RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: e05
Target: Plasmodium falciparum (P. falciparum) erythrocyte membrane protein 1 (PfEMP1)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5′CGACUGCAGAGCUUGCUACGGUGACCACGCGGAUAAAUGAAUCAAAAACAACAACCAGGGCCGUUCGACUACGCUAAUUAUCCCGGGUACCGAGCUCGAAUUCCC3′
Sequence length: 105
GC content: 0.5238095238095238
Affinity: Not reported
Pool type: 5′-CGACTGCAGAGCTTGCTACG-N50-GGTACCGAGCTCGAATTCCC-3′
Pool random region: 50
Binding buffer/conditions: PBSM (PBS, 1 mM MgCl2)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " The var-gene encoding Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is known to play a major role in the pathogenicity of the P. falciparum parasite. The protein enables the parasite to adhere to the endothelial linings of small blood vessels (cytoadherence) as well as to non-infected erythrocytes (rosetting), thus preventing clearance from the bloodstream. The described results show that RNA aptamers are promising candidates for adjunct therapy in severe malaria."
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.
The DNA library was generated using oligo B (5′-CGACTGCAGAGCTTGCTACG (N)50 GGTACCGAGCTCGAATTCCC-3′) and oligo A (5′-GCGTAATACGACTCACTATAGGGAATTCGAGCTCGGTACC-3′), sequence for T7 promoter underlined.
2′F-modified library (ATP, GTP, 2′F-dCTP, 2′F-dUTP)
Reference (2009, Parasitol Res ): Barfod, A., Persson, T., & Lindh, J. (2009). In vitro selection of RNA aptamers against a conserved region of the Plasmodium falciparum erythrocyte membrane protein 1. Parasitology research, 105(6), 1557–1566. https://doi.org/10.1007/s00436-009-1583-x
Aptamer: aptamer 1
Target: SARS-CoV nucleocapsid (N) protein
Type of nucleic acid: ssRNA
Sequence: 5'GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG3'
Sequence length: 83
GC content: 0.5903614457831325
Affinity: Kd: 1.65 ± 0.41 nM
Pool type: 5′-GGGAGAGCGGAAGCGUGCUGGGCC-N40-CAUAACCCAGAGGUCGAUGGAUCCCCCC-3′
Pool random region: 40
Binding buffer/conditions: 30 mM Tris-HCl, pH 7.5, 150 mM NaCl, 10 mM MgCl2, 2 mM DTT, 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: Detection and Diagnostic: "The SARS-CoV nucleocapsid (N) protein is one of the most abundant structural proteins and serves as a diagnostic marker for accurate and sensitive detection of the virus. Using a chemiluminescence immunosorbent assay and a nanoarray aptamer chip with the selected aptamer as an antigen-capturing agent, we could sensitively detect N protein at a concentration as low as 2 pg/ml. These aptamer-antibody hybrid immunoassays may be useful for rapid, sensitive detection of SARS-CoV N protein."
Reference (2009, Analyst ): Ahn, D. G., Jeon, I. J., Kim, J. D., Song, M. S., Han, S. R., Lee, S. W., Jung, H., & Oh, J. W. (2009). RNA aptamer-based sensitive detection of SARS coronavirus nucleocapsid protein. The Analyst, 134(9), 1896–1901. https://doi.org/10.1039/b906788d
Aptamer: D10/DA24
Target: Diclofenac (DCF)
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTACACACCGAGACCGCACTTGTACTCCCTAGCCGCCTCCGTAGATAGTAAGTGCAATCT3′
Sequence length: 76
GC content: 0.4736842105263157
Affinity: Kd: 100.64 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl pH 7.6, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% Tween 20
Divalent salt: MgCl/CaCl
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: Drug Delivery and Detection: "A series of 56 ssDNA aptamer variants that bind to diclofenac (DCF) were selected from an initial pool of 2.4x10^(14) ssDNA molecules by Flu-Mag SELEX process. DCF aptamers selected can be potential candidates for drug-delivery systems, specific detection of DCF and its derivatives in pharmaceutical preparations and contaminants"
Reference (2009, Bioorg Med Chem ): Joeng, C. B., Niazi, J. H., Lee, S. J., & Gu, M. B. (2009). ssDNA aptamers that recognize diclofenac and 2-anilinophenylacetic acid. Bioorganic & medicinal chemistry, 17(15), 5380–5387. https://doi.org/10.1016/j.bmc.2009.06.044
Aptamer: D22
Target: Diclofenac (DCF)
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGGCAGTAGGTGTACATGCAAAGCCAGTGTGGGTCCCTGTGTAGATAGTAAGTGCAATCT3′
Sequence length: 77
GC content: 0.4415584415584415
Affinity: Kd: 166.34 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl pH 7.6, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% Tween 20
Divalent salt: MgCl/CaCl
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: Drug Delivery and Detection: "A series of 56 ssDNA aptamer variants that bind to diclofenac (DCF) were selected from an initial pool of 2.4x10^(14) ssDNA molecules by Flu-Mag SELEX process. DCF aptamers selected can be potential candidates for drug-delivery systems, specific detection of DCF and its derivatives in pharmaceutical preparations and contaminants"
Reference (2009, Bioorg Med Chem ): Joeng, C. B., Niazi, J. H., Lee, S. J., & Gu, M. B. (2009). ssDNA aptamers that recognize diclofenac and 2-anilinophenylacetic acid. Bioorganic & medicinal chemistry, 17(15), 5380–5387. https://doi.org/10.1016/j.bmc.2009.06.044
Aptamer: D3
Target: Diclofenac (DCF)
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGCAACGTGGCGGTCAGTCAGCGGGTGGTGGGTTCGGTCCAGATAGTAAGTGCAATCT3′
Sequence length: 75
GC content: 0.5066666666666667
Affinity: Kd: 42.7 nM
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris–HCl pH 7.6, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% Tween 20
Divalent salt: MgCl/CaCl
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: Drug Delivery and Detection: "A series of 56 ssDNA aptamer variants that bind to diclofenac (DCF) were selected from an initial pool of 2.4x10^(14) ssDNA molecules by Flu-Mag SELEX process. DCF aptamers selected can be potential candidates for drug-delivery systems, specific detection of DCF and its derivatives in pharmaceutical preparations and contaminants"
Reference (2009, Bioorg Med Chem ): Joeng, C. B., Niazi, J. H., Lee, S. J., & Gu, M. B. (2009). ssDNA aptamers that recognize diclofenac and 2-anilinophenylacetic acid. Bioorganic & medicinal chemistry, 17(15), 5380–5387. https://doi.org/10.1016/j.bmc.2009.06.044
Aptamer: Aptamer 32, 34
Target: Streptavidin
Type of nucleic acid: ssDNA
Sequence: 5′TAATACGACTCACTATAGCAATGGTACGGTACTTCCTATAACGCCCGTGTTGCTCGGTTATCAAAAGTGCACGCTACTTTG3′
Sequence length: 81
GC content: 0.4444444444444444
Affinity: Kd: 69.277 ± 4.323 nM
Pool type: 5′-TAATACGACTCACTATAGCAATGGTACGGTACTTCC-N25-CAAAAGTGCACGCTACTTTG-3′
Pool random region: 25
Binding buffer/conditions: 5 mM of MgCl2 in PBS
Divalent salt: MgCl
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: " The streptavidin-specific aptamers obtained in this work can be used as tools for characterization of the occupancy of streptavidin-modified surfaces with biotinylated target molecules. The method described in the study is also generally applicable to target molecules other than streptavidin."
Reference (2009, Acta Biochim Biophys Sin (Shanghai) ): Wang, C., Yang, G., Luo, Z., & Ding, H. (2009). In vitro selection of high-affinity DNA aptamers for streptavidin. Acta biochimica et biophysica Sinica, 41(4), 335–340. https://doi.org/10.1093/abbs/gmp022
Aptamer: MT32
Target: Virus coat protein of two apple stem pitting virus (ASPV) isolates: MT32 and PSA‐H
Type of nucleic acid: ssDNA
Sequence: 5′AGCCTCGTCTGTTCTCCCGGGGTGGTGGGTTCTTTTTGTGGTATTGGTGTGGGGGGCAGGGAAGACAAGCAGACGT3′
Sequence length: 76
GC content: 0.5789473684210527
Affinity: Kd: 55 nM for MT32 protein & 83 nM for PSA‐H protein, both via SPR
Pool type: 5′‐AGCCTCGTCTGTTCTCCC‐40N‐GGGAAGACAAGCAGACGT‐3′
Pool random region: 40
Binding buffer/conditions: PBS‐T solution: 10 mM Na2HPO4,2mMKH2PO4, 2.7 mM KCl, 137 mM NaCl, and 0.05% Triton‐X; pH 7.5 containing 0.1 µg/ml dIdC and 1 µg/ml BSA
Buffer type: PBS/phosphate buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection and Diagnostic: Although the significance of molecular diagnostics in routine plant virus detection is rapidly growing, the preferred methods are still antibody-based enzyme immunoassays. Summarily, our results present the selection and practical utilization of first plant virus-specific aptamers. Most important, the first application of ELONA for virus detection is demonstrated, which proposes a novel, more flexible, and cost-effective means of virus diagnostics."
Reference (2010, FASEB J ): Balogh Z, Lautner G, Bardóczy V, Komorowska B, Gyurcsányi RE, Mészáros T. Selection and versatile application of virus-specific aptamers. FASEB J. 2010 Nov;24(11):4187-95. doi: 10.1096/fj.09-144246. Epub 2010 Jul 12. PMID: 20624933.
Aptamer: PSA‐H
Target: Virus coat protein of two apple stem pitting virus (ASPV) isolates: MT32 and PSA‐H
Type of nucleic acid: ssDNA
Sequence: 5′AGCCTCGTCTGTTCTCCCAGCAAGGTTTGGTGTTGGTTGGTTGCTGGTTTTGGTTTCGGGAAGACAAGCAGACGT3′
Sequence length: 75
GC content: 0.52
Affinity: Kd: 8.0 nM for PSA‐H protein & 290 nM for MT32 protein, both via SPR
Pool type: 5′‐AGCCTCGTCTGTTCTCCC‐40N‐GGGAAGACAAGCAGACGT‐3′
Pool random region: 40
Binding buffer/conditions: PBS‐T solution: 10 mM Na2HPO4,2mMKH2PO4, 2.7 mM KCl, 137 mM NaCl, and 0.05% Triton‐X; pH 7.5 containing 0.1 µg/ml dIdC and 1 µg/ml BSA
Buffer type: PBS/phosphate buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection and Diagnostic: Although the significance of molecular diagnostics in routine plant virus detection is rapidly growing, the preferred methods are still antibody-based enzyme immunoassays. Summarily, our results present the selection and practical utilization of first plant virus-specific aptamers. Most important, the first application of ELONA for virus detection is demonstrated, which proposes a novel, more flexible, and cost-effective means of virus diagnostics."
Reference (2010, FASEB J ): Balogh Z, Lautner G, Bardóczy V, Komorowska B, Gyurcsányi RE, Mészáros T. Selection and versatile application of virus-specific aptamers. FASEB J. 2010 Nov;24(11):4187-95. doi: 10.1096/fj.09-144246. Epub 2010 Jul 12. PMID: 20624933.
Aptamer: Apta 5A
Target: 17 beta-Estradiol (17β-Estradiol) (E2）
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGTTCGTCCATTATTCTGGTAGCGTTGAACAACATTCAACACGCCCCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.5
Affinity: Kd: 27 μM
Pool type: 5′-AGCAGCACAGAGGTCAGTTC-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 10 mM HEPES, pH 7.4
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: Detection: " Aptamers targeting different functional groups of 17β-estradiol.The selected aptamers with affinities for different functional groups of E2 can potentially be applied to develop a cross-reactive aptasensor. This aptasensor introduces a promising tool for the future of in-field real-time monitoring of a wide range of steroid hormones."
Reference (2010, J Steroid Biochem Mol Biol ): Vanschoenbeek K, Vanbrabant J, Hosseinkhani B, Vermeeren V, Michiels L. Aptamers targeting different functional groups of 17β-estradiol. J Steroid Biochem Mol Biol. 2015 Mar;147:10-6. doi: 10.1016/j.jsbmb.2014.10.013. Epub 2014 Oct 22. PMID: 25465478.
Aptamer: Apta 6A
Target: 17 beta-Estradiol (17β-Estradiol) (E2）
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGTTCGTCGAATCAGCACCTCTGCATAGGTTACGTTTATACTGCGCCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.5125
Affinity: Kd: 36 μM
Pool type: 5′-AGCAGCACAGAGGTCAGTTC-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 10 mM HEPES, pH 7.4
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: Detection: " Aptamers targeting different functional groups of 17β-estradiol.The selected aptamers with affinities for different functional groups of E2 can potentially be applied to develop a cross-reactive aptasensor. This aptasensor introduces a promising tool for the future of in-field real-time monitoring of a wide range of steroid hormones."
Reference (2010, J Steroid Biochem Mol Biol ): Vanschoenbeek K, Vanbrabant J, Hosseinkhani B, Vermeeren V, Michiels L. Aptamers targeting different functional groups of 17β-estradiol. J Steroid Biochem Mol Biol. 2015 Mar;147:10-6. doi: 10.1016/j.jsbmb.2014.10.013. Epub 2014 Oct 22. PMID: 25465478.
Aptamer: Apta 8A
Target: 17 beta-Estradiol (17β-Estradiol) (E2）
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGTTCAGCGTCCTCTGCATAGTGATTTACGCTATGTGTACAGTGCCCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.5125
Affinity: Kd: 124 μM
Pool type: 5′-AGCAGCACAGAGGTCAGTTC-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 10 mM HEPES, pH 7.4
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: Detection: " Aptamers targeting different functional groups of 17β-estradiol.The selected aptamers with affinities for different functional groups of E2 can potentially be applied to develop a cross-reactive aptasensor. This aptasensor introduces a promising tool for the future of in-field real-time monitoring of a wide range of steroid hormones."
Reference (2010, J Steroid Biochem Mol Biol ): Vanschoenbeek K, Vanbrabant J, Hosseinkhani B, Vermeeren V, Michiels L. Aptamers targeting different functional groups of 17β-estradiol. J Steroid Biochem Mol Biol. 2015 Mar;147:10-6. doi: 10.1016/j.jsbmb.2014.10.013. Epub 2014 Oct 22. PMID: 25465478.
Aptamer: Apta 9A
Target: 17 beta-Estradiol (17β-Estradiol) (E2）
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGTTCCATGACTCTGCATAGGTCTAATGAAACTAGTTCTTATTTACCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.4375
Affinity: Kd: 52 μM
Pool type: 5′-AGCAGCACAGAGGTCAGTTC-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 10 mM HEPES, pH 7.4
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: Detection: " Aptamers targeting different functional groups of 17β-estradiol.The selected aptamers with affinities for different functional groups of E2 can potentially be applied to develop a cross-reactive aptasensor. This aptasensor introduces a promising tool for the future of in-field real-time monitoring of a wide range of steroid hormones."
Reference (2010, J Steroid Biochem Mol Biol ): Vanschoenbeek K, Vanbrabant J, Hosseinkhani B, Vermeeren V, Michiels L. Aptamers targeting different functional groups of 17β-estradiol. J Steroid Biochem Mol Biol. 2015 Mar;147:10-6. doi: 10.1016/j.jsbmb.2014.10.013. Epub 2014 Oct 22. PMID: 25465478.
Aptamer: Apta 11A
Target: 17 beta-Estradiol (17β-Estradiol) (E2）
Type of nucleic acid: ssDNA
Sequence: 5'AGCAGCACAGAGGTCAGTTCCAAGTCGTACGACACAGGGTAATCCTGTTTGGTAAAACGACCTATGCGTGCTACCGTGAA3'
Sequence length: 80
GC content: 0.5
Affinity: Kd: 51 μM
Pool type: 5′-AGCAGCACAGAGGTCAGTTC-N40-CCTATGCGTGCTACCGTGAA-3′
Pool random region: 40
Binding buffer/conditions: 10 mM HEPES, pH 7.4
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: Detection: " Aptamers targeting different functional groups of 17β-estradiol.The selected aptamers with affinities for different functional groups of E2 can potentially be applied to develop a cross-reactive aptasensor. This aptasensor introduces a promising tool for the future of in-field real-time monitoring of a wide range of steroid hormones."
Reference (2010, J Steroid Biochem Mol Biol ): Vanschoenbeek K, Vanbrabant J, Hosseinkhani B, Vermeeren V, Michiels L. Aptamers targeting different functional groups of 17β-estradiol. J Steroid Biochem Mol Biol. 2015 Mar;147:10-6. doi: 10.1016/j.jsbmb.2014.10.013. Epub 2014 Oct 22. PMID: 25465478.
Aptamer: Apta 19B
Target: 17 beta-Estradiol (17β-Estradiol) (E2）
Type of nucleic acid: ssDNA
Sequence: 5'TGTGTGTGAGACTTCGTTCCCCCGGTCGGTGGGGTAGGGGGCGTGGAGTCACCGGGGGGGCAGCAAGGCATCAGAGGTAT3'
Sequence length: 80
GC content: 0.65
Affinity: Kd: 6 μM
Pool type: 5'-TGTGTGTGAGACTTCGTTCC-N40-CAGCAAGGCATCAGAGGTAT-3'
Pool random region: 40
Binding buffer/conditions: PBS with 10% ethanol, 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: " Aptamers targeting different functional groups of 17β-estradiol.The selected aptamers with affinities for different functional groups of E2 can potentially be applied to develop a cross-reactive aptasensor. This aptasensor introduces a promising tool for the future of in-field real-time monitoring of a wide range of steroid hormones."
Reference (2010, J Steroid Biochem Mol Biol ): Vanschoenbeek K, Vanbrabant J, Hosseinkhani B, Vermeeren V, Michiels L. Aptamers targeting different functional groups of 17β-estradiol. J Steroid Biochem Mol Biol. 2015 Mar;147:10-6. doi: 10.1016/j.jsbmb.2014.10.013. Epub 2014 Oct 22. PMID: 25465478.
Aptamer: Apt10L
Target: Sulforhodamine analogue (ASR) fluorogen
Type of nucleic acid: ssRNA
Sequence: 5'GAAGCUUGGGAAUUCGAGCUCCUGACAGCAGGACCCUCACCUCGGUGAUGAUGGAGGGGCGCAAGGUUAACCGCCUCAGGGUCCUCGAUUCGAAGACGUCCAGCUGAUCUAGAUUCUAUAGUGUCACCUAAAU3'
Sequence length: 133
GC content: 0.5338345864661654
Affinity: Kd: 39.1 ± 7.6 μM (if purified with a G-25 column without denaturing and renaturing subsequent to in vitro transcription), 3.5 ± 1.5 μM (if purified using 6% polyacrylamide-7M urea gel) 
Pool type: 5'-GAAGCUUGGGAAUUCGAGCUCCUGACA-N60-AUUCGAAGACGUCCAGCUGAUCUAGAUUCUAUAGUGUCACCUAAAU-3'
Pool random region: 60
Binding buffer/conditions: PBS buffer (pH 7.4) containing 1 mM MgCl2
Divalent salt: MgCl
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 report here a new small molecule fluorogen and RNA aptamer pair for RNA labeling. This study demonstrates the value of combining in vitro SELEX and E. coli fluorescence screening with rational modifications in discovering and optimizing new fluorogen-RNA aptamer labeling pairs."
Additional information: *pool static regions determined by sequences
Reference (2010, ACS Chem Biol ): Lee, J., Lee, K. H., Jeon, J., Dragulescu-Andrasi, A., Xiao, F., & Rao, J. (2010). Combining SELEX screening and rational design to develop light-up fluorophore-RNA aptamer pairs for RNA tagging. ACS chemical biology, 5(11), 1065–1074. https://doi.org/10.1021/cb1001894
Aptamer: Apt10T3 (88mer)
Target: Sulforhodamine analogue (ASR) fluorogen
Type of nucleic acid: ssRNA
Sequence: 5'GGACAGCAGGACCCUCACCUCGGUGAUGAUGGAGGGGCGCAAGGUUAACCGCCUCAGGGUCCUCGACUCGAAGACGUCCAGCUGAUCC3'
Sequence length: 88
GC content: 0.625
Affinity: Kd: 26.9 ± 2.2 uM
Pool type: 5'-GAAGCUUGGGAAUUCGAGCUCCUGACA-N60-AUUCGAAGACGUCCAGCUGAUCUAGAUUCUAUAGUGUCACCUAAAU-3'
Pool random region: 60
Binding buffer/conditions: PBS buffer (pH 7.4) containing 1 mM MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Tuncation. To elucidate the interaction between the ASR probe and the RNA aptamer, we systematically modified both the ASR structure and the aptamer sequence and identified the structural elements important for binding affinity and fluorescence activation. A rationally designed ASR analogue displayed a 33-fold improvement in the binding affinity compared to the original ASR probe.
Application as quoted in the referenced paper: Detection: " We report here a new small molecule fluorogen and RNA aptamer pair for RNA labeling. This study demonstrates the value of combining in vitro SELEX and E. coli fluorescence screening with rational modifications in discovering and optimizing new fluorogen-RNA aptamer labeling pairs."
Additional information: *pool static regions determined by sequences
Reference (2010, ACS Chem Biol ): Lee, J., Lee, K. H., Jeon, J., Dragulescu-Andrasi, A., Xiao, F., & Rao, J. (2010). Combining SELEX screening and rational design to develop light-up fluorophore-RNA aptamer pairs for RNA tagging. ACS chemical biology, 5(11), 1065–1074. https://doi.org/10.1021/cb1001894
Aptamer: aptamer 807
Target: Recombinant human erythropoietin-alpha (rHuEPO-α)
Type of nucleic acid: ssDNA
Sequence: 5′CTTCTGCCCGCCTCCTTCCGATTGAAAGGTCTGTTTTTGGGGTTGGTTTGGGTCAATAGGAGACGAGATAGGCGGACACT3′
Sequence length: 80
GC content: 0.525
Affinity: Kd: 82 ± 32 nM
Pool type: 5′-CTTCTGCCCGCCTCCTTCC-N39-GGAGACGAGATAGGCGGACACT-3′
Pool random region: 39
Binding buffer/conditions: 20 mM Tris, 140 mM NaCl, 5 mM MgCl2, and 5 mM KCl (pH 7.4)
Divalent salt: MgCl
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: Diagnostic: " A lectin-mediated affinity chromatographic SELEX technique was developed to generate functional ssDNA aptamers for recombinant human erythropoietin-α (rHuEPO-α), an important pharmaceutical glycoprotein for the first time. Aptamer 807-39nt also exhibited a specific recognition for human bladder carcinoma cells and human urothelium tumors, which might provide a novel way to probe such tumors with overexpressed EPOs."
Additional information: WGA lectin-mediated affinity chromatographic SELEX
Reference (2010, Bioorg Med Chem ): Zhang, Z., Guo, L., Guo, A., Xu, H., Tang, J., Guo, X., & Xie, J. (2010). In vitro lectin-mediated selection and characterization of rHuEPO-α-binding ssDNA aptamers. Bioorganic & medicinal chemistry, 18(22), 8016–8025. https://doi.org/10.1016/j.bmc.2010.09.024
Aptamer: C13
Target: Protein tyrosine phosphatase 1B (PTP1B)
Type of nucleic acid: ssRNA
Sequence: 5'GGGAAUGGAUCCACAUCUACUGUGAUCAAUUUGGCAAUCCGCCACACGAGACUGCAGACUUGACGAAGCUU3'
Sequence length: 71
GC content: 0.4929577464788732
Affinity: Ki: 200 pM
Pool type: 5'-GGGAAUGGAUCCACAUCUAC‐N30-ACUGCAGACUUGACGAAGCUU-3'
Pool random region: 30
Binding buffer/conditions: HEPES (20 mM), MgCl2 (5 mM) and NaCl (125 mM) at pH 7.2
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " SELEX was used to create an RNA aptamer targeted to protein tyrosine phosphatase 1B (PTP1B), an enzyme implicated in type 2 diabetes, breast cancer and obesity. We also investigated various single-nucleotide modifications to probe their effects on the aptamer's secondary structure and inhibition properties. This family of aptamers represents an exciting option for the development of lead nucleotide-based compounds in combating several human cancers and metabolic diseases."
Reference (2010, Chembiochem ): Townshend B, Aubry I, Marcellus RC, Gehring K, Tremblay ML. An RNA aptamer that selectively inhibits the enzymatic activity of protein tyrosine phosphatase 1B in vitro. Chembiochem. 2010 Jul 26;11(11):1583-93. doi: 10.1002/cbic.201000208. PMID: 20572251.