RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: m010
Target: Sphingosylphosphorylcholine (SPC)
Type of nucleic acid: ssRNA
Sequence: 5'GGAUCUACGAAUUCUACCGUUAUUGGUGUCACCGAAGAUCC3'
Sequence length: 41
GC content: 0.4634146341463415
Affinity: Kd: 252 ± 7.04 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: m012
Target: Sphingosylphosphorylcholine (SPC)
Type of nucleic acid: ssRNA
Sequence: 5'GGCGAAUUCUUCCGUUAUUGGAGCCAAGUCGCC3'
Sequence length: 33
GC content: 0.5454545454545454
Affinity: Kd: 196 ± 2.98 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: Two Arm
Target: Escherichia coli (E. coli) O157:H7
Type of nucleic acid: ssRNA
Sequence: 5'GGGAUACCAGCUUAUUCAAUUUGAUUCCAUCUUCCUGGACUGUCGAAAAUUCAGUAUCGGGAGGUUACGUAUUUGGUUUAUAGAUAGUAAGUGCAAUCU3'
Sequence length: 99
GC content: 0.3838383838383838
Affinity: Kd: 110 nM
Pool type: 5′-GGGAUACCAGCUUAUUCAAUU-N60-AGAUAGUAAGUGCAAUCU-3′
Pool random region: 60
Binding buffer/conditions: 200 ul (30 mM Tris-HCl, ph 7.5, 150 mM NaCl, 1.5 mM MgCl2, 2mM dithiothreitol, 1% BSA)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated to: 5'-gggtcttccthhacthtchaaaattcagtatcgggaggttacgtatttggtttatagatagtaa-3'
Application as quoted in the referenced paper: Diagnostic: " In this study, a RNA aptamer-based ligand which can specifically distinguish the pathogen E. coli O157:H7 from others was developed by a subtractive cell-SELEX method. This novel O157:H7-specific aptamer could be of potential application as a diagnostic ligand against the pathogen-related food borne illness."
Reference (2011, Biochem Biophys Res Commun ): Lee, Y. J., Han, S. R., Maeng, J. S., Cho, Y. J., & Lee, S. W. (2012). In vitro selection of Escherichia coli O157:H7-specific RNA aptamer. Biochemical and biophysical research communications, 417(1), 414–420. https://doi.org/10.1016/j.bbrc.2011.11.130
Aptamer: H1
Target: Hirame rhabdovirus (HIRRV)
Type of nucleic acid: ssRNA
Sequence: 5'GGUGUAUAGGUAUUGAAUCAAUUGUUUUAGCGUUGUCUUA3'
Sequence length: 40
GC content: 0.325
Affinity: Not reported
Pool type: 5′‐GGGCCAGGCAGCGAG-N40‐CCGACCACACGCGTCCGAGA‐3′
Pool random region: 40
Binding buffer/conditions: 2.5 mm MgCl2, 100 mm NaCl, 20 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: Therapeutic: " Here, we describe four Hirame rhabdovirus (HIRRV)-RNA aptamers (H1, H2, H3 and H4) that we obtained from an in vitro process called the systematic evolution of ligands by exponential enrichment (SELEX). The HIRRV-RNA aptamers specifically bind to HIRRV. Thus, the recombinant R. sulfidophilum might be a powerful tool for the prevention of HIRRV in aquaculture."
Reference (2012, J Fish Dis ): Hwang, S. D., Midorikawa, N., Punnarak, P., Kikuchi, Y., Kondo, H., Hirono, I., & Aoki, T. (2012). Inhibition of Hirame rhabdovirus growth by RNA aptamers. Journal of fish diseases, 35(12), 927–934. https://doi.org/10.1111/jfd.12000
Aptamer: N32
Target: N-glycolylneuraminic acid (Neu5Gc)
Type of nucleic acid: ssDNA
Sequence: 5'CATCTGCAGTGTGGCACCATGGGATCCGGGAGGGACGTTTTCTAGTACGGTCCGTTGGGTACGTGCTGAGCGTGAATTCGC3'
Sequence length: 81
GC content: 0.5802469135802469
Affinity: Kd: 6.49 nM
Pool type: 5′-CATCTGCAGTGTGGCACCATG-N40-CGTGCTGAGCGTGAATTCGC-3′
Pool random region: 40
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: Diagnostic: " The aptamers selected in this study will provide a novel analytical probe for the development of a biosensor to detect Neu5Gc in tissues and sera from patients with tumors as well as to detect Neu5Gc in animal-derived foods. In addition, the successful aptamer candidate can solve the problem that antibody is difficult to prepare in immunological assays. Thus, the discovery of novel aptamers specific for Neu5Gc is important for developing new methods of detecting Neu5Gc for the diagnosis and prevention of cancer as well as food poisoning."
Reference (2013, Biosens Bioelectron ): Gong, S., Ren, H. L., Tian, R. Y., Lin, C., Hu, P., Li, Y. S., Liu, Z. S., Song, J., Tang, F., Zhou, Y., Li, Z. H., Zhang, Y. Y., & Lu, S. Y. (2013). A novel analytical probe binding to a potential carcinogenic factor of N-glycolylneuraminic acid by SELEX. Biosensors & bioelectronics, 49, 547–554. https://doi.org/10.1016/j.bios.2013.05.024
Aptamer: anti-KpnI RNA Aptamer 24
Target: KpnI isoschizomer Acc65I
Type of nucleic acid: ssRNA
Sequence: 5'GGGAUAUCCUUCAUGGUGUGAUUAAACGUAAUCUCAAUCGAUCAUGCAUGAAGCGUUCCAUAUUUUU3'
Sequence length: 67
GC content: 0.373134328358209
Affinity: Kd: 28.7 ± 5.2 nM
Pool type: 5′-TA2TACGACTCACTATAG3ATATC2TC2ATGAT-N10-G-TA2-N9-ATCATGCATGA2GCGT2C2ATAT5-3'
Pool random region: 19
Binding buffer/conditions: Selection buffer for KpnI (10 mM HEPES pH 7.5, 100 mM NaCl, 1 mM CaCl2)
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection and Therapeutic: " Restriction endonucleases (REases) recognize and cleave short palindromic DNA sequences, protecting bacterial cells against bacteriophage infection by attacking foreign DNA. We are interested in the potential of folded RNA to mimic DNA, a concept that might be applied to inhibition of DNA-binding proteins. Anti-REase RNA aptamers could have value in studies of REase mechanism and may give clues to a code for designing RNAs that competitively inhibit DNA binding proteins including transcription factors."
Additional information: The structured RNA libraries (Figure ​(Figure1A)1A) used for selection were 67-nt in length with a potential tetraloop (GUAA) flanked by two random regions: 10 nt upstream and 9 nt downstream of the tetraloop. 

The synthetic DNA template for the selection pool was 5′-TA2TACGACTCACTATAG3ATATC2TC2ATGATN10G-TA2N9ATCATGCATGA2GCGT2C2ATAT5 where N indicates any base. Nucleotides in the random region were synthesized from a mixture of phosphoramidites adjusted for the relative coupling efficiency of each monomer. The library template was amplified by PCR using primers LJM-4485 5′-TA2TACGACTCACTATAG3ATATC2 and LJM-4486 5′A5TATG2A2CGCT2CATGCAT.
Reference (2015, Nucleic Acids Res ): Mondragón, E., & Maher, L. J. (2015). RNA aptamer inhibitors of a restriction endonuclease. Nucleic Acids Research, 43(15), 7544-7555. doi:10.1093/nar/gkv702
Aptamer: F4
Target: Soluble pleiotropic cytokine interleukin-6 receptor (sIL-6R) and interleukin-6 receptor domain 3 (IL-6R D3)
Type of nucleic acid: ssRNA
Sequence: 5'AAUGCGAAGAAAGAGGUCUGAGACAUUCUUAAAAACGGCCCAUCGUUUGGCRCUGUGGGAGUGGAGGGUGGAUGGUGUUAAGCGAUUCUUCUGGAGUUGACGUUGCUU3'
Sequence length: 107
GC content: 0.4859813084112149
Affinity: Kd: 34.8 ± 5.8 nM
Pool type: 5'-AATGCGAAGAAAGAGGTCTGAGACATTCT-N60-CTTCTGGAGTTGACGTTGCTT-3'
Pool random region: 60
Binding buffer/conditions: 1 × PBS (137 mM NaCl; 2.7 mM KCl; 6.5 mM Na2HPO4; 1.5 mM KH2PO4) supplemented with 3 mM MgCl2
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: Therapeutic: " Classic IL-6 signaling is believed to contribute to tissue regeneration and anti-inflammatory processes, whereas trans-signaling is considered to be mainly pro-inflammatory and plays a significant role in autoimmune and chronic inflammatory diseases as well as inflammation-driven cancers. Here we report the selection, characterization and post-selective modification of a 34 nucleotide (nt) RNA aptamer for a non-dominant, novel target site (domain 3) of the interleukin-6 receptor (IL-6R)."
Additional information: In the first 3 cycles of selection, immobilized sIL-6R was used to ensure enrichment of unmodified RNA aptamers that bind to the native soluble cytokine receptor. Domain 3 of the IL-6R was used as the target for 8 additional selection cycles, aiming at aptamers specific for this site of the receptor.
Reference (2015, RNA Biol ): Mittelberger, F., Meyer, C., Waetzig, G. H., Zacharias, M., Valentini, E., Svergun, D. I., Berg, K., Lorenzen, I., Grötzinger, J., Rose-John, S., & Hahn, U. (2015). RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity. RNA biology, 12(9), 1043–1053. https://doi.org/10.1080/15476286.2015.1079681
Aptamer: Ec3
Target: Escherichia coli (E.coli) DH5 alpha (DH5α)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'AUACCAGCUUAUUCAAUUGCACGAAUUUGCUGUGUUUUUGGGGGGGUCGGGGAGUAUAAGAUAGUAAGUGCAAUCU3'
Sequence length: 76
GC content: 0.4210526315789473
Affinity: Kd: 225 nM
Pool type: 5'-AUACCAGCUUAUUCAAUU-N40-AGAUAGUAAGUGCAAUCU-3'
Pool random region: 40
Binding buffer/conditions: 50 mM Tris pH7.4, 5 mM KCl, 100 mM NaCl, 1 mM MgCl2, 0.02% Tween 20, 0.1 mg/ml yeast tRNA and 1 mg/ml BSA
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: " Escherichia coli are important indicator organisms, used routinely for the monitoring of water and food safety. For quick, sensitive and real-time detection of E. coli we developed a 2'F modified RNA aptamer Ec3, by Cell-SELEX. We believe that our developed method can step towards more complex and real sample application."
Additional information: 2′F modified RNA aptamers
Reference (2016, Mol Cells ): Dua, P., Ren, S., Lee, S. W., Kim, J. K., Shin, H. S., Jeong, O. C., Kim, S., & Lee, D. K. (2016). Cell-SELEX Based Identification of an RNA Aptamer for Escherichia coli and Its Use in Various Detection Formats. Molecules and cells, 39(11), 807–813. https://doi.org/10.14348/molcells.2016.0167
Aptamer: E3 aptamer
Target: Prostate cancer cell line PC-3
Type of nucleic acid: ssRNA
Sequence: 5'GGGAGGACGAUGCGGGGCUUUCGGGCUUUCGGCAACAUCAGCCCCUCAGCCAUUUCUCCUACUGGGAUAGGUGGAUUAU3'
Sequence length: 79
GC content: 0.569620253164557
Affinity: Kd: 146-410 nM
Pool type: 5'-GGGAGGACGATGCGG-N40-ATTTCTCCTACTGGGATAGGTGGATTAT-3'
Pool random region: 40
Binding buffer/conditions: Hepes Buffered Saline with 1mM MgCl2,1mM CaCl2 and 2.7mM KCl
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " With the goal of developing an improved drug-targeting strategy, we turned to a new class of targeted anticancer therapeutics: aptamers conjugated to highly toxic chemotherapeutics. The E3 aptamer targets tumors in vivo and treatment with the MMAF-E3 conjugate significantly inhibits prostate cancer growth in mice, demonstrating the in vivo utility of aptamer-drug conjugates. Additionally, we report the use of antidotes to block E3 aptamer-drug conjugate cytotoxicity, providing a safety switch in the unexpected event of normal cell killing in vivo."
Reference (2018, Proc Natl Acad Sci U S A ): Powell Gray, B., Kelly, L., Ahrens, D. P., Barry, A. P., Kratschmer, C., Levy, M., & Sullenger, B. A. (2018). Tunable cytotoxic aptamer-drug conjugates for the treatment of prostate cancer. Proceedings of the National Academy of Sciences of the United States of America, 115(18), 4761–4766. https://doi.org/10.1073/pnas.1717705115
Aptamer: CEA A02
Target: Homo sapien - CEA
Type of nucleic acid: ssRNA
Sequence: 5'AUCGUUACCUUAGAAGCUUAACGGCAUGACCUAACCUGGAGGCGCAUCAGGAUCCGACACGACCCUAUAGUGAGUCGUAUUA3'
Sequence length: 82
GC content: 0.4878048780487805
Affinity: Kd: 156.0 nM
Pool type: 5'-ATCGTTACCTTAGAAGCTT-N30-GGATCCGACACGACCCTATAGTGAGTCGTATTA-3'
Pool random region: 30
Binding buffer/conditions: BSA 1mg/ml in Dulbecco's PBS without calcium and magnesium (pH 7.3), Mg2Cl 5mM, glucose 4.5g/L, Salmon Sperm DNA 0.1 mg/ml and yeast tRNA 0.1 mg/ml
Buffer type: PBS/phosphate buffers
pH: 7.3
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therpaeutic: " these novel RNA aptamers targeting gastrointestinal cancer biomarker CEA, CA50 and CA72-4 will aid further development and standardization of clinical diagnostic method with better sensitivity and specificity, and potentially future therapeutics development of gastric cancer. It is possible that such aptamers would become applicable in clinical applications or even therapeutics in the near future with better sensitivity and specificity, and without the limitations of immunoassays."
Reference (2018, PLoS One ): Pan, Q., Law, C., Yung, M., Han, K. C., Pon, Y. L., & Lau, T. (2018). Novel RNA aptamers targeting gastrointestinal cancer biomarkers CEA, CA50 and CA72-4 with superior affinity and specificity. PloS one, 13(10), e0198980. https://doi.org/10.1371/journal.pone.0198980
Aptamer: CA72-4 A02
Target: Homo sapien - CA72-4
Type of nucleic acid: ssRNA
Sequence: 5'AUCGUUACCUUAGAAGCUUCCCAAAAAGGAUUGGGGCGUCUGCAUGACCGGAUCCGACACGACCCUAUAGUGAGUCGUAUUA3'
Sequence length: 82
GC content: 0.4878048780487805
Affinity: Kd: 71.2 nM
Pool type: 5'-ATCGTTACCTTAGAAGCTT-N30-GGATCCGACACGACCCTATAGTGAGTCGTATTA-3'
Pool random region: 30
Binding buffer/conditions: BSA 1mg/ml in Dulbecco's PBS without calcium and magnesium (pH 7.3), Mg2Cl 5mM, glucose 4.5g/L, Salmon Sperm DNA 0.1 mg/ml and yeast tRNA 0.1 mg/ml
Buffer type: PBS/phosphate buffers
pH: 7.3
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therpaeutic: " these novel RNA aptamers targeting gastrointestinal cancer biomarker CEA, CA50 and CA72-4 will aid further development and standardization of clinical diagnostic method with better sensitivity and specificity, and potentially future therapeutics development of gastric cancer. It is possible that such aptamers would become applicable in clinical applications or even therapeutics in the near future with better sensitivity and specificity, and without the limitations of immunoassays."
Reference (2018, PLoS One ): Pan, Q., Law, C., Yung, M., Han, K. C., Pon, Y. L., & Lau, T. (2018). Novel RNA aptamers targeting gastrointestinal cancer biomarkers CEA, CA50 and CA72-4 with superior affinity and specificity. PloS one, 13(10), e0198980. https://doi.org/10.1371/journal.pone.0198980
Aptamer: TN29
Target: Triple-negative breast cancer (TNBC) cell line MDA-MB-234
Type of nucleic acid: ssRNA
Sequence: 5'UAGGGAAGAGAAGGACAUAUGAUCCUGCCCCAACCAUCGCUUCCUCGACGCGCGUUGUCGGCAUUGACUAGUACAUGACCACUUGA3'
Sequence length: 86
GC content: 0.5232558139534884
Affinity: Kd: 9.84 ± 1.63 by streptavidin-biotin colorimetric assay and 10.77 ± 2.41 by flow cytometric assay
Pool type: 5'-TAGGGAAGAGAAGGACATATGAT-N40-TTGACTAGTACATGACCACTTGA-3'
Pool random region: 40
Binding buffer/conditions: 0.3 M NaAc buffer containing 2 mM EDTA (Invitrogen)
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " These aptamers inhibit TNBC cell capacity of growing in vitro as mammospheres, indicating they could also act as anti-tumor agents. Therefore, our newly identified aptamers are a valuable tool for selectively dealing with TNBC. Further, these aptamers interfere with the TNBC cells’ capacity of growing in vitro as mammospheres, a feature associated with the malignant phenotype, thus indicating they could be employed as important anti-tumor agents. In addition to therapeutic utility, TNBC aptamers may be useful as specific probes for molecular imaging, thus increasing a repertoire that is currently extremely scarce."
Reference (2020, iScience ): Camorani, S., Granata, I., Collina, F., Leonetti, F., Cantile, M., Botti, G., Fedele, M., Guarracino, M. R., & Cerchia, L. (2020). Novel Aptamers Selected on Living Cells for Specific Recognition of Triple-Negative Breast Cancer. IScience, 23(4), 100979. https://doi.org/10.1016/j.isci.2020.100974
Aptamer: DUX4 aptamer
Target: Double homeobox protein 4 (DUX4)
Type of nucleic acid: ssRNA
Sequence: 5′AUCCAGAGUGACGCAGCUAACUUAAUCAACCGCAGGUUGAUUAGCCCAUUAGCUGGACACGGUGGCUUAGU3′
Sequence length: 71
GC content: 0.4929577464788732
Affinity: Kd: 20 nM
Pool type: 5′-ATCCAGAGTGACGCA-N45-TGGACACGGTGGCTTAGT-3′
Pool random region: 45
Binding buffer/conditions: 50 mM of Tris‐HCl pH 7.5, 150 mM of NaCl, 5 mM of MgCl2, 0.1% of BSA, and 0.1% of Triton X‐100
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: " The development of treatment strategies against FSHD and other DUX4‐mediated diseases might benefit from this study. We have shown that a bulge loop at a distinct position within the binding motif strongly increases the affinity of the aptamer. Specificity can be customized by small changes of the motif at non‐conserved regions with mild consequences on the affinity toward DUX4. Such sequence and structural alterations may improve the impact of current therapeutic strategies like transcription factor oligodeoxynucleotide decoys. In addition, the bulge loops can potentially act as platforms for chemical and biological modifications that could be conducive not only to study protein‐DNA interaction, but also for therapeutic purposes."
Reference (2020, FASEB J ): Klingler, C., Ashley, J., Shi, K., Stiefvater, A., Kyba, M., Sinnreich, M., Aihara, H., & Kinter, J. (2020). DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD. The FASEB Journal, 34(3), 4573–4590. https://doi.org/10.1096/fj.201902696
Aptamer: truncated C5C6
Target: C5 component of human complement (serum glycoprotein)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'CGAUGCGGUCUCAUGCGUCGAGUGUGAGUUUACCUUCG3'
Sequence length: 38
GC content: 0.5526315789473685
Affinity: Not reported
Pool type: 5'-GGGAGGACGATGCGG-N30-CAGACGACTCGCCCGA-3'
Pool random region: 30
Binding buffer/conditions: Phosphate-buffered saline containing 1 mM MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 210 kDa
Post-SELEX modifications: 38-mer truncated aptamer derived from c5c6 aptamer
Application as quoted in the referenced paper: Therapeutic: " The human and rat aptamers are being evaluated for complement inhibition in vitro and in vivo as potential therapeutics for treatment of human disease The selected C5 aptamer has the properties to make it useful as a therapeutic complement inhibitor: the aptamer inhibits both C5 pathways, and does not interfere with beneficial complement properties; the aptamer binds with low nanomolar affinity and gives total complement inhibition at a therapeutically feasible dose the aptamer is specific and does not interact with other proteins of the complement pathway; and the aptamer is made synthetically with advantages of scale and reproducibility difficult to achieve with culture systems."
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.
Reference (1999, Immunopharmacology ): Biesecker, G., Dihel, L., Enney, K., & Bendele, R. A. (1999). Derivation of RNA aptamer inhibitors of human complement C5. Immunopharmacology, 42(1-3), 219–230. https://doi.org/10.1016/s0162-3109(99)00020-x
Aptamer: A21
Target: Hemagglutinin (HA) glycoprotein; Influenza virus
Type of nucleic acid: ssDNA
Sequence: 5′AATTAACCCTCACTAAAGGGCGCTTATTTGTTCAGGTTGGGTCTTCCTATTATGGTCGAATAAGTTAA3′
Sequence length: 68
GC content: 0.3823529411764705
Affinity: Not reported
Pool type: 5′-AATTAACCCTCACTAAAGGG-N30-TATGGTCGAATAAGTTAA-3′
Pool random region: 30
Binding buffer/conditions: 50 mM Tris-HCl, pH 7.4, 5 mM KCl, 100 mM NaCl, 1 mM MgCl2, 100 μg tRNA, 0.2% bovine serum albumin
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Design of a novel molecule, comprising a ssDNA aptamer, which inhibits influenza infection by interfering with the virus-host cell interaction, via blocking of the receptor-binding region of the surface glycoprotein HA. This novel aptamer is therefore of interest, as it might be considered a suitable candidate for development as an alternative, selective inhibitory anti-influenza agent."
Additional information: The pool specifies N30 but is only 29nt long after the selection (39 contant region + 30 random regions was the anticipated result)
Reference (2004, J Biol Chem ): Jeon, S. H., Kayhan, B., Ben-Yedidia, T., & Arnon, R. (2004). A DNA aptamer prevents influenza infection by blocking the receptor binding region of the viral hemagglutinin. The Journal of biological chemistry, 279(46), 48410–48419. https://doi.org/10.1074/jbc.M409059200