RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: 77
Target: Unr (Upstream of N-Ras) protein, Human
Type of nucleic acid: ssRNA
Sequence: 5′GGGCCACCAACGACAUUAAGAAAGAACGGAACCAUGGUUGAUAUAAAUAGUGCCCA3′
Sequence length: 56
GC content: 0.4464285714285714
Affinity: Kd: 10 nM
Pool type: 5′-CCCGGTGGTTGCTGTAA-N20-CAACTATATTTATCACGGGT-3′
Pool random region: 20
Binding buffer/conditions: 25 µg/ml BSA, 25 µg/ml tRNA, 5 U/ml RNAguard (Pharmacia), 1 mM PMSF, 1 mM β-mercaptoethanol and 1 µg/ml of leupeptin, antipain and aprotinin, in TNG buffer
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 85 kDa
Application as quoted in the referenced paper: Research: " In our initial characterization of the human Unr protein, we have determined that it has the capacity to interact in vitro with single-stranded RNA and DNA; To further characterize the RNA-binding specificity of Unr and eventually identify RNA ligands, we have used an in vitro selection/amplification approach"
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, Nucleic Acids Res ): Triqueneaux, G., Velten, M., Franzon, P., Dautry, F., & Jacquemin-Sablon, H. (1999). RNA binding specificity of Unr, a protein with five cold shock domains. Nucleic acids research, 27(8), 1926–1934. https://doi.org/10.1093/nar/27.8.1926
Aptamer: 78
Target: Unr (Upstream of N-Ras) protein, Human
Type of nucleic acid: ssRNA
Sequence: 5′GGGCCACCAACGACAUUGAAAAAAAAACAAGAAGAAGGUUGAUAUAAAUAGUGCCCA3′
Sequence length: 57
GC content: 0.3859649122807017
Affinity: Kd: 8 nM
Pool type: 5′-CCCGGTGGTTGCTGTAA-N20-CAACTATATTTATCACGGGT-3′
Pool random region: 20
Binding buffer/conditions: 25 µg/ml BSA, 25 µg/ml tRNA, 5 U/ml RNAguard (Pharmacia), 1 mM PMSF, 1 mM β-mercaptoethanol and 1 µg/ml of leupeptin, antipain and aprotinin, in TNG buffer
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 85 kDa
Application as quoted in the referenced paper: Research: " In our initial characterization of the human Unr protein, we have determined that it has the capacity to interact in vitro with single-stranded RNA and DNA; To further characterize the RNA-binding specificity of Unr and eventually identify RNA ligands, we have used an in vitro selection/amplification approach"
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, Nucleic Acids Res ): Triqueneaux, G., Velten, M., Franzon, P., Dautry, F., & Jacquemin-Sablon, H. (1999). RNA binding specificity of Unr, a protein with five cold shock domains. Nucleic acids research, 27(8), 1926–1934. https://doi.org/10.1093/nar/27.8.1926
Aptamer: C5C6
Target: C5 component of human complement (serum glycoprotein)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGAGGACGAUGCGGUCUCAUGCGUCGAGUGUGAGUUUACCUUCGUCAGACGACUCGCCCGA3'
Sequence length: 62
GC content: 0.5967741935483871
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
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: 1-5
Target: Integration host factor (IHF)
Type of nucleic acid: ssDNA
Sequence: 5′GCCTGCTTTTTTATACTAAGTTGGCATCTGCCGCTAAGTTGTTGATTCCAATTTGTTGCAACGAACAGGTCACTA3′
Sequence length: 75
GC content: 0.4133333333333333
Affinity: IC50: 3.2 nM
Pool type: 5′-GCCTGCTTTTTTATACTAAGTTGGCA-N21-CAATTTGTTGCAACGAACAGGTCACTA-3′
Pool random region: 21
Binding buffer/conditions: 50 mM Tris-Cl–50 mM KCl–50 μg of bovine serum albumin (BSA) per ml–3.75 μg of salmon sperm DNA per ml–10% glycerol–1 mM EDTA at pH 7.8
Buffer type: Tris Buffers
pH: 7.8
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Integration host factor (IHF) is a bacterial protein that binds and severely bends a specific DNA target. To understand the essential determinants of IHF function, a similar selection will be used with recombination as the partition selector in order to ask how efficient recombination is associated with DNA affinity."
Additional information: high-affinity class I site, proficient in excisive recombination and modest in integrative recombination
Reference (1999, J Bacteriol ): Goodman, S. D., Velten, N. J., Gao, Q., Robinson, S., & Segall, A. M. (1999). In vitro selection of integration host factor binding sites. Journal of bacteriology, 181(10), 3246–3255. https://doi.org/10.1128/JB.181.10.3246-3255.1999
Aptamer: 1-46
Target: Integration host factor (IHF)
Type of nucleic acid: ssDNA
Sequence: 5′GCCTGCTTTTTTATACTAAGTTGGCAACCGTCGCATATGTAAGGAATTCAATTTGTTGCAACGAACAGGTCACTA3′
Sequence length: 75
GC content: 0.4
Affinity: IC50: 3.9 nM
Pool type: 5′-GCCTGCTTTTTTATACTAAGTTGGCA-N21-CAATTTGTTGCAACGAACAGGTCACTA-3′
Pool random region: 21
Binding buffer/conditions: 50 mM Tris-Cl–50 mM KCl–50 μg of bovine serum albumin (BSA) per ml–3.75 μg of salmon sperm DNA per ml–10% glycerol–1 mM EDTA at pH 7.8
Buffer type: Tris Buffers
pH: 7.8
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Integration host factor (IHF) is a bacterial protein that binds and severely bends a specific DNA target. To understand the essential determinants of IHF function, a similar selection will be used with recombination as the partition selector in order to ask how efficient recombination is associated with DNA affinity."
Additional information: high-affinity class I site but recombination deficient
Reference (1999, J Bacteriol ): Goodman, S. D., Velten, N. J., Gao, Q., Robinson, S., & Segall, A. M. (1999). In vitro selection of integration host factor binding sites. Journal of bacteriology, 181(10), 3246–3255. https://doi.org/10.1128/JB.181.10.3246-3255.1999
Aptamer: 1-50
Target: Integration host factor (IHF)
Type of nucleic acid: ssDNA
Sequence: 5′GCCTGCTTTTTTATACTAAGTTGGCAATGAATCTTGGATAGTCGGCAGCAATTTGTTGCAACGAACAGGTCACTA3′
Sequence length: 75
GC content: 0.4133333333333333
Affinity: IC50: 10 nM
Pool type: 5′-GCCTGCTTTTTTATACTAAGTTGGCA-N21-CAATTTGTTGCAACGAACAGGTCACTA-3′
Pool random region: 21
Binding buffer/conditions: 50 mM Tris-Cl–50 mM KCl–50 μg of bovine serum albumin (BSA) per ml–3.75 μg of salmon sperm DNA per ml–10% glycerol–1 mM EDTA at pH 7.8
Buffer type: Tris Buffers
pH: 7.8
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Integration host factor (IHF) is a bacterial protein that binds and severely bends a specific DNA target. To understand the essential determinants of IHF function, a similar selection will be used with recombination as the partition selector in order to ask how efficient recombination is associated with DNA affinity."
Additional information: lowest-affinity class I site, modest in both excisive and integrative recombination and with the most accelerated migration in complexes with IHF
Reference (1999, J Bacteriol ): Goodman, S. D., Velten, N. J., Gao, Q., Robinson, S., & Segall, A. M. (1999). In vitro selection of integration host factor binding sites. Journal of bacteriology, 181(10), 3246–3255. https://doi.org/10.1128/JB.181.10.3246-3255.1999
Aptamer: 2-16
Target: Trypanosome variant surface glycoprotein (VSG)
Type of nucleic acid: ssRNA
Sequence: 5'GAAUUCAGUCGGACAGCGUCGGGUGGCCCGUGUCUGAGCGGGGACGGCCACUUGAGCGCGAUGGACGAAUAUCGUCUCCC3'
Sequence length: 80
GC content: 0.6375
Affinity: Kd: 60 ± 17 nM
Pool type: 5'-GAATTCAGTCGGACAGCG-N40-GATGGACGAATATCGTCTCCC-3'
Pool random region: 40
Binding buffer/conditions: 20 mM NaxHyPO4, pH 7.4, 2 mM MgCl2, 130 mM NaCl, 5 mM KCl, 20 mM glucose, 0.2 mM β-mercaptoethanol
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 42 kDa
Post-SELEX modifications: Biotinylation of aptamer 2–16 was performed by in vitro transcription
Application as quoted in the referenced paper: Diagnostic and Therapeutic: "The identified RNA aptamers show high affinity binding and specificity for a single protein and as such they have the potential to be used as diagnostic as well as therapeutic tools. Their ability to bind to an invariant element on the trypanosome surface opens up the possibility of side-stepping the antigenic variation of the VSG coat."
Additional information: 32P-phosphate labelled RNA. DNA oligonucleotides were synthesised b automated solid suupport chemsistry using O-cyanoethyl-N,N-dissopropyl-phosphoramidites . The starting pool library was a 79mer DNA of sequence. Fluorescence labelling of aptamer 2–16 was achieved by tagging the bodipy tmr-c5 fluorophore (molecular probes) to the 5′-end of the rna, 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, Nucleic Acids Res ): Homann, M., & Göringer, H. U. (1999). Combinatorial selection of high affinity RNA ligands to live African trypanosomes. Nucleic acids research, 27(9), 2006–2014. https://doi.org/10.1093/nar/27.9.2006
Aptamer: R-06
Target: Trans-activation responsive (TAR) RNA element of HIV-1
Type of nucleic acid: ssRNA
Sequence: 5'GGUUACCAGCCUUCACUGCGGGCCACGAUUGUCGAGUCCAUCAACAGGUCCCAGACGUGUUGAACUGGAGAUCCCCCCGCACCACGGUCGGUCACAC3'
Sequence length: 97
GC content: 0.6082474226804123
Affinity: Kd: 30 nM
Pool type: 5'-GGUUACCAGCCUUCACUGC-N60-GCACCACGGUCGGUCACAC-3'
Pool random region: 60
Binding buffer/conditions: R buffer (20 mM HEPES, pH 7.3, at 208C contain-ing 20 mM sodium acetate, 140 mM potassium acetate,and 3 mM magnesium acetate)
Buffer type: Other Buffers
pH: 7.3
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Numerous RNA structures act as regulatory domains of gene expression, generally through the binding of proteins. Tertiary RNA interactions are known to play a key role in several biological processes. A pseudo-knot is responsible for the ribosomal frame-shifting on the mRNA of the Infectious Bronchitis Virus. Loop–loop interactions are also involved in the regulation of the copy number of the plasmid ColE1. Ligands specific for such structures would constitute an efficient means for interfering with the regulatory processes that they mediate. This strategy offered a way to identify key determinants of loop–loop interactions and to generate high affinity ligands of TAR RNA structure."
Reference (1999, RNA ): Ducongé, F., & Toulmé, J. J. (1999). In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA (New York, N.Y.), 5(12), 1605–1614. https://doi.org/10.1017/s1355838299991318
Aptamer: R-42
Target: Trans-activation responsive (TAR) RNA element of HIV-1
Type of nucleic acid: ssRNA
Sequence: 5'GGUUACCAGCCUUCACUGCCCAGCGCAAUGACGACCCCCAGUCCCAGAUGGGAGGUCAUAGUCAUAGUCGGACUCACCGCGGCACCACGGUCGGUCACAC3'
Sequence length: 100
GC content: 0.62
Affinity: Not reported 
Pool type: 5'-GGUUACCAGCCUUCACUGC-N60-GCACCACGGUCGGUCACAC-3'
Pool random region: 60
Binding buffer/conditions: R buffer (20 mM HEPES, pH 7.3, at 208C contain-ing 20 mM sodium acetate, 140 mM potassium acetate,and 3 mM magnesium acetate)
Buffer type: Other Buffers
pH: 7.3
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " Numerous RNA structures act as regulatory domains of gene expression, generally through the binding of proteins. Tertiary RNA interactions are known to play a key role in several biological processes. A pseudo-knot is responsible for the ribosomal frame-shifting on the mRNA of the Infectious Bronchitis Virus. Loop–loop interactions are also involved in the regulation of the copy number of the plasmid ColE1. Ligands specific for such structures would constitute an efficient means for interfering with the regulatory processes that they mediate. This strategy offered a way to identify key determinants of loop–loop interactions and to generate high affinity ligands of TAR RNA structure."
Additional information: slightly weaker binder than R-06 24
Reference (1999, RNA ): Ducongé, F., & Toulmé, J. J. (1999). In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA (New York, N.Y.), 5(12), 1605–1614. https://doi.org/10.1017/s1355838299991318
Aptamer: R-06 24
Target: Trans-activation responsive (TAR) RNA element of HIV-1
Type of nucleic acid: ssRNA
Sequence: 5'UCAACACGGUCCCAGACGUGUUGA3'
Sequence length: 24
GC content: 0.5416666666666666
Affinity: Kd: 32 ± 8 nM 
Pool type: 5'-GGUUACCAGCCUUCACUGC-N60-GCACCACGGUCGGUCACAC-3'
Pool random region: 60
Binding buffer/conditions: R buffer (20 mM HEPES, pH 7.3, at 208C contain-ing 20 mM sodium acetate, 140 mM potassium acetate,and 3 mM magnesium acetate)
Buffer type: Other Buffers
pH: 7.3
Molecular weight of target: Not reported
Post-SELEX modifications: 24-mer truncated aptamer derived from r-06 aptamer
Application as quoted in the referenced paper: Detection: " Numerous RNA structures act as regulatory domains of gene expression, generally through the binding of proteins. Tertiary RNA interactions are known to play a key role in several biological processes. A pseudo-knot is responsible for the ribosomal frame-shifting on the mRNA of the Infectious Bronchitis Virus. Loop–loop interactions are also involved in the regulation of the copy number of the plasmid ColE1. Ligands specific for such structures would constitute an efficient means for interfering with the regulatory processes that they mediate. This strategy offered a way to identify key determinants of loop–loop interactions and to generate high affinity ligands of TAR RNA structure."
Reference (1999, RNA ): Ducongé, F., & Toulmé, J. J. (1999). In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA (New York, N.Y.), 5(12), 1605–1614. https://doi.org/10.1017/s1355838299991318
Aptamer: IV-04
Target: Human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element
Type of nucleic acid: ssDNA
Sequence: 5′GCAGTCTCGTCGACACCCAGCAGCGCATGTAACTCCCATATCATGTGTGTGCTGGATCCGACGCAG3'
Sequence length: 66
GC content: 0.5757575757575758
Affinity: Kd: 20 nM
Pool type: 5′-GCAGTCTCGTCGACACCC-N30-GTGCTGGATCCGACGCAG-3'
Pool random region: 30
Binding buffer/conditions: 10 mmTris-HCl, pH 7.5, 10 mm MgCl2, 50 mm NaCl, and 1 mm dithioerythritol
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " In vitro selection was performed in a DNA library, made of oligonucleotides with a 30-nucleotide random sequence, to identify ligands of the human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element. These results, which allowed the identification of a new type of complex, DNA-RNA kissing complex, demonstrate the interest of in vitro selection for identifying non-antisense oligonucleotide ligands of RNA structures that are of potential value for artificially modulating gene expression."
Reference (1999, J Biol Chem ): Boiziau, C., Dausse, E., Yurchenko, L., & Toulmé, J. J. (1999). DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes. The Journal of biological chemistry, 274(18), 12730–12737. https://doi.org/10.1074/jbc.274.18.12730
Aptamer: III-25 39
Target: Human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element
Type of nucleic acid: ssDNA
Sequence: 5′CCCACGGGAGAATACTCCCATCATTGAATCCCGTGCTGG3'
Sequence length: 39
GC content: 0.5641025641025641
Affinity: Kd: 50 nM
Pool type: 5′-GCAGTCTCGTCGACACCC-N30-GTGCTGGATCCGACGCAG-3'
Pool random region: 30
Binding buffer/conditions: 10 mmTris-HCl, pH 7.5, 10 mm MgCl2, 50 mm NaCl, and 1 mm dithioerythritol
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " In vitro selection was performed in a DNA library, made of oligonucleotides with a 30-nucleotide random sequence, to identify ligands of the human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element. These results, which allowed the identification of a new type of complex, DNA-RNA kissing complex, demonstrate the interest of in vitro selection for identifying non-antisense oligonucleotide ligands of RNA structures that are of potential value for artificially modulating gene expression."
Reference (1999, J Biol Chem ): Boiziau, C., Dausse, E., Yurchenko, L., & Toulmé, J. J. (1999). DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes. The Journal of biological chemistry, 274(18), 12730–12737. https://doi.org/10.1074/jbc.274.18.12730
Aptamer: III-33 39
Target: Human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element
Type of nucleic acid: ssDNA
Sequence: 5′CCACAGTACGTTAACTCCCATATACACGTATGGTGCTGG3'
Sequence length: 39
GC content: 0.4871794871794871
Affinity: Kd: 50 nM
Pool type: 5′-GCAGTCTCGTCGACACCC-N30-GTGCTGGATCCGACGCAG-3'
Pool random region: 30
Binding buffer/conditions: 10 mmTris-HCl, pH 7.5, 10 mm MgCl2, 50 mm NaCl, and 1 mm dithioerythritol
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " In vitro selection was performed in a DNA library, made of oligonucleotides with a 30-nucleotide random sequence, to identify ligands of the human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element. These results, which allowed the identification of a new type of complex, DNA-RNA kissing complex, demonstrate the interest of in vitro selection for identifying non-antisense oligonucleotide ligands of RNA structures that are of potential value for artificially modulating gene expression."
Reference (1999, J Biol Chem ): Boiziau, C., Dausse, E., Yurchenko, L., & Toulmé, J. J. (1999). DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes. The Journal of biological chemistry, 274(18), 12730–12737. https://doi.org/10.1074/jbc.274.18.12730
Aptamer: IV-04 39
Target: Human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element
Type of nucleic acid: ssDNA
Sequence: 5′CCAGCAGCGCATGTAACTCCCATATCATGTGTGTGCTGG3'
Sequence length: 39
GC content: 0.5384615384615384
Affinity: Kd: 50 nM
Pool type: 5′-GCAGTCTCGTCGACACCC-N30-GTGCTGGATCCGACGCAG-3'
Pool random region: 30
Binding buffer/conditions: 10 mmTris-HCl, pH 7.5, 10 mm MgCl2, 50 mm NaCl, and 1 mm dithioerythritol
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " In vitro selection was performed in a DNA library, made of oligonucleotides with a 30-nucleotide random sequence, to identify ligands of the human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element. These results, which allowed the identification of a new type of complex, DNA-RNA kissing complex, demonstrate the interest of in vitro selection for identifying non-antisense oligonucleotide ligands of RNA structures that are of potential value for artificially modulating gene expression."
Reference (1999, J Biol Chem ): Boiziau, C., Dausse, E., Yurchenko, L., & Toulmé, J. J. (1999). DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes. The Journal of biological chemistry, 274(18), 12730–12737. https://doi.org/10.1074/jbc.274.18.12730
Aptamer: IV-40 38
Target: Human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element
Type of nucleic acid: ssDNA
Sequence: 5′CCAGTAGGACATTACTCCCACACTGATGTCCGTGCTGG3'
Sequence length: 38
GC content: 0.5526315789473685
Affinity: Kd: 120 nM
Pool type: 5′-GCAGTCTCGTCGACACCC-N30-GTGCTGGATCCGACGCAG-3'
Pool random region: 30
Binding buffer/conditions: 10 mmTris-HCl, pH 7.5, 10 mm MgCl2, 50 mm NaCl, and 1 mm dithioerythritol
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research: " In vitro selection was performed in a DNA library, made of oligonucleotides with a 30-nucleotide random sequence, to identify ligands of the human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element. These results, which allowed the identification of a new type of complex, DNA-RNA kissing complex, demonstrate the interest of in vitro selection for identifying non-antisense oligonucleotide ligands of RNA structures that are of potential value for artificially modulating gene expression."
Reference (1999, J Biol Chem ): Boiziau, C., Dausse, E., Yurchenko, L., & Toulmé, J. J. (1999). DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes. The Journal of biological chemistry, 274(18), 12730–12737. https://doi.org/10.1074/jbc.274.18.12730
Aptamer: 8-5 aptamer
Target: Rex fusion protein of Human T-lymphotropic virus 1 (HTLV-1)
Type of nucleic acid: ssDNA
Sequence: 5'GGGAACTCGATGAAGCGAATTCTGTAGGCGACGGTACGCAAGTACTCTTGCGCCACAGGCCTATCTATCGGATCCACG3'
Sequence length: 78
GC content: 0.5512820512820513
Affinity: Kapp: 25 nM & 30 nM
Pool type: 5'-GGGAACTCGATGAAGCGAATTCTGT-N6.9-GTACGCAAGTAC-N6.9-ACAGGCCTATCTATCGGATCCACG-3'
Pool random region: 15
Binding buffer/conditions: 50 mM Tris-HCl [pH 8.0], 50 mM KCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic and Research: "RNA molecules that bind tightly and specifically to a Rex fusion protein have been isolated from a conformationally constrained pool of random sequence RNAs. The anti-Rex aptamers can functionally substitute for the XBE in vivo, a result which supports a previously proposed model for mRNA transport in which the viral genome serves as a platform for assembling a nucleoprotein complex that can co-opt the cellular transport apparatus. Overall, these studies suggest that anti-Rex aptamers may serve as RNA decoys of the Rex protein."
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, J Virol ): Baskerville, S., Zapp, M., & Ellington, A. D. (1999). Anti-Rex aptamers as mimics of the Rex-binding element. Journal of virology, 73(6), 4962–4971. https://doi.org/10.1128/JVI.73.6.4962-4971.1999