGTCAGATAGTAAGTGCAATCT3′
Sequence length: 76
GC content: 0.3815789473684211
Affinity: Kd: 5.2 uM
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% Tween 20, pH 7.6
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection and Therapeutic: "Single stranded DNA aptamers that can bind to ibuprofen, a widely used anti-inflammation drug, were selected from random DNA library of 1015 nucleotides by FluMag-SELEX process. The affinity of five ssDNA aptamers isolated was in a range of 1.5–5.2 μM. In addition, all of these five aptamers did not show any affinity to analogues of ibuprofen in its profen’s group (fenoprofen, flubiprofen, and naproxen) and the antibiotics of oxytetracycline, another control."
Reference (2010, Bioorg Med Chem ): Kim, Y. S., Hyun, C. J., Kim, I. A., & Gu, M. B. (2010). Isolation and characterization of enantioselective DNA aptamers for ibuprofen. Bioorganic & medicinal chemistry, 18(10), 3467–3473. https://doi.org/10.1016/j.bmc.2010.03.074
Aptamer: 3XABA
Target: Anti-FLAG M2 antibody
Type of nucleic acid: ssDNA
Sequence: 5′GCGTCGACAAGCTTTCTAGATCGATTTCCTTAGTTGTCTTCCTTAGTTGTCTTCCTTAGTTGTCTTCCTTAGTGAGGAATTCGGATCCCTCGAGCG3′
Sequence length: 96
GC content: 0.4583333333333333
Affinity: Kd: 80 ± 7 nM
Pool type: 5′-GCGTCGACAAGCTTTCTAGA-N35-GAATTCGGATCCCTCGAGCG-3′
Pool random region: 35
Binding buffer/conditions: 1X binding buffer (4% glycerol, 1 mM MgCl2, 1 mM DTT, 50 mM NaCl, 10 mM Tris-HCl pH 7.5)
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: Therapuetic: " Using SELEX (systematic evolution of ligands by exponential enrichment), we serendipitously discovered a ssDNA aptamer that binds selectively to the anti-FLAG M2 antibody. These findings demonstrate the feasibility of using SELEX to develop ssDNA aptamers that block the function of a specific antibody, a capability that could lead to the development of novel therapeutic modalities for patients with systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases."
Reference (2011, J Nucleic Acids ): Lakamp, A. S., & Ouellette, M. M. (2011). A ssDNA Aptamer That Blocks the Function of the Anti-FLAG M2 Antibody. Journal of nucleic acids, 2011, 720798. https://doi.org/10.4061/2011/720798
Aptamer: CLN0020
Target: Fc-gamma receptor III (FcγRIII) (CD16α)
Type of nucleic acid: ssDNA
Sequence: 5′GGAGGGAAAAGTTATCAGGCCACTGCGGGGGTCTATACGTGAGGAAGAAGTGGGCAGGTCGATTAGTTTTGGAGTACTCGCTCC3′
Sequence length: 84
GC content: 0.5357142857142857
Affinity: Kd: 45 ± 28 nM
Pool type: 5′-GGAGGGAAAAGTTATCAGGC-N40-GATTAGTTTTGGAGTACTCGCTCC-3′
Pool random region: 40
Binding buffer/conditions: 200 μl of 0.05% BSA in DPBS
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: " Antibody-dependent cellular cytotoxicity plays a pivotal role in antibody-based tumor therapies and is based on the recruitment of natural killer cells to antibody-bound tumor cells via binding of the Fcγ receptor III (CD16). Here we describe the generation of chimeric DNA aptamers that simultaneously bind to CD16α and c-Met, a receptor that is overexpressed in many tumors. These results represent the first gain of a tumor-effective function of two distinct oligonucleotides by linkage into a bi-specific aptamer mediating cellular cytotoxicity."
Reference (2011, J Biol Chem ): Boltz, A., Piater, B., Toleikis, L., Guenther, R., Kolmar, H., & Hock, B. (2011). Bi-specific aptamers mediating tumor cell lysis. The Journal of biological chemistry, 286(24), 21896–21905. https://doi.org/10.1074/jbc.M111.238261
Aptamer: 16-1
Target: Small cell lung cancer (SCLC) cell lines (SBC3 cells)
Type of nucleic acid: ssDNA
Sequence: 5'ATACCAGCTTATTCAATTGAATCCTTCTTTGTCCCGGGCCCGTAGATAGTAAGTGCAATCT3'
Sequence length: 61
GC content: 0.4262295081967213
Affinity: Not reported
Pool type: 5'-ATACCAGCTTATTCAATT-N25-AGATAGTAAGTGCAATCT-3'
Pool random region: 25
Binding buffer/conditions: (0.1 mg mL−1 yeast tRNA, 1 mg mL−1 BSA, 4.5 g L−1glucose and 5 mM MgCl2 in phosphate buffered saline, pH 7.4
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: Detection: " We applied Systematic Evolution of Ligands by EXponential enrichment using Small Cell Lung Cancer (SCLC) cells. Our results showed that the DNA aptamer binds to molecules that exist predominantly on target SCLC cell surfaces compared with other types of SCLC cells."
Reference (2011, Analyst ): Kunii, T., Ogura, S., Mie, M., & Kobatake, E. (2011). Selection of DNA aptamers recognizing small cell lung cancer using living cell-SELEX. The Analyst, 136(7), 1310–1312. https://doi.org/10.1039/c0an00962h