RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: pe35
Target: L-Tyrosinamide
Type of nucleic acid: ssDNA
Sequence: 5'AATTCGCTAGCTGGAGCTTGGATTGATGTGGTGTGTGAGTGCGGTGCCC3'
Sequence length: 49
GC content: 0.5510204081632653
Affinity: Kd: 45±4 μM
Pool type: 5'-CGTACGGAATTCGCTAGC-N60-GGATCCGAGCTCCACGTG-3'
Pool random region: 60
Binding buffer/conditions: Tris 20 mM, pH 7.6, NaCl 300 mM and MgCl2 5 mM
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: The paper does not state the static regions were removed from the original aptamer, however the reported sequence untilized in the kd determination was the random region only. We have reported the seqeunce utilized in the kd determination.
Application as quoted in the referenced paper: Biosensor: " We have applied SELEX (Systematic Evolution of Ligands by Exponential enrichment), a combinatorial method that employs biopolymers for drug discovery, to identify single stranded DNA sequences able to bind l-Tyrosinamide, a simple mimic of Tyrosine, an amino acid essential to the catalytic activity of several enzymes of pharmaceutical interest."
Reference (2001, Bioorg Med Chem ): Vianini, E., Palumbo, M., & Gatto, B. (2001). In vitro selection of DNA aptamers that bind L-tyrosinamide. Bioorganic & medicinal chemistry, 9(10), 2543–2548. https://doi.org/10.1016/s0968-0896(01)00054-2
Aptamer: pe38
Target: L-Tyrosinamide
Type of nucleic acid: ssDNA
Sequence: 5'AATTCGCTAGCCGAGCAGACGGCGTACGGAATTCGAGCTCGGTACCCGGGGATCC3'
Sequence length: 55
GC content: 0.6181818181818182
Affinity: Kd: 760±21 μM
Pool type: 5'-CGTACGGAATTCGCTAGC-N60-GGATCCGAGCTCCACGTG-3'
Pool random region: 60
Binding buffer/conditions: Tris 20 mM, pH 7.6, NaCl 300 mM and MgCl2 5 mM
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: The paper does not state the static regions were removed from the original aptamer, however the reported sequence untilized in the kd determination was the random region only. We have reported the seqeunce utilized in the kd determination.
Application as quoted in the referenced paper: Biosensor: " We have applied SELEX (Systematic Evolution of Ligands by Exponential enrichment), a combinatorial method that employs biopolymers for drug discovery, to identify single stranded DNA sequences able to bind l-Tyrosinamide, a simple mimic of Tyrosine, an amino acid essential to the catalytic activity of several enzymes of pharmaceutical interest."
Reference (2001, Bioorg Med Chem ): Vianini, E., Palumbo, M., & Gatto, B. (2001). In vitro selection of DNA aptamers that bind L-tyrosinamide. Bioorganic & medicinal chemistry, 9(10), 2543–2548. https://doi.org/10.1016/s0968-0896(01)00054-2
Aptamer: aptamer A.2
Target: Nonstructural 5B (NS5B) polymerase, hepatitis C virus (HCV) NS5BΔC55 protein
Type of nucleic acid: ssRNA
Sequence: 5'GGGAUGCUUCGGCAUCCCAGUCGAUGCGUAUCGCAGACUAUGUGGCUUCGGCCGUUGGAGUUGGUACCGCUUCGGCGGUACGUAAGCUUGGG3'
Sequence length: 92
GC content: 0.5978260869565217
Affinity: Kd: 16 ± 1.6 nM
Pool type: 5'-GGGAUGCUUCGGCAUCCC-N25-GGCUUCGGCC-N10-GUACCGCUUCGGCGGUACGTAAGCTTGGG-3'
Pool random region: 35
Binding buffer/conditions: 50 mM Tris-Cl (pH 7.5)-100 mM KCl-50 mM NaCl-5 mM MgCl2 (5B-selection buffer)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: 66 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Experiments are in progress to test whether the B.2 RNA is able to affect NS5B activity in cells supporting subgenomic replication. This possibility would open up a new experimental avenue for identifying vital functional domains of the HCV polymerase by genetic approaches and could also provide an alternative approach for HCV therapy."
Reference (2002, J Virol ): Biroccio, A., Hamm, J., Incitti, I., De Francesco, R., & Tomei, L. (2002). Selection of RNA aptamers that are specific and high-affinity ligands of the hepatitis C virus RNA-dependent RNA polymerase. Journal of virology, 76(8), 3688–3696. https://doi.org/10.1128/jvi.76.8.3688-3696.2002
Aptamer: aptamer B.2
Target: Nonstructural 5B (NS5B) polymerase, hepatitis C virus (HCV) NS5BΔC55 protein
Type of nucleic acid: ssRNA
Sequence: 5'GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG3'
Sequence length: 92
GC content: 0.6739130434782609
Affinity: Kd: 1.5 ± 0.2 nM
Pool type: 5'-GGGAUGCUUCGGCAUCCC-N25-GGCUUCGGCC-N10-GUACCGCUUCGGCGGUACGTAAGCTTGGG-3'
Pool random region: 35
Binding buffer/conditions: 50 mM Tris-Cl (pH 7.5)-100 mM KCl-50 mM NaCl-5 mM MgCl2 (5B-selection buffer)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: 66 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Experiments are in progress to test whether the B.2 RNA is able to affect NS5B activity in cells supporting subgenomic replication. This possibility would open up a new experimental avenue for identifying vital functional domains of the HCV polymerase by genetic approaches and could also provide an alternative approach for HCV therapy."
Reference (2002, J Virol ): Biroccio, A., Hamm, J., Incitti, I., De Francesco, R., & Tomei, L. (2002). Selection of RNA aptamers that are specific and high-affinity ligands of the hepatitis C virus RNA-dependent RNA polymerase. Journal of virology, 76(8), 3688–3696. https://doi.org/10.1128/jvi.76.8.3688-3696.2002
Aptamer: aptamer B.3
Target: Nonstructural 5B (NS5B) polymerase, hepatitis C virus (HCV) NS5BΔC55 protein
Type of nucleic acid: ssRNA
Sequence: 5'GGGAUGCUUCGGCAUCCCGCUCUGGGCCGAAUAUGGACCACGUGGCUUCGGCCGCCAGCUCGUGUACCGCUUCGGCGGUACGUAAGCUUGGG3'
Sequence length: 92
GC content: 0.6521739130434783
Affinity: Kd: 10 ± 1.6 nM
Pool type: 5'-GGGAUGCUUCGGCAUCCC-N25-GGCUUCGGCC-N10-GUACCGCUUCGGCGGUACGTAAGCTTGGG-3'
Pool random region: 35
Binding buffer/conditions: 50 mM Tris-Cl (pH 7.5)-100 mM KCl-50 mM NaCl-5 mM MgCl2 (5B-selection buffer)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: 66 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Experiments are in progress to test whether the B.2 RNA is able to affect NS5B activity in cells supporting subgenomic replication. This possibility would open up a new experimental avenue for identifying vital functional domains of the HCV polymerase by genetic approaches and could also provide an alternative approach for HCV therapy."
Reference (2002, J Virol ): Biroccio, A., Hamm, J., Incitti, I., De Francesco, R., & Tomei, L. (2002). Selection of RNA aptamers that are specific and high-affinity ligands of the hepatitis C virus RNA-dependent RNA polymerase. Journal of virology, 76(8), 3688–3696. https://doi.org/10.1128/jvi.76.8.3688-3696.2002
Aptamer: aptamer B.2 SLII
Target: Nonstructural 5B (NS5B) polymerase, hepatitis C virus (HCV) NS5BΔC55 protein
Type of nucleic acid: ssRNA
Sequence: 5'CGAAGCCGCGCUAUGGACCAGUGGCGCGGCUUCG3'
Sequence length: 34
GC content: 0.7058823529411765
Affinity: Kd: >>200 nM
Pool type: 5'-GGGAUGCUUCGGCAUCCC-N25-GGCUUCGGCC-N10-GUACCGCUUCGGCGGUACGTAAGCTTGGG-3'
Pool random region: 35
Binding buffer/conditions: 50 mM Tris-Cl (pH 7.5)-100 mM KCl-50 mM NaCl-5 mM MgCl2 (5B-selection buffer)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: 66 kDa
Post-SELEX modifications: Insertion of bases (gc) and deletion of last 13 bases
Application as quoted in the referenced paper: Detection: " Experiments are in progress to test whether the B.2 RNA is able to affect NS5B activity in cells supporting subgenomic replication. This possibility would open up a new experimental avenue for identifying vital functional domains of the HCV polymerase by genetic approaches and could also provide an alternative approach for HCV therapy."
Reference (2002, J Virol ): Biroccio, A., Hamm, J., Incitti, I., De Francesco, R., & Tomei, L. (2002). Selection of RNA aptamers that are specific and high-affinity ligands of the hepatitis C virus RNA-dependent RNA polymerase. Journal of virology, 76(8), 3688–3696. https://doi.org/10.1128/jvi.76.8.3688-3696.2002
Aptamer: SA19 Aptamer
Target: Streptavidin (SA)
Type of nucleic acid: ssRNA
Sequence: 5'AAUUAACCCUCACUAAAGGGAACUGUUGUGAGUCUCAUGUCGAACUUUCCUAGCGCACAUGCGACCUCUAUGCGUAAUACGAACGUUGACGGUUUGAGCGUCUAGUCUUGUCU3'
Sequence length: 113
GC content: 0.4601769911504424
Affinity: Kd: 7 ± 1.8 nM
Pool type: 5'-AATTAACCCTCACTAAAGGGAACTGTTGTGAGTCTCATGTCGAA-N49-TTGAGCGTCTAGTCTTGTCT-3'
Pool random region: 49
Binding buffer/conditions: 20 mM HEPES–NaOH pH 7.5, 100 mM NaCl, 50 mM KCl, 10 mM MgCl2
Divalent salt: MgCl
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: " We describe the isolation of 2′-Fluoro (2′-F)-substituted RNA aptamers that bind to SA with an affinity comparable with the peptide aptamers described above. We go on to show that our SA-binding aptamers can be used to exploit the specificity of other RNA ligands in general protein capture and detection systems, by generating hetero-bi-functional ligands through the interaction of complementary adapter sequences."
Reference (2002, Nucleic Acids Res ): Tahiri-Alaoui, A., Frigotto, L., Manville, N., Ibrahim, J., Romby, P., & James, W. (2002). High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands. Nucleic acids research, 30(10), e45. https://doi.org/10.1093/nar/30.10.e45
Aptamer: DP3
Target: Neuropeptide Y (NPY)
Type of nucleic acid: ssRNA
Sequence: 5′UCGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC3′
Sequence length: 91
GC content: 0.5714285714285714
Affinity: Kd: 0.37 μM
Pool type: 5′-TCGGAGAAAGGGAAGCTTGAG-N40-AGAAGAAGGAACGAGCGTACGGATCCGATC-3′
Pool random region: 40
Binding buffer/conditions: PBS binding buffer (Invitrogen, 155 mM NaCl, 1.1 mMKH2PO4, 3 mMNa2HPO4·7H2O, 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: " We describe here two main classes of novel 2′-amino-2′-deoxypyrimidine-modified RNA aptamers that bind to neuropeptide Y with affinities between 370 and 470 nm. These binding affinities compare well with other in vitroselections performed with peptide targets."
Reference (2002, J Biol Chem ): Proske, D., Höfliger, M., Söll, R. M., Beck-Sickinger, A. G., & Famulok, M. (2002). A Y2 receptor mimetic aptamer directed against neuropeptide Y. The Journal of biological chemistry, 277(13), 11416–11422. https://doi.org/10.1074/jbc.M109752200
Aptamer: W2
Target: Complement 5 protein (C5 protein)
Type of nucleic acid: ssRNA
Sequence: 5'CGUCCCUUCGCAACCCUUUAAGACUUGGGACCCUGCUCUU3'
Sequence length: 40
GC content: 0.55
Affinity: Kd: 3.6 nM
Pool type: 5'-GUCCC-N20-GGGAC-3'
Pool random region: 20
Binding buffer/conditions: 20 mM K±HEPES, pH 8.0, 400 mM NH4OAc, 10 mM Mg(OAc)2, 0.01% (v/v) Nonidet P-40 and 5% glycerol
Buffer type: Other Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " The characterization of RNA aptamers binding to C5 protein is a starting point towards understanding its function as an RNA-binding protein. Elucidating the RNA-binding mechanism of C5 protein would provide a molecular basis for explaining the effects of the protein on RNase P function. In addition, this RNA motif may be used as an artificial inhibitor of bacterial RNase P."
Reference (2002, Nucleic Acids Res ): Lee, J. H., Kim, H., Ko, J., & Lee, Y. (2002). Interaction of C5 protein with RNA aptamers selected by SELEX. Nucleic acids research, 30(24), 5360–5368. https://doi.org/10.1093/nar/gkf694
Aptamer: RNA7
Target: Release factor 1 (RF1), Thermus thermophilus (T. thermophilus)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAGAGGAUACUACACGUGGAAAGCUGAAAGUGAACGGAGUAUCACAGAGAACCCGGAAAAGUGGAGCCAUUGCAUGUAGCAGAAGCUUCCG3'
Sequence length: 93
GC content: 0.5053763440860215
Affinity: Kd: 2 x 10^-5 M
Pool type: 5'-GGGAGAGGAUACUACACGUG-N50-CCAUUGCAUGUAGCAGAAGCUUCCG-3'
Pool random region: 50
Binding buffer/conditions: 50 mM Tris^HCl, pH 7.5, 50 mM NaCl and 7 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: Research: " Specific inhibition of RF1 by RF1 aptamers leads to increased efficiency of read-through of mRNA amber codons during in vitro translation. This effect may be of particular interest in all cases where increased efficiency of suppression is desirable, e.g. to facilitate incorporation of unnatural amino acids into protein via suppression of non-sense codons"
Reference (2002, FEBS Lett ): Szkaradkiewicz, K., Nanninga, M., Nesper-Brock, M., Gerrits, M., Erdmann, V. A., & Sprinzl, M. (2002). RNA aptamers directed against release factor 1 from Thermus thermophilus. FEBS letters, 514(1), 90–95. https://doi.org/10.1016/s0014-5793(02)02308-6
Aptamer: SE RNA #1
Target: Nuclear factor of activated T cells NFATc DNA binding domain (DBD)
Type of nucleic acid: ssRNA
Sequence: 5′GGGAGAGCGGAAGCGUGCUGGGCCUCUGUUCCCAAGGGAAUACYGGUCGUGUUGGAUCAGGUUGGCAUAACCCAGAGGUCGAUGGAUCCCCCC3′
Sequence length: 92
GC content: 0.6086956521739131
Affinity: Kd: 30 nM
Pool type: 5′-GGGAGAGCGGAAGCGUGCUGGGCC-N41-CAUAACCCAGAGGUCGAUGGAUCCCCCC-3′
Pool random region: 41
Binding buffer/conditions: 30 mM Tris–HCl, pH 7.5, 150 mM NaCl, 1.5 mM MgCl2, 2 mM dithiothreitol, and 1% BSA
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 " and Inhibition: We have recently shown that in vitro selected RNA aptamers to autoantibodies could be utilized as potent agents against autoimmune diseases by blocking the binding of antibodies to their self-antigens. Therefore, RNA molecules directed against NFAT could be potential candidates to act as specific and effective immunosuppressors."
Reference (2002, Biochem Biophys Res Commun ): Bae, S. J., Oum, J. H., Sharma, S., Park, J., & Lee, S. W. (2002). In vitro selection of specific RNA inhibitors of NFATc. Biochemical and biophysical research communications, 298(4), 486–492. https://doi.org/10.1016/s0006-291x(02)02490-7
Aptamer: xPSM-A9
Target: Prostate-specificmembrane antigen (PSMA) of prostate cancer cells
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGAGGACGAUGCGGACCGAAAAAGACCUGACUUCUAUACUAAGUCUACGUUCCCAGACGACUCGCCCGA3'
Sequence length: 70
GC content: 0.5428571428571428
Affinity: Ki: 2.1 nM
Pool type: 5′-GGGAGGACGAUGCGG-40N-CAGACGACUCGCCCGA-3'
Pool random region: 40
Binding buffer/conditions: HBSMCIT [HBSMC [HEPES buffered saline (pH 7.4), 1 mm MgCl2, and 1 mm CaCl2], 0.01% I-block (Tropix Inc., Bedford, MA), and 0.05% Tween 20]
Divalent salt: MgCl/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: " These are the first reported RNA aptamers selected to bind a tumor-associated membrane antigen and the first application of RNA aptamers to a prostate specific cell marker. These aptamers may be used clinically as NAALADase inhibitors or be modified to carry imaging agents and therapeutic agents directed to prostate cancer cells."
Additional information: pool modified with 2′F-CTP, 2′F-UTP, ATP, GTP. 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 (2002, Cancer Res ): Lupold, S. E., Hicke, B. J., Lin, Y., & Coffey, D. S. (2002). Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer research, 62(14), 4029–4033.
Aptamer: xPSM-A10
Target: Prostate-specificmembrane antigen (PSMA) of prostate cancer cells
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′GGGAGGACGAUGCGGAUCAGCCAUGUUUACGUCACUCCUUGUCAAUCCUCAUCGGCAGACGACUCGCCCGA3'
Sequence length: 71
GC content: 0.5774647887323944
Affinity: Ki: 11.9 nM
Pool type: 5′-GGGAGGACGAUGCGG-40N-CAGACGACUCGCCCGA-3'
Pool random region: 40
Binding buffer/conditions: HBSMCIT [HBSMC [HEPES buffered saline (pH 7.4), 1 mm MgCl2, and 1 mm CaCl2], 0.01% I-block (Tropix Inc., Bedford, MA), and 0.05% Tween 20]
Divalent salt: MgCl/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: " These are the first reported RNA aptamers selected to bind a tumor-associated membrane antigen and the first application of RNA aptamers to a prostate specific cell marker. These aptamers may be used clinically as NAALADase inhibitors or be modified to carry imaging agents and therapeutic agents directed to prostate cancer cells."
Additional information: pool modified with 2′F-CTP, 2′F-UTP, ATP, GTP. 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 (2002, Cancer Res ): Lupold, S. E., Hicke, B. J., Lin, Y., & Coffey, D. S. (2002). Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer research, 62(14), 4029–4033.
Aptamer: bU118
Target: C8-linked ATP agarose
Type of nucleic acid: ssRNA
Sequence: 5′GGGAAAAGCGAAUCAUACACAAGACUUAGGAGGAAGAAACUGCACAAUACACAGAUCACGCGAAAGGAUAAUGCGUUCUGCGGAUUGUGGGCCUGGGCAUAAGGUAUUUAAUUCCAUA3′
Sequence length: 118
GC content: 0.4406779661016949
Affinity: Not reported
Pool type: 5′-GGGAAAAGCGAAUCAUACACAAGA-70N-GGGCAUAAGGUAUUUAAUUCCAUA-3′
Pool random region: 70
Binding buffer/conditions: 50 mM Bis–Tris pH 6.4, 200 mM NaCl, 10 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 6.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " The borano group plays an essential role, as yet undefined, in target recognition or RNA structure. We conclude that the bG and bU nucleotides are fully compatible with SELEX, and that these analogs could be used to make boronated aptamers as therapeutics for BNCT."
Reference (2002, Nucleic Acids Res ): Lato, S. M., Ozerova, N. D., He, K., Sergueeva, Z., Shaw, B. R., & Burke, D. H. (2002). Boron-containing aptamers to ATP. Nucleic acids research, 30(6), 1401–1407. https://doi.org/10.1093/nar/30.6.1401
Aptamer: bU320
Target: C8-linked ATP agarose
Type of nucleic acid: ssRNA
Sequence: 5′GGGAAAAGCGAAUCAUACACAAGAGCAAUCUUGUUAACGGUGGAGGACGUAUGAAGGAAACUUAGGAAUCCCUGGUCCACGAAUCUGACCGUGUGGGCAUAAGGUAUUUAAUUCCAUA3′
Sequence length: 118
GC content: 0.4406779661016949
Affinity: Not reported
Pool type: 5′-GGGAAAAGCGAAUCAUACACAAGA-70N-GGGCAUAAGGUAUUUAAUUCCAUA-3′
Pool random region: 70
Binding buffer/conditions: 50 mM Bis–Tris pH 6.4, 200 mM NaCl, 10 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 6.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " The borano group plays an essential role, as yet undefined, in target recognition or RNA structure. We conclude that the bG and bU nucleotides are fully compatible with SELEX, and that these analogs could be used to make boronated aptamers as therapeutics for BNCT."
Reference (2002, Nucleic Acids Res ): Lato, S. M., Ozerova, N. D., He, K., Sergueeva, Z., Shaw, B. R., & Burke, D. H. (2002). Boron-containing aptamers to ATP. Nucleic acids research, 30(6), 1401–1407. https://doi.org/10.1093/nar/30.6.1401
Aptamer: bU321
Target: C8-linked ATP agarose
Type of nucleic acid: ssRNA
Sequence: 5′GGGAAAAGCGAAUCAUACACAAGAAAGAACGUGAUGAAACGGUAACCAUAUCGCGUGCUCAAACUACAACGGAAAAUGAGGAGGAACGUGCUCAUGGGCAUAAGGUAUUUAAUUCCAUA3′
Sequence length: 119
GC content: 0.4201680672268907
Affinity: Not reported
Pool type: 5′-GGGAAAAGCGAAUCAUACACAAGA-70N-GGGCAUAAGGUAUUUAAUUCCAUA-3′
Pool random region: 70
Binding buffer/conditions: 50 mM Bis–Tris pH 6.4, 200 mM NaCl, 10 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 6.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " The borano group plays an essential role, as yet undefined, in target recognition or RNA structure. We conclude that the bG and bU nucleotides are fully compatible with SELEX, and that these analogs could be used to make boronated aptamers as therapeutics for BNCT."
Reference (2002, Nucleic Acids Res ): Lato, S. M., Ozerova, N. D., He, K., Sergueeva, Z., Shaw, B. R., & Burke, D. H. (2002). Boron-containing aptamers to ATP. Nucleic acids research, 30(6), 1401–1407. https://doi.org/10.1093/nar/30.6.1401
Aptamer: E2F-E1
Target: E2F transcription factor
Type of nucleic acid: ssRNA
Sequence: 5'GUCGAUGUGAUAAGUAGGACGGAGGUGGUCGAU3'
Sequence length: 33
GC content: 0.5151515151515151
Affinity: Kd:2–4 nM
Pool type: 5'-AAACAGAACAGCAGAGTGGCTGGGATG-N10-GCTAGCATC-GACCACCTCCGTCCTACTTATCACATCGACGCTAGC-N10-C-ATCCCAGCGCAGCGGTACG-3'
Pool random region: 20
Binding buffer/conditions: 20 mM Hepes, pH 7.9, 150 mM KCl, 6 mM MgCl2, and 1 mM dithiothreitol
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.9
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " These chimeric tRNA-E2F aptamers are functional and can inhibit E2F-mediated transactivation by up to 80% in human 293 cells. Expression cassette SELEX should greatly facilitate the use of aptamers for a variety of gene therapy applications."
Reference (2002, Mol Ther ): Martell, R. E., Nevins, J. R., & Sullenger, B. A. (2002). Optimizing aptamer activity for gene therapy applications using expression cassette SELEX. Molecular therapy : the journal of the American Society of Gene Therapy, 6(1), 30–34. https://doi.org/10.1006/mthe.2002.0624
Aptamer: beta 55
Target: Beta amyloid peptide (βA4(1–40))
Type of nucleic acid: ssRNA
Sequence: 5'UUACCGUAAGGCCUGUCUUCGUUUGACAGCGGCUUGUUGACCCUCACACUUUGUACCUGCUGCCAA3'
Sequence length: 66
GC content: 0.5151515151515151
Affinity: Kd: 29–48 nM
Pool type: 5'-CCAAGCTTGCATGCCTGCAG-N70-GGTACCGAGCTCGAATTCCC-3
Pool random region: 70
Binding buffer/conditions: 10 mM Tris–HCl, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM EDTA
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: Diagnostic: " The chemical synthesis of these nucleic acids enables tailor-made modifications. By introduction of specific reporter groups these RNAs can become suitable tools for analytical and diagnostic purposes. Thus, this study may introduce a new approach for diagnosis of the Alzheimer's disease."
Reference (2002, Biochem Biophys Res Commun ): Ylera, F., Lurz, R., Erdmann, V. A., & Fürste, J. P. (2002). Selection of RNA aptamers to the Alzheimer's disease amyloid peptide. Biochemical and biophysical research communications, 290(5), 1583–1588. https://doi.org/10.1006/bbrc.2002.6354