RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: I-3
Target: Ff gene 5 protein (g5p)
Type of nucleic acid: ssDNA
Sequence: 5‘CGGGATCCAACGTTTTGGGGTCAGGCTGGGGTTGTGCAGGTCAAGAGGCAGAATTCGC3‘
Sequence length: 58
GC content: 0.5862068965517241
Affinity: Kωapp at 10 mM NaCl: 3.0 ± 0.7 (10-5 M-1)
Kωapp at 200 mM NaCl: >300 (10-5 M-1)
Pool type: 5‘-CGGGATCCAACGTTTT-N26-AAGAGGCAGAATTCGC-3‘
Pool random region: 26
Binding buffer/conditions: 200 mM NaCl at 37 °C for 15 min in TE buffer (10 mM Tris-HCl, pH 7.4, 1 mM EDTA)
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: Research: " We present the first application of SELEX using a cooperative ssDNA binding protein, the Ff g5p. The g5p binds with a large, positive cooperativity factor, ω, so that the protein tends to saturate all nucleic acid sequences. Nevertheless, our results show that the SELEX strategy can be used to efficiently select high-affinity ssDNA sequences. The gist of our results is that the initiation of cooperative binding, when the binding is least dependent on ω, can be very dependent on the ssDNA sequence and structure."
Reference (2001, Biochemistry ): Wen, J. D., & Gray, D. M. (2002). The Ff gene 5 single-stranded DNA-binding protein binds to the transiently folded form of an intramolecular G-quadruplex. Biochemistry, 41(38), 11438–11448. https://doi.org/10.1021/bi020276e
Aptamer: I-3c26
Target: Ff gene 5 protein (g5p)
Type of nucleic acid: ssDNA
Sequence: 5‘GGGGTCAGGCTGGGGTTGTGCAGGTC3'
Sequence length: 26
GC content: 0.6923076923076923
Affinity: Kωapp at 10 mM NaCl: 2.4 ± 0.2 (10-5 M-1)
Kωapp at 200 mM NaCl: 2.1 ± 0.1 (10-5 M-1)
Pool type: 5‘-CGGGATCCAACGTTTT-N26-AAGAGGCAGAATTCGC-3‘
Pool random region: 26
Binding buffer/conditions: 200 mM NaCl at 37 °C for 15 min in TE buffer (10 mM Tris-HCl, pH 7.4, 1 mM EDTA)
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated version of i-3 (removed primer region) to 26 nucleotides
Application as quoted in the referenced paper: Research: " We present the first application of SELEX using a cooperative ssDNA binding protein, the Ff g5p. The g5p binds with a large, positive cooperativity factor, ω, so that the protein tends to saturate all nucleic acid sequences. Nevertheless, our results show that the SELEX strategy can be used to efficiently select high-affinity ssDNA sequences. The gist of our results is that the initiation of cooperative binding, when the binding is least dependent on ω, can be very dependent on the ssDNA sequence and structure."
Reference (2001, Biochemistry ): Wen, J. D., & Gray, D. M. (2002). The Ff gene 5 single-stranded DNA-binding protein binds to the transiently folded form of an intramolecular G-quadruplex. Biochemistry, 41(38), 11438–11448. https://doi.org/10.1021/bi020276e
Aptamer: C2
Target: Disaccharide analogue of moenomycin A
Type of nucleic acid: 2'-amino-RNA
Sequence: 5'GGAGGUCGACCUCGCGCGAGGAGGGUGGAGGGUCGUAGAGCGCGUAGGAGG3'


Sequence length: 51
GC content: 0.7058823529411765
Affinity: Kd: 300 to 400 nM
Pool type: 5′-TCGGAGAGACAAGCTTGGGTC-N40-AGAAGAGAAAGAGAAGTTAATTAAGGATCCTCAC-3′
Pool random region: 40
Binding buffer/conditions: 20 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM MgCl2
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated of a4 rna clone omitting any terminal primer binding sites: no difference in the binding behaviour to immobilized moenomycin was detectable, indicating that the primer binding sites are not required for moenomycin complexation
Application as quoted in the referenced paper: Dectection and nhibition: " We have isolated aptamers that are capable of recognizing a disaccharide analogue of moenomycin A. This property should be useful as an analytical tool for the isolation of biogenetic precursors of moenomycin A from cultures of deletion mutants of Streptomyces ghanaensis that do not produce the full-length moenomycins."
Additional information: nuclease-resistant 2′-aminopyrimidine-modified RNA
Reference (2001, Bioorg Med Chem ): Schürer, H., Stembera, K., Knoll, D., Mayer, G., Blind, M., Förster, H. H., Famulok, M., Welzel, P., & Hahn, U. (2001). Aptamers that bind to the antibiotic moenomycin A. Bioorganic & medicinal chemistry, 9(10), 2557–2563. https://doi.org/10.1016/s0968-0896(01)00030-x
Aptamer: A6
Target: Disaccharide analogue of moenomycin A
Type of nucleic acid: 2'-amino-RNA
Sequence: 5'UCUAAUACGACUCACUAUAGGGAGAGACAAGCUUGGGUCUCAUCGGAGGAGCGGUGUGGUGAGGUGACGCGGAAAAGGUAGAAGAGAAAGAGAAGUUAAUUAAGGAUCCUCAC3′
Sequence length: 113
GC content: 0.4778761061946903
Affinity: Kd: 300 to 400 nM
Pool type: 5′-TCGGAGAGACAAGCTTGGGTC-N40-AGAAGAGAAAGAGAAGTTAATTAAGGATCCTCAC-3′
Pool random region: 40
Binding buffer/conditions: 20 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM MgCl2
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated of a4 rna clone omitting any terminal primer binding sites: no difference in the binding behaviour to immobilized moenomycin was detectable, indicating that the primer binding sites are not required for moenomycin complexation
Application as quoted in the referenced paper: Dectection and Inhibition: " We have isolated aptamers that are capable of recognizing a disaccharide analogue of moenomycin A. This property should be useful as an analytical tool for the isolation of biogenetic precursors of moenomycin A from cultures of deletion mutants of Streptomyces ghanaensis that do not produce the full-length moenomycins."
Additional information: nuclease-resistant 2′-aminopyrimidine-modified RNA
Reference (2001, Bioorg Med Chem ): Schürer, H., Stembera, K., Knoll, D., Mayer, G., Blind, M., Förster, H. H., Famulok, M., Welzel, P., & Hahn, U. (2001). Aptamers that bind to the antibiotic moenomycin A. Bioorganic & medicinal chemistry, 9(10), 2557–2563. https://doi.org/10.1016/s0968-0896(01)00030-x
Aptamer: Clone 5
Target: Sialyl Lewis X (sLeX)-expressing HL60 cells
Type of nucleic acid: ssRNA
Sequence: 5'CCGUAAUACGACUCACUAUAGGGGAGCUCGGUACCGAAUUCAAGGYACUCUGUGCUUGUCGAUGUGYAUUGAUGGCACUUUCGAGUCAACGAGUUGACAGRACAAGUAGUCAAGCUUUGCAGAGAGGAUCCUU3'
Sequence length: 130
GC content: 0.4662
Affinity: Kd: 0.085 nM and 3.3 nM via SPR
Pool type: 5'-CCGUAAUACGACUCACUAUAGGGGAGCUCGGUACCGAAUUC-N70-AAGCUUUGCAGAGAGGAUCCUU-3'
Pool random region: 70
Binding buffer/conditions: 150 mM NaCl, 20 mM Hepes (pH 7.4), 1 mMCaCl2, 1 mM MgCl2
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 RNA aptamer against the sLeX sugar was likely act as an inhibitor for the cell adhesion, as shown in this study. Specific inhibitors for cell adhesion mediated by selectin and sLeX is hoped to be an extremely useful therapeutic agents for chronic inflammation and cancer cell metastasis. High affinity sLeX -specific RNA aptamer that we presented in this paper might shed light on the development of a lead molecule for the cell adhesion blocking anti-inflammatory therapy"
Additional information: In sequence: Y = pyrimidine, R = purine. Static region obtained from pool
Reference (2001, Biochem Biophys Res Commun ): Jeong, S., Eom, T., Kim, S., Lee, S., & Yu, J. (2001). In vitro selection of the RNA aptamer against the Sialyl Lewis X and its inhibition of the cell adhesion. Biochemical and biophysical research communications, 281(1), 237–243. https://doi.org/10.1006/bbrc.2001.4327
Aptamer: cb28 aptamer
Target: Class I typical tetracyclins
Type of nucleic acid: ssRNA
Sequence: 5'GCAUGCUAAUACGACUCACUAUAGGAGCUCAGCCUUCACUGCUGCUUAAAGCCUAAAACAUACCAGAUCGCCACCCGCGCUUUAAUCUGGAGAGGUGAAGAAUUCGACCACCUAGGCUGCACCACAAGCUU3'
Sequence length: 131
GC content: 0.4961832061068702
Affinity: Kd: ~1 μM
Pool type: 5'-GCATGCGAGCTCAGCCTTCACTGCT-N74-CACCTAGGCTGCACCACAAGCTT-3'
Pool random region: 74
Binding buffer/conditions: 10 mM Tris–HCl pH 7.6, 5 mM MgCl2, 250 mM NaCl
Divalent salt: MgCl
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: Research: " Tetracycline is an antibiotic which inhibits prokaryotic translation by interfering with binding of the aminoacyl-tRNA to the ribosomal A-site.1,2 It is a widely used therapeutic agent of low toxicity, active against most common pathogens, which has also been used at subtherapeutic levels in animal feed to stimulate weight gain, as well as for prophylactic disease control. To study the mode of interaction of tetracycline with RNA, we isolated aptamers with high affinity to this antibiotic via in vitro selection."
Reference (2001, Bioorg Med Chem ): Berens, C., Thain, A., & Schroeder, R. (2001). A tetracycline-binding RNA aptamer. Bioorganic & medicinal chemistry, 9(10), 2549–2556. https://doi.org/10.1016/s0968-0896(01)00063-3
Aptamer: cb28 minimer
Target: Class I typical tetracyclins
Type of nucleic acid: ssRNA
Sequence: 5'GGCCUAAAACAUACCAGAUUUCGAUCUGGAGAGGUGAAGAAUUCGACCACCUAGGCCGGU3'
Sequence length: 60
GC content: 0.5
Affinity: Not reported
Pool type: 5'-GCATGCGAGCTCAGCCTTCACTGCT-N74-CACCTAGGCTGCACCACAAGCTT-3'
Pool random region: 74
Binding buffer/conditions: 10 mM Tris–HCl pH 7.6, 5 mM MgCl2, 250 mM NaCl
Divalent salt: MgCl
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: Research: " Tetracycline is an antibiotic which inhibits prokaryotic translation by interfering with binding of the aminoacyl-tRNA to the ribosomal A-site.1,2 It is a widely used therapeutic agent of low toxicity, active against most common pathogens, which has also been used at subtherapeutic levels in animal feed to stimulate weight gain, as well as for prophylactic disease control. To study the mode of interaction of tetracycline with RNA, we isolated aptamers with high affinity to this antibiotic via in vitro selection."
Additional information: Truncated from cb28 aptamer
Reference (2001, Bioorg Med Chem ): Berens, C., Thain, A., & Schroeder, R. (2001). A tetracycline-binding RNA aptamer. Bioorganic & medicinal chemistry, 9(10), 2549–2556. https://doi.org/10.1016/s0968-0896(01)00063-3
Aptamer: Tuda-2
Target: Tubulin purified, Calf brain
Type of nucleic acid: ssDNA
Sequence: 5′TAGGGAATTCGTCGTCGTCGACGGATCCGTTGGGCTACAGTACTTCCCCTTTTTTCTCTTCCTCCTTCCTATCGCTCTCCCTGCAGGTCGACGCATGCGCCG3′
Sequence length: 102
GC content: 0.5686274509803921
Affinity: Kd: 1.94×10−5 M
Pool type: 5′-TAGGGAATTCGTCGTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3′
Pool random region: 59
Binding buffer/conditions: 100 mM PIPES pH 6.9, 1 mM EGTA, 5 mM MgSO4, 100 mM NaCl
Buffer type: Other Buffers
pH: 6.9
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Acquisition of DNA aptamers that bind to tubulin using SELEX. Tubulin is the main component of microtubules, which are involvedin a variety of biological events such as intracellular transport, cellular motility, and construction of cytoskeletons.5 These cytoskeletal elements also act pivotal roles in mitotic spindle assembly and cell division. Numerous ligands that bind to tubulin and affect its assembly have been employedas anticancer drug candidates. Tubulin ligands have been also believed as useful probes for studying the structures of tubulin molecules."
Reference (2001, Bioorg Med Chem Lett ): Fukusaki, E., Hasunuma, T., Kajiyama, S., Okazawa, A., Itoh, T. J., & Kobayashi, A. (2001). SELEX for tubulin affords specific T-rich DNA aptamers. Systematic evolution of ligands by exponeential enrichment. Bioorganic & medicinal chemistry letters, 11(22), 2927–2930. https://doi.org/10.1016/s0960-894x(01)00584-4
Aptamer: III.1
Target: Endothelial regulatory protein pigpen (YPEN-1)
Type of nucleic acid: ssDNA
Sequence: 5'ATACCAGCTTATTCAATTAGGCGGTGCATTGTGGTTGGTAGTATACATGAGGTTTGGTTGAGACTAGTCGCAAGATATAGATAGTAAGTGCAATCT3'
Sequence length: 96
GC content: 0.3958333333333333
Affinity: Not reported
Pool type: 5′-ATACCAGCTTATTCAATT- N60-AGATAGTAAGTGCAATCT-3′
Pool random region: 60
Binding buffer/conditions: 50 mM Tris·HCl (pH 7.4), 5 mM KCl, 100 mM NaCl, 1 mM MgCl2, and 0.1% NaN3
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: 67-kDa 
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Applied Systematic Evolution ofLigands by EXponential enrichment (SELEX) against transformed endothelial cells as a complex target to select single-stranded DNA-ligands (aptamers) that function as histological markers to detect microvessels of rat experimental glioma, a fatal brain tumor that is highly vascularized."
Reference (2001, J Biol Chem ): Blank, M., Weinschenk, T., Priemer, M., & Schluesener, H. (2001). Systematic evolution of a DNA aptamer binding to rat brain tumor microvessels. selective targeting of endothelial regulatory protein pigpen. The Journal of biological chemistry, 276(19), 16464–16468. https://doi.org/10.1074/jbc.M100347200
Aptamer: ADR7
Target: Monocyte chemoattractant protein‐1 (MCP‐1)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′GGGAGGACGAUGCGGGAACUCACCGGGAAGAAGCCCGUUCCGUCACAGACAUGUUCCGCAUCGUCCUCCC3′
Sequence length: 70
GC content: 0.6285714285714286
Affinity: Kd: 180 pM
Pool type: 5′‐GGGAGGACGAUGCGG‐N40‐CCGCATCGTCCTCCC‐3′
Pool random region: 40
Binding buffer/conditions: SCHMK buffer (110 mM NaCl, 1 mM MgCl2, 20 mM HEPES pH 7.0, 1 mM CaCl2, 5 mM KCl)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Monocyte chemoattractant protein-1 (MCP-1) has been implicated as a powerful pro-inflammatory mediator and may represent a potentially important, therapeutic opportunity for treatment of inflammatory disease and atherosclerosis. To further investigate the role of MCP-1 in inflammatory disorders we have isolated a series of RNA aptamers that bind specifically to mouse MCP-1. The aptamers may be used as a tool to further investigate the role of MCP-1 in inflammatory disorders and may also have a role as a therapeutic agent."
Additional information: 2′-Fluoropyrimidine modified RNA containing a randomised region of 40 nucleotides was prepared by in vitro transcription from synthetic random DNA templates. 
Reference (2001, FEBS Lett ): Rhodes, A., Smithers, N., Chapman, T., Parsons, S., & Rees, S. (2001). The generation and characterisation of antagonist RNA aptamers to MCP-1. FEBS letters, 506(2), 85–90. https://doi.org/10.1016/s0014-5793(01)02895-2
Aptamer: ADR22
Target: Monocyte chemoattractant protein‐1 (MCP‐1)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′GGGAGGACGAUGCGGAAAAAUCUAGGCGCUGAAGCCCCGCUUCCUUACCUUCACCCGCAUCGUCCUCCC3′
Sequence length: 69
GC content: 0.6086956521739131
Affinity: Kd: 370 pM
Pool type: 5′‐GGGAGGACGAUGCGG‐N40‐CCGCATCGTCCTCCC‐3′
Pool random region: 40
Binding buffer/conditions: SCHMK buffer (110 mM NaCl, 1 mM MgCl2, 20 mM HEPES pH 7.0, 1 mM CaCl2, 5 mM KCl)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Monocyte chemoattractant protein-1 (MCP-1) has been implicated as a powerful pro-inflammatory mediator and may represent a potentially important, therapeutic opportunity for treatment of inflammatory disease and atherosclerosis. To further investigate the role of MCP-1 in inflammatory disorders we have isolated a series of RNA aptamers that bind specifically to mouse MCP-1. The aptamers may be used as a tool to further investigate the role of MCP-1 in inflammatory disorders and may also have a role as a therapeutic agent."
Additional information: 2′-Fluoropyrimidine modified RNA containing a randomised region of 40 nucleotides was prepared by in vitro transcription from synthetic random DNA templates. 
Reference (2001, FEBS Lett ): Rhodes, A., Smithers, N., Chapman, T., Parsons, S., & Rees, S. (2001). The generation and characterisation of antagonist RNA aptamers to MCP-1. FEBS letters, 506(2), 85–90. https://doi.org/10.1016/s0014-5793(01)02895-2
Aptamer: ODNs 93
Target: Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT)
Type of nucleic acid: ssDNA
Sequence: 5'CCCCTCGAGGTGATTTTGCTCAAGTGGGGGTGGGAGGAGGGTAGGCCTTAGGTTTCTGAAGTATCGCTAATCAGGCGGATA3'
Sequence length: 81
GC content: 0.5432098765432098
Affinity: Not reported
Pool type: 5'-CCCCTCGAGGTGATTTTGCTCAAGT-N35-AGTATCGCTAATCAGGCGGATA-3'
Pool random region: 35
Binding buffer/conditions: 50 mM Tris-HCl (pH 8.0), 6 mM Mg2+, and 10 mM dithiothreitol.
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 117 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " The DNA polymerase of the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is a target widely used to inhibit HIV-1 replication. In addition to the inhibition of HIV-1 RNase H observed in a cell free system, these ODNs were able to strongly diminish the infectivity of HIV-1 in human infected cells. Oligonucleotides described here may serve as leading compounds for the development of specific inhibitors of this key retroviral enzyme activity."
Reference (2001, Biochemistry ): Andreola, M. L., Pileur, F., Calmels, C., Ventura, M., Tarrago-Litvak, L., Toulmé, J. J., & Litvak, S. (2001). DNA aptamers selected against the HIV-1 RNase H display in vitro antiviral activity. Biochemistry, 40(34), 10087–10094. https://doi.org/10.1021/bi0108599
Aptamer: ODNs 112
Target: Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT)
Type of nucleic acid: ssDNA
Sequence: 5'CCCCTCGAGGTGATTTTGCTCAAGTCCAGTGGCGGGTGGGTGGGTGGTGGGGGGACTTGGAGTATCGCTAATCAGGCGGATA3'
Sequence length: 82
GC content: 0.5975609756097561
Affinity: Not reported
Pool type: 5'-CCCCTCGAGGTGATTTTGCTCAAGT-N35-AGTATCGCTAATCAGGCGGATA-3'
Pool random region: 35
Binding buffer/conditions: 50 mM Tris-HCl (pH 8.0), 6 mM Mg2+, and 10 mM dithiothreitol.
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: 117 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " The DNA polymerase of the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is a target widely used to inhibit HIV-1 replication. In addition to the inhibition of HIV-1 RNase H observed in a cell free system, these ODNs were able to strongly diminish the infectivity of HIV-1 in human infected cells. Oligonucleotides described here may serve as leading compounds for the development of specific inhibitors of this key retroviral enzyme activity."
Reference (2001, Biochemistry ): Andreola, M. L., Pileur, F., Calmels, C., Ventura, M., Tarrago-Litvak, L., Toulmé, J. J., & Litvak, S. (2001). DNA aptamers selected against the HIV-1 RNase H display in vitro antiviral activity. Biochemistry, 40(34), 10087–10094. https://doi.org/10.1021/bi0108599
Aptamer: TTA1
Target: Tenascin-C (TN-C) (Fibrinogen-like domain of TN-C)
Type of nucleic acid: 2'-fluoro/O-Me-RNA
Sequence: 5'GGGAGGGACGCGUCGCCGUAAUGGAUGUUUUGCUCCCUG3'
Sequence length: 39
GC content: 0.6153846153846154
Affinity: Kd: 5 × 10−9 M.
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: Aptamer TTA1, a truncated version of aptamer TN-9, was chosen to test species cross-reactivity. Nucleotides 10–26 have been deleted. The oligonucleotide is synthesized with a 3′–3′ linkage and a 5′ primary amine incorporated by phosphoramidite coupling. TTA1.NB is a nonbinding sequence that is identical to TTA1 except that it contains a deletion in which CCCUG-3′-3′-T is replaced by 3′-3′-T.
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: All pyrimidines are 2′-F and all purines are 2′-OCH3
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.ezproxy.lib.utexas.edu/10.1074/jbc.M104651200
Aptamer: Toggle-25
Target: Thrombin, Human and porcine
Type of nucleic acid: ssRNA
Sequence: 5‘GGGAGAGAGGAAGAGGGAUGGGGAACAAAGCUGAAGUACUUACCCAAGAUCAUCCCGAACGACAUAACCCAGAGGUCGAU3‘
Sequence length: 80
GC content: 0.5125
Affinity: Kd: (Human: 2.8 ± 0.7 nM, Porcine: 83 ± 3 pM)
Pool type: 5‘-GGGAGAGAGGAAGAGGGAUGGG-N40-CAUAACCCAGAGGUCGAU-3‘
Pool random region: 40
Binding buffer/conditions: 20 mM HEPES, pH 7.4, 150 mM NaCl, 2 mM CaCl2, and 0.01% BSA
Divalent salt: CaCl
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 and Diagnostic: "We describe an in vitro selection strategy in which RNA ligands (aptamers) that bind both human and porcine thrombin were selected by “toggling” the protein target between human and porcine thrombin during alternating rounds of selection. This strategy should facilitate the isolation of ligands with needed properties for gene therapy and other therapeutic and diagnostic applications."
Reference (2001, Mol Ther ): White, R., Rusconi, C., Scardino, E., Wolberg, A., Lawson, J., Hoffman, M., & Sullenger, B. (2001). Generation of Species Cross-reactive Aptamers Using “Toggle” SELEX. In Molecular Therapy (Vol. 4, Issue 6, pp. 567–573). Elsevier BV. https://doi.org/10.1006/mthe.2001.0495
Aptamer: 12 E4
Target: N6-adenine
Type of nucleic acid: ssRNA
Sequence: 5'GCGAAUUCGGAGAGGAUACUACACGUGAUAGGACGAUUAUCGAAAAUCACCAGAUUGGACCCUGGUUAACGAUCGGAAGCUUCUGCUACAUGCAAUGG3'
Sequence length: 98
GC content: 0.4693877551020408
Affinity: Kd: 10 μM
Pool type: 5′-CGGAAGCTTCTGCTACATGCAATGG-N50-CACGTGTAGTATCCTCTCCC-3′
Pool random region: 50
Binding buffer/conditions: 100 mM HEPES, 500 mM NaCl, 5 mM MgCl2, pH 7.3
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.3
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " RNA aptamers that are able to complex free adenine have been isolated by a SELEX (systematic evolution of ligands by exponential enrichment) procedure. Such binding is of great interest because the imidazole moiety is not trapped in the binding site, and would easily be available for catalytic activity."
Reference (2002, J Biol Chem ): Meli, M., Vergne, J., Décout, J. L., & Maurel, M. C. (2002). Adenine-aptamer complexes: a bipartite RNA site that binds the adenine nucleic base. The Journal of biological chemistry, 277(3), 2104–2111. https://doi.org/10.1074/jbc.M107130200