RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: M9-9DEL 60 (DEL60)
Target: Antibody-mediated inhibition of cytotoxic T cell antigen-4 (CTLA-4)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGGGAAUUCUAAUACGACUCACUAUAGGGAGAGAGGAAGAGGGAUAGGGCCGACGUGCCGCA3'
Sequence length: 63
GC content: 0.5555555555555556
Affinity: Kd: 60 nM
Pool type: 5'-ATCGACCTCTGGGTTATG-N40-CCCATCCCTCTTCCTC-3'
Pool random region: 40
Binding buffer/conditions: Binding buffer for Assay: HEPES wash buffer (20mM HEPES pH 7.4, 0.15M NaCl, 2mM CaCl2)  + 0.01% BSA
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated version of m9a-9 by 60 deletions
Application as quoted in the referenced paper: Therapeutic: " Development of RNA aptamers that bind CTLA-4 with high affinity and specificity. These aptamers inhibit CTLA-4 function in vitro and enhance tumor immunity in mice. Moreover, assembly of the aptamers into tetrameric forms significantly enhances their bioactivity in vitro and in vivo. These results demonstrate that aptamers can be used to manipulate the immune system for therapeutic applications and that multivalent versions of aptamers may be particularly potent agents in vivo."
Additional information: The contant region drived from figure 1 is 5'-GGGAGAGAGGAAGAGGGATAGGG-N40-CATAACCCAGAGGTCGATAGTACTGGATCCCCCC-3'
The pool/library in the supplement was reported in pool randon region
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 (2003, Cancer Res ): Santulli-Marotto, S., Nair, S. K., Rusconi, C., Sullenger, B., & Gilboa, E. (2003). Multivalent RNA aptamers that inhibit CTLA-4 and enhance tumor immunity. Cancer research, 63(21), 7483–7489.
Aptamer: M9-9DEL 60 (DEL60)
Target: CD28 receptor on T cell
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGGGAAUUCUAAUACGACUCACUAUAGGGAGAGAGGAAGAGGGAUAGGGCCGACGUGCCGCA3'
Sequence length: 63
GC content: 0.5555555555555556
Affinity: Kd: >1 μM
Pool type: 5'-ATCGACCTCTGGGTTATG-N40-CCCATCCCTCTTCCTC-3'
Pool random region: 40
Binding buffer/conditions: Binding buffer for Assay: HEPES wash buffer (20mM HEPES pH 7.4, 0.15M NaCl, 2mM CaCl2)  + 0.01% BSA
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated version of m9a-9 by 60 deletions
Application as quoted in the referenced paper: Therapeutic: " Development of RNA aptamers that bind CTLA-4 with high affinity and specificity. These aptamers inhibit CTLA-4 function in vitro and enhance tumor immunity in mice. Moreover, assembly of the aptamers into tetrameric forms significantly enhances their bioactivity in vitro and in vivo. These results demonstrate that aptamers can be used to manipulate the immune system for therapeutic applications and that multivalent versions of aptamers may be particularly potent agents in vivo."
Additional information: The contant region drived from figure 1 is 5'-GGGAGAGAGGAAGAGGGATAGGG-N40-CATAACCCAGAGGTCGATAGTACTGGATCCCCCC-3'
The pool/library in the supplement was reported in pool randon region
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 (2003, Cancer Res ): Santulli-Marotto, S., Nair, S. K., Rusconi, C., Sullenger, B., & Gilboa, E. (2003). Multivalent RNA aptamers that inhibit CTLA-4 and enhance tumor immunity. Cancer research, 63(21), 7483–7489.
Aptamer: pRNAwt
Target: ATP (Adenosine triphosphate)
Type of nucleic acid: ssRNA
Sequence: 5'UCAAUGGUACGGUACUUCCAUUGUCAUGUGUAUGUUGGGGAUUAAACCCUGAUUGAGUUCAGconCCCACAUACUUUGUUGAUUGGUUGUCAAUCAUGGCAAAAGUGCACGCUACUUUGA3'
Sequence length: 118
GC content: 0.423728813559322
Affinity: Apparent Kd: 1.3 ± 0.8 mM
Pool type: 5'-UCAAUGGUACGGUACUUCCAUUGUCAUGUGUA-N40-UACUUUGUUGAUUGGUUGUCAAUCAUGGCAAAAGUGCACGCUACUUUGA-3'
Pool random region: 40
Binding buffer/conditions: 300 mM NaCl, 20 mM Tris, pH 7.6, 5 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research and Detection: " The presence of an astonishing variety of unknown RNA species in cells and the finding that RNA has enzymatic activity have bred the notion that RNA might not be excluded from the group of ATPases that has long been believed to be only proteins. One method for the examination of this idea is the chemical approach using the in vitro selection-amplification technique to identify ATP-binding RNA dubbed aptamers from synthesized random RNA pools. Here we report that the central region of pRNA is similar to the ATP-binding RNA aptamer in sequence and structure. We also demonstrate that phi29 pRNA directly binds ATP."
Additional information: Gcon enlarged is a conserved base essential for ATP binding
Reference (2003, J Biol Chem ): Shu, D., & Guo, P. (2003). A viral RNA that binds ATP and contains a motif similar to an ATP-binding aptamer from SELEX. The Journal of biological chemistry, 278(9), 7119–7125. https://doi.org/10.1074/jbc.M209895200
Aptamer: aptRNA1
Target: ATP (Adenosine triphosphate)
Type of nucleic acid: ssRNA
Sequence: 5'UCAAUGGUACGGUACUUCCAUUGUCAUGUGUAGGGUUGGGAAGAAACUGUGGCACUUCGGUGCCAGconCAACCCUACUUUGUUGAUUGGUUGUCAAUCAUGGCAAAAGUGCACGCUACUUUGA3'
Sequence length: 122
GC content: 0.4672131147540984
Affinity: Apperant Kd: 0.1 ± 0.06 mM
Pool type: 5'-UCAAUGGUACGGUACUUCCAUUGUCAUGUGUA-N40-UACUUUGUUGAUUGGUUGUCAAUCAUGGCAAAAGUGCACGCUACUUUGA-3'
Pool random region: 40
Binding buffer/conditions: 300 mM NaCl, 20 mM Tris, pH 7.6, 5 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research and Detection: " The presence of an astonishing variety of unknown RNA species in cells and the finding that RNA has enzymatic activity have bred the notion that RNA might not be excluded from the group of ATPases that has long been believed to be only proteins. One method for the examination of this idea is the chemical approach using the in vitro selection-amplification technique to identify ATP-binding RNA dubbed aptamers from synthesized random RNA pools. Here we report that the central region of pRNA is similar to the ATP-binding RNA aptamer in sequence and structure. We also demonstrate that phi29 pRNA directly binds ATP."
Additional information: Gcon enlarged is a conserved base essential for ATP binding
Reference (2003, J Biol Chem ): Shu, D., & Guo, P. (2003). A viral RNA that binds ATP and contains a motif similar to an ATP-binding aptamer from SELEX. The Journal of biological chemistry, 278(9), 7119–7125. https://doi.org/10.1074/jbc.M209895200
Aptamer: tMG RNA
Target: MAb198 antibody, Rat
Type of nucleic acid: ssRNA
Sequence: 5'GGGCCGGAGGUUAGCUUGCCCAUGGCAAGCAGGGCGCCACGGACCC3'
Sequence length: 46
GC content: 0.717391304347826
Affinity: Kd: 30 nM
Pool type: 5'-GGGAGAGCGGAAGCGUGCUGGGCC-N40-CAUAACCCAGAGGUCGAUGG-3'
Pool random region: 40
Binding buffer/conditions: 30 mM Tris–HCl, pH 7.5, 150 mM NaCl, 10 mM MgCl2, 2 mM dithiothreitol, and 1% bovine serum albumin
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Mutated version of an aptamer selected in 2000; also tuncated the aptamer and (separately) PEGylated
Application as quoted in the referenced paper: Therapeutic: " To investigate the therapeutic potential of the RNA, we tested the ability of the RNA aptamer to protect the receptors in vivo from mAb198, a rat monoclonal antibody that recognizes the main immunogenic region on the AChR, and a significant fraction of patient autoantibodies with MG"
Additional information: https://www.koreascience.or.kr/article/JAKO200011920816102.pdf
Reference (2003, FEBS Lett ): Hwang, B., Han, K., & Lee, S. W. (2003). Prevention of passively transferred experimental autoimmune myasthenia gravis by an in vitro selected RNA aptamer. FEBS letters, 548(1-3), 85–89. https://doi.org/10.1016/s0014-5793(03)00745-2
Aptamer: #7
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCAAAGGAGTGGCTTTGGGAAGGTTGCCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.5974025974025974
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: #16
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCGTAGGTGTGGCTTTGGGAAGGTTGCCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.6103896103896104
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: #17
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCGGTTGGTGTGGGTATGGGAAGGTACCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.6103896103896104
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: #18
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCTAAGGAATGGCTATGGGAAGGTAGCCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.5844155844155844
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: #25
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCGGAAGGGTTGGCTGTGGGAAGGTACCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.6233766233766234
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: #26
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCAGGCAGGGATGGCTATGGGAAGGGCCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.6363636363636364
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: #27
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCCGAGGTATGGCTTTGGGAAGGTGGCCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.6233766233766234
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: #28
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCAGAAGGATTGGCTATGGAAAGGTCCCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.5844155844155844
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: #31
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCGGCAGGTTTGGCTATGGGAAGGGCCCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.6363636363636364
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: #32
Target: Pro‐urokinase (PLAU), Human
Type of nucleic acid: ssDNA
Sequence: 5′GACACCTGCGGATCCAAAGCGATGGCCAAGGTGTGGCTTTGGGAAGGTGGCCCATCGCAGCCCTGCAGGCTCTTCAG3'
Sequence length: 77
GC content: 0.6233766233766234
Affinity: Not reported
Pool type: 5′‐GACACCTGCGGATCCAAAGCGATGGC-N24-CCCATCGCAGCCCTGCAGGCTCTTCAG-3'
Pool random region: 24
Binding buffer/conditions: Not reported
Buffer type: Not Reported
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Detection of Human pro‐urokinase (PLAU) for thrombolytic therapy of acute myocardial infarction and acute ischemic stroke. We have isolated singlestranded DNA molecules with significantly increased binding affinity for human prourokinase by SELEX (systematic evolution of ligands by exponential enrichment) procedure from a pool of 1015 molecules containing 24 randomized positions which are flanked by defined regions."
Additional information: Selection is done with sDNA from this library that was radiolabelled by polynucleotide kinase and hybridized with a 37-nucleotide helper fixture
Reference (2004, Nucleosides Nucleotides Nucleic Acids ): Skrypina, N. A., Savochkina, L. P., & Beabealashvilli, R. S.h (2004). In vitro selection of single-stranded DNA aptamers that bind human pro-urokinase. Nucleosides, nucleotides & nucleic acids, 23(6-7), 891–893. https://doi.org/10.1081/NCN-200026037
Aptamer: M1
Target: 4,4′-methylenedianiline (MDA)
Type of nucleic acid: ssRNA
Sequence: 5′GCCUGUUGUGAGCCUCCUGUCGAACUGCGAUCAGCGGUAAAUUUCCGCGCAGCCUCCACGCCGCUUGAGCGUUUAUUCUUGUCUCCC3′
Sequence length: 87
GC content: 0.5747126436781609
Affinity: Kd: 0.45 μM
Pool type: 5′-GCCTGTTGTGAGCCTCCTGTCGAA-N40-TTGAGCGTTTATTCTTGTCTCCC-3′
Pool random region: 40
Binding buffer/conditions: 250 mM NaCl/50 mM Tris–HCl/5 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " The modification of cellular DNA by environmental substances is thought to be a crucial event in chemical induced carcinogenesis. Among the environmental carcinogens, aromatic amines are known for the fact that they can induce several types of cancers through the formation of so-called DNA adducts. These results open the possibility of using the SELEX technique to generate RNA molecules as diagnostic tools for the detection of DNA damaging compounds and ultimately DNA adducts."
Reference (2004, Biochem Biophys Res Commun ): Brockstedt, U., Uzarowska, A., Montpetit, A., Pfau, W., & Labuda, D. (2004). In vitro evolution of RNA aptamers recognizing carcinogenic aromatic amines. Biochemical and biophysical research communications, 313(4), 1004–1008. https://doi.org/10.1016/j.bbrc.2003.12.030