RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: Apt-1.4
Target: Major urinary protein 13 (MUP13) (rat urine biomarker)
Type of nucleic acid: ssDNA
Sequence: 5'ATACCAGCTTATTCAATTGTCCACAAAATCCTTATTTTCCTTCATAGGTTACAATTGTACAATCGTAATCAGTTAG3'
Sequence length: 76
GC content: 0.3157894736842105
Affinity: Kd: 25 ± 7 nM
Pool type: 5‘-ATACCAGCTTATTCAATT–N40 –ACAATCGTAATCAGTTAG-3‘
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 5 mM KCl, 1 mM CaCl2
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: 18 kDa
Application as quoted in the referenced paper: Biomarker: " The assay showed that the aptamer could detect recombinant MUP13 spiked in filtered urine and the natural MUP13 in unfiltered urine, as a first step into translation to real world application. These are the first known assays to detect and quantify a MUP biomarker of rats."
Additional information: pool information: 76 bp- consisted of 76 bp oligonucleotides with a central random region flanked by two constant regions that acted as the primer binding sites. pool information was found in another paper doi: 10.1371/journal.pone.0134403

The Kd was obtained from Bead-based binding assay. The sequence of 1.4 and 2.5 aptamer is identical however, their secondary structure differ.
Reference (2022, Talanta ): Lucarelli, V., Colbert, D., Li, S., Cumming, M., Linklater, W., Mitchell, J., Travas-Sejdic, J., & Kralicek, A. (2022). Selection and characterization of DNA aptamers for the rat major urinary protein 13 (MUP13) as selective biorecognition elements for sensitive detection of rat pests. Talanta, 240, 123073. https://doi.org/10.1016/j.talanta.2021.123073
Aptamer: 44626
Target: The fluorophore in Green fluorescent protein (GFP) (Ser65-Tyr66-Gly67)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAGAUACGCUCUAGAAUUCAAUUGCAUGGUGGUCUGGGACAGACGUGUGGACGGCACACAGCGUGAGGCUUUGGUGGGUUAUGGCUGUCAUGCGAGAUAGCUCGAGCAAUGC3'
Sequence length: 114
GC content: 0.543859649122807
Affinity: KD: 406 nM
Pool type: 5ʼ-ATACGCTCTAGAATTCAATT-N70-AGATAGCTCGAGCAATGC-3ʼ
Pool random region: 70
Binding buffer/conditions: 40 mM HEPES pH 7.4 (or 40 mM Bicine pH 8.0), 125 mM KCl, 5 mM MgCl2, and 5% DMSO
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported 
Application as quoted in the referenced paper: Research and Biosensor: " An RNA-fluorophore complex resembling enhanced GFP (EGFP), termed Spinach, emits a green fluorescence comparable in brightness to fluorescent proteins. Spinach is markedly resistant to photobleaching, and Spinach fusion RNAs can be imaged in living cells. These RNA mimics of GFP provide an approach for genetic encoding of fluorescent RNAs. RNAs can be tagged with Spinach, providing a simple strategy for introducing a compact fluorescent tag for live cell imaging of RNAs, while avoiding the problems associated with current methods for tagging RNAs. Spinach is different from GFP in that it exhibits considerable resistance to photobleaching, and fluorescence is observed shortly after Spinach transcription in cells, which contrasts with the delay in acquisition of fluorescence by nascent GFP due to the requirement for fluorophore maturation"
Additional information: Purified single stranded DNA library was then used in a PCR reaction to gently amplify the library and to create double stranded DNA templates for RNA in vitro synthesis.
Reference (2011,Science ): Paige, J. S., Wu, K. Y., & Jaffrey, S. R. (2011). RNA mimics of green fluorescent protein. Science (New York, N.Y.), 333(6042), 642–646. https://doi.org/10.1126/science.1207339
Aptamer: E9P2-2
Target: Tenascin-C (TN-C) 
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGAGGACGAUGCGGUGCCCACUAUGCGUGCCGAAAAACAUUUCCCCCUCUACCCCAGACGACUCGCGCGA3'
Sequence length: 71
GC content: 0.6197183098591549
Affinity: Kd: 4 nM
Pool type: 5′-TCGCGCGAGTCGTCTG-40N-CCGCATCGTCCTCCC-3′
Pool random region: 40
Binding buffer/conditions: Dulbecco's phosphate-buffered saline with MgCl2 and CaCl2 (Life Technologies, Inc.) and 0.05% bovine serum albumin
Divalent salt: MgCl/CaCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 13 kDa
Post-SELEX modifications: Truncation: Family II aptamers E9P2-1 and E9P2-2 together represented 56% of the E9P2 pool. Thus, family II aptamers dominated the advanced pools and displayed high affinity for TN-C withKds of 1–10 × 10−9m.
Application as quoted in the referenced paper: Drug delivery: "targeted delivery of radioisotopes or chemical agents to diseased tissues.A size-minimized and nuclease-stabilized aptamer, TTA1, binds to the fibrinogen-like domain of TN-C with an equilibrium dissociation constant (Kd) of 5 × 10−9m. At 13 kDa, this aptamer is intermediate in size between peptides and single chain antibody fragments, both of which are superior to antibodies for tumor targeting because of their smaller size. TTA1 defines a new class of ligands that are intended for targeted delivery of radioisotopes or chemical agents to diseased tissues."
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 (2001,J Biol Chem): Hicke, B. J., Marion, C., Chang, Y. F., Gould, T., Lynott, C. K., Parma, D., Schmidt, P. G., & Warren, S. (2001). Tenascin-C aptamers are generated using tumor cells and purified protein. The Journal of biological chemistry, 276(52), 48644–48654. https://doi.org/10.1074/jbc.M104651200
Aptamer: C2
Target: Human transferrin receptor (hTfR), CD71 (TfR)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGAGGUGAAUGGUUCUACGAUUCAAACAUCUCACAGAUCAAUCCAAGGCACCUCGUUAAAGGACGACUCCCUUACAUGCGAGAUGACCACGU3'
Sequence length: 93
GC content: 0.4838709677419355
Affinity: Kd:17 nM
Pool type: 5′-GGGAGGTGAATGGTTCTACGAT-N50-TTACATGCGAGATGACCACGTAATTGAATTAAATGCCCGCCATGACCAG-3′
Pool random region: 50
Binding buffer/conditions: HBSS (Hank's Buffered Saline Solution; Invitrogen)
Buffer type: Not Reported
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Drug Delivery: "Selected aptamers were specific for the human receptor, rapidly endocytosed by cells and shared a common core structure. A minimized variant was found to compete with the natural ligand, transferrin, for receptor binding and cell uptake, but performed ~twofold better than it in competition experiments. Using this molecule, we generated aptamer-targeted siRNA-laden liposomes. Aptamer targeting enhanced both uptake and target gene knockdown in cells grown in culture when compared to nonmodified or nontargeted liposomes. The aptamer should prove useful as a surrogate for transferrin in many applications including cell imaging and targeted drug delivery."
Additional information: "The 2′F modification can be readily incorporated during transcription by substituting 2′F CTP and 2′F UTP instead of the natural CTP and UTP and using the mutant T7 RNA polymerase protein Y639F"
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..
"additional 3′ constant region used for hybridization of a fluorescent probe for flow cytometry"
Reference (2012,Mol Ther Nucleic Acids
): Wilner, S. E., Wengerter, B., Maier, K., de Lourdes Borba Magalhães, M., Del Amo, D. S., Pai, S., Opazo, F., Rizzoli, S. O., Yan, A., & Levy, M. (2012). An RNA alternative to human transferrin: a new tool for targeting human cells. Molecular therapy. Nucleic acids, 1(5), e21. https://doi.org/10.1038/mtna.2012.14
Aptamer: E07
Target: Human epidermal growth factor receptor (hEGFR)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGCGCUCCGACCUUAGUCUCUGUGCCGCUAUAAUGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCGGAACCGUGUAGCACAGCAGA3'
Sequence length: 93
GC content: 0.5268817204301075
Affinity: Kd: 2.4 ± 0.2 nM
Pool type: 5'-GGCGCTCCGACCTTAGTCTCTG-N62-GAACCGTGTAGCACAGCAGA-3′
Pool random region: 62
Binding buffer/conditions: 1X DPBS and 5 mM MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Therapeutic: "One of the selected aptamers, E07, bound tightly to the wild-type receptor (Kd = 2.4 nM). This aptamer can compete with EGF for binding, binds to a novel epitope on EGFR, and also binds a deletion mutant, EGFRvIII, that is commonly found in breast and lung cancers, and especially in grade IV glioblastoma multiforme, a cancer which has for the most part proved unresponsive to current therapies. The aptamer binds to cells expressing EGFR, blocks receptor autophosphorylation, and prevents proliferation of tumor cells in three-dimensional matrices. In short, the aptamer is a promising candidate for further development as an anti-tumor therapeutic. In addition, Aptamer E07 is readily internalized into EGFR-expressing cells, raising the possibility that it might be used to escort other anti-tumor or contrast agents."
Additional information: In vitro selection of anti-EGFR 2′-fluoropyrimidine RNA aptamers
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 (2011,PLoS One
): Li, N., Nguyen, H. H., Byrom, M., & Ellington, A. D. (2011). Inhibition of cell proliferation by an anti-EGFR aptamer. PloS one, 6(6), e20299. https://doi.org/10.1371/journal.pone.0020299
Aptamer: E07
Target: Mouse epidermal growth factor receptor (mEGFR)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGCGCUCCGACCUUAGUCUCUGUGCCGCUAUAAUGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCGGAACCGUGUAGCACAGCAGA3'
Sequence length: 93
GC content: 0.5268817204301075
Affinity: Kd: 36 ± 4 nM
Pool type: 5'-GGCGCTCCGACCTTAGTCTCTG-N62-GAACCGTGTAGCACAGCAGA-3′
Pool random region: 62
Binding buffer/conditions: 1X DPBS and 5 mM MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Therapeutic: "One of the selected aptamers, E07, bound tightly to the wild-type receptor (Kd = 2.4 nM). This aptamer can compete with EGF for binding, binds to a novel epitope on EGFR, and also binds a deletion mutant, EGFRvIII, that is commonly found in breast and lung cancers, and especially in grade IV glioblastoma multiforme, a cancer which has for the most part proved unresponsive to current therapies. The aptamer binds to cells expressing EGFR, blocks receptor autophosphorylation, and prevents proliferation of tumor cells in three-dimensional matrices. In short, the aptamer is a promising candidate for further development as an anti-tumor therapeutic. In addition, Aptamer E07 is readily internalized into EGFR-expressing cells, raising the possibility that it might be used to escort other anti-tumor or contrast agents."
Additional information: In vitro selection of anti-EGFR 2′-fluoropyrimidine RNA aptamers
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 (2011,PLoS One
): Li, N., Nguyen, H. H., Byrom, M., & Ellington, A. D. (2011). Inhibition of cell proliferation by an anti-EGFR aptamer. PloS one, 6(6), e20299. https://doi.org/10.1371/journal.pone.0020299
Aptamer: GL21.T
Target: Extracellular domain of AXL 
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′AUGAUCAAUCGCCUCAAUUCGACAGGAGGCUCAC3′
Sequence length: 34
GC content: 0.5
Affinity: Kd: 12 nmol/l
Pool type: Not Reported 
Pool random region: 45
Binding buffer/conditions: Not Reported 
Buffer type: Not Reported
Molecular weight of target: ~10 kDa
Post-SELEX modifications: Truncation: "designed a 34mer truncated version of the 92mer original molecule, named GL21.T, that contains the active site of GL21 and preserves high binding affinity to the U87MG cells"
Application as quoted in the referenced paper: Therapeutic:"We have thus generated and characterized a selective RNA-based aptamer, GL21.T that binds the extracellular domain of Axl at high affinity (12 nmol/l) and inhibits its catalytic activity. GL21.T blocked Axl-dependent transducing events in vitro, including Erk and Akt phosphorylation, cell migration and invasion, as well as in vivo lung tumor formation in mice xenografts. In this respect, the GL21.T aptamer represents a promising therapeutic molecule for Axl-dependent cancers whose importance is highlighted by the paucity of available Axl-specific inhibitory molecules."
Reference (2012,Mol Ther
): Cerchia, L., Esposito, C. L., Camorani, S., Rienzo, A., Stasio, L., Insabato, L., Affuso, A., & de Franciscis, V. (2012). Targeting Axl with an high-affinity inhibitory aptamer. Molecular therapy : the journal of the American Society of Gene Therapy, 20(12), 2291–2303. https://doi.org/10.1038/mt.2012.163
Aptamer: ΔPSap4#5
Target: Prostate specific antigen (PSA)
Type of nucleic acid: ssDNA
Sequence: 5'TTTTTAATTAAAGCTCGCCATCAAATAGCTTT3'
Sequence length: 32
GC content: 0.28125
Affinity: Kd: "ΔPSap4#5 showed the highest PSA-binding ability and it was 48-fold higher than that of the parent oligonucleotide", (parent's 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: This is a truncated fourth generation sequence from the original PSap4#5 (100-00-800) aptamer.
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."
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