RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: Aptamer 10-10
Target: Guanosine triphosphate (GTP)
Type of nucleic acid: ssRNA
Sequence: 5′GUGACGCGACUAGUUACGGAUGCUCAACAGUAGCCAACACGAGUACUGCUUCGGCAGUGGAACCAACGUAGUAUGUUUAGCAUUCAUUCAGUUGGCGCCUCCUAUAGUGAGUCGUAUUACAU3'
Sequence length: 122
GC content: 0.4754098360655737
Affinity: Kd: 28 nM
Pool type: 5′-GTGACGCGACTAGTTACGGA-N26-CTGCCGAAGCAG-N26-TTCATTCAGTTGGCGCCTCCTATAGTGAGTCGTATTACAT-3'
Pool random region: 52
Binding buffer/conditions: 200 mM KCl/10 mM potassium phosphate/5 mM MgCl2/0.1 mM EDTA, pH 6.2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 6.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research: " To see whether higher-affinity aptamers can be isolated from partially structured RNA libraries, we selected for aptamers that bind GTP, starting from a mixture of fully random and partially structured libraries. The engineered stem-loop was present in the three highest affinity aptamers, and in 12 of 13 independent isolates with a single consensus sequence, suggesting that its inclusion increased the abundance of high-affinity aptamers in the starting pool."
Reference (2002, Proc Natl Acad Sci U S A ): Davis, J. H., & Szostak, J. W. (2002). Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11616–11621. https://doi.org/10.1073/pnas.182095699
Aptamer: Class I
Target: Guanosine triphosphate (GTP)
Type of nucleic acid: ssRNA
Sequence: 5′GUGACGCGACUAGUUACGGACUUUCCGaAGuGGUUGGGCUGCUUCGGCAGuGuGAAAaCGGAGAGUUCAUUCAGUUGGCGCCUCCUAUAGUGAGUCGUAUUACAU3'
Sequence length: 105
GC content: 0.5047619047619047
Affinity: Kd: 60–300 nM
Pool type: 5′-GTGACGCGACTAGTTACGGA-N64-TTCATTCAGTTGGCGCCTCCTATAGTGAGTCGTATTACAT-3'
5′-GTGACGCGACTAGTTACGGA-N26-CTGCCGAAGCAG-N26-TTCATTCAGTTGGCGCCTCCTATAGTGAGTCGTATTACAT-3'
Pool random region: 58
Binding buffer/conditions: 200 mM KCl/10 mM potassium phosphate/5 mM MgCl2/0.1 mM EDTA, pH 6.2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 6.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research: " To see whether higher-affinity aptamers can be isolated from partially structured RNA libraries, we selected for aptamers that bind GTP, starting from a mixture of fully random and partially structured libraries. The engineered stem-loop was present in the three highest affinity aptamers, and in 12 of 13 independent isolates with a single consensus sequence, suggesting that its inclusion increased the abundance of high-affinity aptamers in the starting pool."
Additional information: RNA transcribed from these two initial libraries was mixed together in a 1:1 ratio before the start of the selection
Reference (2002, Proc Natl Acad Sci U S A ): Davis, J. H., & Szostak, J. W. (2002). Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11616–11621. https://doi.org/10.1073/pnas.182095699
Aptamer: Aptamer 10-59
Target: Guanosine triphosphate (GTP)
Type of nucleic acid: ssRNA
Sequence: 5′GUGACGCGACUAGUUACGGAGAUAAGUUCCCAAGGCGGGUUGGAAGAGAUAUCAUAGGAGCUUGUCUUCAUUCAGUUGGCGCCUCCUAUAGUGAGUCGUAUUACAU3'
Sequence length: 106
GC content: 0.4716981132075472
Affinity: Kd: 200 nM
Pool type: 5′-GTGACGCGACTAGTTACGGA-N64-TTCATTCAGTTGGCGCCTCCTATAGTGAGTCGTATTACAT-3'
Pool random region: 64
Binding buffer/conditions: 200 mM KCl/10 mM potassium phosphate/5 mM MgCl2/0.1 mM EDTA, pH 6.2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 6.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research: " To see whether higher-affinity aptamers can be isolated from partially structured RNA libraries, we selected for aptamers that bind GTP, starting from a mixture of fully random and partially structured libraries. The engineered stem-loop was present in the three highest affinity aptamers, and in 12 of 13 independent isolates with a single consensus sequence, suggesting that its inclusion increased the abundance of high-affinity aptamers in the starting pool."
Reference (2002, Proc Natl Acad Sci U S A ): Davis, J. H., & Szostak, J. W. (2002). Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11616–11621. https://doi.org/10.1073/pnas.182095699
Aptamer: Aptamer 9-12
Target: Guanosine triphosphate (GTP)
Type of nucleic acid: ssRNA
Sequence: 5′GUGACGCGACUAGUUACGGAUCUAGCAGUUCAGGUAACCACGUAAGAUACGGGUCUAGAUUCAUUCAGUUGGCGCCUCCUAUAGUGAGUCGUAUUACAU3'
Sequence length: 99
GC content: 0.4646464646464646
Affinity: Kd:  250 nM
Pool type: 5′-GTGACGCGACTAGTTACGGA-N64-TTCATTCAGTTGGCGCCTCCTATAGTGAGTCGTATTACAT-3'
Pool random region: 64
Binding buffer/conditions: 200 mM KCl/10 mM potassium phosphate/5 mM MgCl2/0.1 mM EDTA, pH 6.2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 6.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research: " To see whether higher-affinity aptamers can be isolated from partially structured RNA libraries, we selected for aptamers that bind GTP, starting from a mixture of fully random and partially structured libraries. The engineered stem-loop was present in the three highest affinity aptamers, and in 12 of 13 independent isolates with a single consensus sequence, suggesting that its inclusion increased the abundance of high-affinity aptamers in the starting pool."
Reference (2002, Proc Natl Acad Sci U S A ): Davis, J. H., & Szostak, J. W. (2002). Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11616–11621. https://doi.org/10.1073/pnas.182095699
Aptamer: Aptamer 10-24
Target: Guanosine triphosphate (GTP)
Type of nucleic acid: ssRNA
Sequence: 5′GUGACGCGACUAGUUACGGAGGCAUCUAUAUACUGCUUCGGCAGGGAACUCUACUAAGCACCGAUGUCUUCAUUCAGUUGGCGCCUCCUAUAGUGAGUCGUAUUACAU3'
Sequence length: 108
GC content: 0.4814814814814814
Affinity: Kd:  250 nM
Pool type: 5′-GTGACGCGACTAGTTACGGA-N26-CTGCCGAAGCAG-N26-TTCATTCAGTTGGCGCCTCCTATAGTGAGTCGTATTACAT-3'
Pool random region: 52
Binding buffer/conditions: 200 mM KCl/10 mM potassium phosphate/5 mM MgCl2/0.1 mM EDTA, pH 6.2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 6.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research: " To see whether higher-affinity aptamers can be isolated from partially structured RNA libraries, we selected for aptamers that bind GTP, starting from a mixture of fully random and partially structured libraries. The engineered stem-loop was present in the three highest affinity aptamers, and in 12 of 13 independent isolates with a single consensus sequence, suggesting that its inclusion increased the abundance of high-affinity aptamers in the starting pool."
Reference (2002, Proc Natl Acad Sci U S A ): Davis, J. H., & Szostak, J. W. (2002). Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11616–11621. https://doi.org/10.1073/pnas.182095699
Aptamer: Aptamer 10-6
Target: Guanosine triphosphate (GTP)
Type of nucleic acid: ssRNA
Sequence: 5′GUGACGCGACUAGUUACGGAAAUGAAGAUAGUCGGGACCACUUCCCUGAGUCUGCUUCGGCAGUAACUCCAAGGAGAAAGGUCGUCAUUUUCAUUCAGUUGGCGCCUCCUAUAGUGAGUCGUAUUACAU3'
Sequence length: 129
GC content: 0.4806201550387597
Affinity: Kd: 500 nM
Pool type: 5′-GTGACGCGACTAGTTACGGA-N26-CTGCCGAAGCAG-N26-TTCATTCAGTTGGCGCCTCCTATAGTGAGTCGTATTACAT-3'
Pool random region: 52
Binding buffer/conditions: 200 mM KCl/10 mM potassium phosphate/5 mM MgCl2/0.1 mM EDTA, pH 6.2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 6.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research: " To see whether higher-affinity aptamers can be isolated from partially structured RNA libraries, we selected for aptamers that bind GTP, starting from a mixture of fully random and partially structured libraries. The engineered stem-loop was present in the three highest affinity aptamers, and in 12 of 13 independent isolates with a single consensus sequence, suggesting that its inclusion increased the abundance of high-affinity aptamers in the starting pool."
Reference (2002, Proc Natl Acad Sci U S A ): Davis, J. H., & Szostak, J. W. (2002). Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11616–11621. https://doi.org/10.1073/pnas.182095699
Aptamer: C1
Target: Mitochondria
Type of nucleic acid: ssRNA
Sequence: 5'GGAAUUCUAAUACGACUCACUAUAGGGACGCAGGGACUGUACCUUCUAGGCUGGGUCAUGUGACUGUAGCGG3'
Sequence length: 72
GC content: 0.5138888888888888
Affinity: Kd: 1 nM
Pool type: 5'-GGAATTCGGACGCAGGGACTGTA- N16 -ATGTGACTGTAGCGG-3'
Pool random region: 16
Binding buffer/conditions: 10 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 1 mM DTT, and 4 mM ATP
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: " A large number of cytoplasmic tRNAs are imported into the kinetoplast-mitochondrion of Leishmania by a receptor-mediated process. Two types of aptamers were discernible: the A arm and D arm homologues (type I), which were efficiently transferred across the inner mitochondrial membrane, and the V-T homologues (type II), which were not. Such cooperative and antagonistic interactions may allow the use of a limited number of receptors to recognize a large number of tRNAs of variable affinity and enable the maintenance of a properly balanced tRNA pool for mitochondrial translation."
Reference (2002, Mol Cell Biol ): Bhattacharyya, S. N., Chatterjee, S., & Adhya, S. (2002). Mitochondrial RNA import in Leishmania tropica: aptamers homologous to multiple tRNA domains that interact cooperatively or antagonistically at the inner membrane. Molecular and cellular biology, 22(12), 4372–4382. https://doi.org/10.1128/MCB.22.12.4372-4382.2002
Aptamer: C16
Target: Mitochondria
Type of nucleic acid: ssRNA
Sequence: 5'GGAAUUCUAAUACGACUCACUAUAGGGACGCAGGGACUGUACGGUAAGUCCCCGGGCAUGUGACUGUAGCGG3'
Sequence length: 72
GC content: 0.5416666666666666
Affinity: Kd: 0.46 nM
Pool type: 5'-GGAATTCGGACGCAGGGACTGTA- N16 -ATGTGACTGTAGCGG-3'
Pool random region: 16
Binding buffer/conditions: 10 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 1 mM DTT, and 4 mM ATP
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: " A large number of cytoplasmic tRNAs are imported into the kinetoplast-mitochondrion of Leishmania by a receptor-mediated process. Two types of aptamers were discernible: the A arm and D arm homologues (type I), which were efficiently transferred across the inner mitochondrial membrane, and the V-T homologues (type II), which were not. Such cooperative and antagonistic interactions may allow the use of a limited number of receptors to recognize a large number of tRNAs of variable affinity and enable the maintenance of a properly balanced tRNA pool for mitochondrial translation."
Reference (2002, Mol Cell Biol ): Bhattacharyya, S. N., Chatterjee, S., & Adhya, S. (2002). Mitochondrial RNA import in Leishmania tropica: aptamers homologous to multiple tRNA domains that interact cooperatively or antagonistically at the inner membrane. Molecular and cellular biology, 22(12), 4372–4382. https://doi.org/10.1128/MCB.22.12.4372-4382.2002
Aptamer: C20
Target: Mitochondria
Type of nucleic acid: ssRNA
Sequence: 5'GGAAUUCUAAUACGACUCACUAUAGGGACGCAGGGACUGUAUGGUUUUCUGGGGUUUAUGUGACUGUAGCGG3'
Sequence length: 72
GC content: 0.4722222222222222
Affinity: Kd: 1.19 nM
Pool type: 5'-GGAATTCGGACGCAGGGACTGTA- N16 -ATGTGACTGTAGCGG-3'
Pool random region: 16
Binding buffer/conditions: 10 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 1 mM DTT, and 4 mM ATP
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: " A large number of cytoplasmic tRNAs are imported into the kinetoplast-mitochondrion of Leishmania by a receptor-mediated process. Two types of aptamers were discernible: the A arm and D arm homologues (type I), which were efficiently transferred across the inner mitochondrial membrane, and the V-T homologues (type II), which were not. Such cooperative and antagonistic interactions may allow the use of a limited number of receptors to recognize a large number of tRNAs of variable affinity and enable the maintenance of a properly balanced tRNA pool for mitochondrial translation."
Reference (2002, Mol Cell Biol ): Bhattacharyya, S. N., Chatterjee, S., & Adhya, S. (2002). Mitochondrial RNA import in Leishmania tropica: aptamers homologous to multiple tRNA domains that interact cooperatively or antagonistically at the inner membrane. Molecular and cellular biology, 22(12), 4372–4382. https://doi.org/10.1128/MCB.22.12.4372-4382.2002
Aptamer: C32
Target: Mitochondria
Type of nucleic acid: ssRNA
Sequence: 5'GGAAUUCUAAUACGACUCACUAUAGGGACGCAGGGACUGUACGGAUCAGAGUCUCCUAUGUGACUGUAGCGG3'
Sequence length: 72
GC content: 0.5
Affinity: Kd: 0.1 nM
Pool type: 5'-GGAATTCGGACGCAGGGACTGTA- N16 -ATGTGACTGTAGCGG-3'
Pool random region: 16
Binding buffer/conditions: 10 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 1 mM DTT, and 4 mM ATP
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: " A large number of cytoplasmic tRNAs are imported into the kinetoplast-mitochondrion of Leishmania by a receptor-mediated process. Two types of aptamers were discernible: the A arm and D arm homologues (type I), which were efficiently transferred across the inner mitochondrial membrane, and the V-T homologues (type II), which were not. Such cooperative and antagonistic interactions may allow the use of a limited number of receptors to recognize a large number of tRNAs of variable affinity and enable the maintenance of a properly balanced tRNA pool for mitochondrial translation."
Reference (2002, Mol Cell Biol ): Bhattacharyya, S. N., Chatterjee, S., & Adhya, S. (2002). Mitochondrial RNA import in Leishmania tropica: aptamers homologous to multiple tRNA domains that interact cooperatively or antagonistically at the inner membrane. Molecular and cellular biology, 22(12), 4372–4382. https://doi.org/10.1128/MCB.22.12.4372-4382.2002
Aptamer: Aptamer F4
Target: Receptor fibronectin, Trypanosoma cruzi (T. cruzi) parasite
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′ACCGAGUCCAGAAGCUUGUAGUACUGACCCUUCCCGACGCACGGACCAGUGAUGCCAACCCACCCGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC3′
Sequence length: 107
GC content: 0.5327102803738317
Affinity: Kd: 142 ± 94 nM
Pool type: 5′-ACCGAGTCCAGAAGCTTGTAGTACT-N40-GCCTAGATGGAGTTGAATTCTCCCTATAGTGAGTCGTATTAC-3′
Pool random region: 40
Binding buffer/conditions: PBS, 20 mm glucose (phosphate-buffered saline, 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: Therapeutic: " Select RNA aptamers that bind to infectious human cytomegalovirus and inhibit viral infection in vitro, showing the feasibility of the SELEX technique for the evolution of novel compounds that protect cells against infection by pathogens (Trypanosoma cruzi)"
Additional information: Two′-fluoro-pyrimidines (2′F-dCTP and 2′F-dUTP) were from TriLink BioTechnologies (San Diego, CA).[α-32P]ATP and 1 mm 2′-OH-(ATP and GTP) and 3 mm2′-F-(dCTP and dUTP), the latter to provide stability of the transcript against RNase activity
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, J Biol Chem ): Ulrich, H., Magdesian, M. H., Alves, M. J., & Colli, W. (2002). In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion. The Journal of biological chemistry, 277(23), 20756–20762. https://doi.org/10.1074/jbc.M111859200
Aptamer: Aptamer T6
Target: Receptor fibronectin, Trypanosoma cruzi (T. cruzi) parasite
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′ACCGAGUCCAGAAGCUUGUAGUACUCAAUACUCAAGCAAGCCCAGCCCUACCAACCCCGGAGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC3′
Sequence length: 103
GC content: 0.4951456310679611
Affinity: Kd: 400 ± 239 nM
Pool type: 5′-ACCGAGTCCAGAAGCTTGTAGTACT-N40-GCCTAGATGGAGTTGAATTCTCCCTATAGTGAGTCGTATTAC-3′
Pool random region: 40
Binding buffer/conditions: PBS, 20 mm glucose (phosphate-buffered saline, 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: Therapeutic: " Select RNA aptamers that bind to infectious human cytomegalovirus and inhibit viral infection in vitro, showing the feasibility of the SELEX technique for the evolution of novel compounds that protect cells against infection by pathogens (Trypanosoma cruzi)"
Additional information: Two′-fluoro-pyrimidines (2′F-dCTP and 2′F-dUTP) were from TriLink BioTechnologies (San Diego, CA).[α-32P]ATP and 1 mm 2′-OH-(ATP and GTP) and 3 mm2′-F-(dCTP and dUTP), the latter to provide stability of the transcript against RNase activity
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, J Biol Chem ): Ulrich, H., Magdesian, M. H., Alves, M. J., & Colli, W. (2002). In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion. The Journal of biological chemistry, 277(23), 20756–20762. https://doi.org/10.1074/jbc.M111859200
Aptamer: Aptamer HS6
Target: Receptor fibronectin, Trypanosoma cruzi (T. cruzi) parasite
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′ACCGAGUCCAGAAGCUUGUAGUACUAUCGCUACUGCGCCGGUUGCGGCUUGCGGUUGCAACGCCAGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC3′
Sequence length: 107
GC content: 0.5233644859813084
Affinity: Kd: 40 ± 14 nM
Pool type: 5′-ACCGAGTCCAGAAGCTTGTAGTACT-N40-GCCTAGATGGAGTTGAATTCTCCCTATAGTGAGTCGTATTAC-3′
Pool random region: 40
Binding buffer/conditions: PBS, 20 mm glucose (phosphate-buffered saline, 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: Therapeutic: " Select RNA aptamers that bind to infectious human cytomegalovirus and inhibit viral infection in vitro, showing the feasibility of the SELEX technique for the evolution of novel compounds that protect cells against infection by pathogens (Trypanosoma cruzi)"
Additional information: Two′-fluoro-pyrimidines (2′F-dCTP and 2′F-dUTP) were from TriLink BioTechnologies (San Diego, CA).[α-32P]ATP and 1 mm 2′-OH-(ATP and GTP) and 3 mm2′-F-(dCTP and dUTP), the latter to provide stability of the transcript against RNase activity
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, J Biol Chem ): Ulrich, H., Magdesian, M. H., Alves, M. J., & Colli, W. (2002). In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion. The Journal of biological chemistry, 277(23), 20756–20762. https://doi.org/10.1074/jbc.M111859200
Aptamer: Aptamer L28
Target: Receptor fibronectin, Trypanosoma cruzi (T. cruzi) parasite
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′ACCGAGUCCAGAAGCUUGUAGUACUUCUCUCAGCCACGUUCUAUGUGACGCAAGCUACCCUGUAUGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC3′
Sequence length: 107
GC content: 0.4672897196261682
Affinity: Kd: 209 ± 99 nM
Pool type: 5′-ACCGAGTCCAGAAGCTTGTAGTACT-N40-GCCTAGATGGAGTTGAATTCTCCCTATAGTGAGTCGTATTAC-3′
Pool random region: 40
Binding buffer/conditions: PBS, 20 mm glucose (phosphate-buffered saline, 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: Therapeutic: " Select RNA aptamers that bind to infectious human cytomegalovirus and inhibit viral infection in vitro, showing the feasibility of the SELEX technique for the evolution of novel compounds that protect cells against infection by pathogens (Trypanosoma cruzi)"
Additional information: Two′-fluoro-pyrimidines (2′F-dCTP and 2′F-dUTP) were from TriLink BioTechnologies (San Diego, CA).[α-32P]ATP and 1 mm 2′-OH-(ATP and GTP) and 3 mm2′-F-(dCTP and dUTP), the latter to provide stability of the transcript against RNase activity
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, J Biol Chem ): Ulrich, H., Magdesian, M. H., Alves, M. J., & Colli, W. (2002). In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion. The Journal of biological chemistry, 277(23), 20756–20762. https://doi.org/10.1074/jbc.M111859200
Aptamer: P19
Target: Rat neurotensin receptor NTS-1
Type of nucleic acid: ssRNA
Sequence: 5'UAAUACGACUACUAUAGGGAGGACGAUGCGGACAGAUACGGAACUACAGAGGUCAAUUACGGUGGCCACGCCAGACGACUCGCCCGA3'
Sequence length: 87
GC content: 0.5402298850574713
Affinity: Kd: 0.37 nM
Pool type: 5'-TAATACGACTACTATAGGGAGGACGATGCGG-N40-CAGACGACTCGCCCGA-3'
Pool random region: 40
Binding buffer/conditions: SHMCK buffer 110 mM NaCl, 20 mM Hepes (pH 7.5 at 25°C), 1 mM MgCl2, 1 mM CaCl2, containing 0.2% (w/v) CHAPS, 0.04% (w/v) CHS, and 0.1% (w/v)LM
Divalent salt: MgCl/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: Therapeutic: " Generate GPCR-specific RNA aptamers for disease therapy and cocrystallization studies using the neurotensin receptor NTS-1, evolve aptamers reactive to minor protein concentrations. To our knowledge this is the first report describing the isolation of a high-affinity RNA aptamer to a GPCR. We have outlined an expression and purification protocol for the generation of functional NTR as the substrate in SELEX experiments and show that the aptamers generated are capable of recognizing this GPCR specifically."
Reference (2002, Anal Biochem ): Daniels, D. A., Sohal, A. K., Rees, S., & Grisshammer, R. (2002). Generation of RNA aptamers to the G-protein-coupled receptor for neurotensin, NTS-1. Analytical biochemistry, 305(2), 214–226. https://doi.org/10.1006/abio.2002.5663