Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 273
Aptamer sequence: CUUAUAGGGGAGGCUGUGGUGAGGGAAUAUUAAGAGAAUUAACGGUCUAGUUCACCUCGA
Target unique ID: P08887
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_268 | AIR-3 | Protein | IL6RA_HUMAN | 19.7 nM | 137 mM NaCl, 2.7 mM KCl, 6.5 mM Na2HPO4, and 3 mM MgCl2 at PH 7.5 | 22258147 |
Structure information of aptamer
| Aptamer Sequence: | CUUAUAGGGGAGGCUGUGGUGAGGGAAUAUUAAGAGAAUUAACGGUCUAGUUCACCUCGA |
| The optimal secondary structure in dot-bracket notation: | .((((((......))))))(((((((((....(((..........))).)))).))))). |
| The centroid secondary structure in dot-bracket notation: | ..(((((......)))))..((((((((.....((..........))..)))).)))).. |
The MFE structure
The Centroid structure
The mountain plot representation
Aptamer information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Aptamer ID | Apta_268 | Description | AIR-3 |
| Aptamer chemistry | RNA | Length | 60 nt |
| GC content | 45.0% | Molecular weight | 19,673.49 Da |
| Molarity of 1 μg/μl solution | 50.83 μM | Number of G-quadruplexes | 2 |
| G-Score | 20 | Function | Targeted binding |
| Sequence | CUUAUAGGGGAGGCUGUGGUGAGGGAAUAUUAAGAGAAUUAACGGUCUAGUUCACCUCGA | ||
| Applications | To deliver bulky cargos, exemplified by fluorescently labeled streptavidin, into IL-6R presenting cells, thereby setting the stage for an aptamer-mediated escort of drug molecules to diseased cell populations or tissues | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P08887 | Protein name | Interleukin-6 receptor subunit alpha (IL-6 receptor subunit alpha) (IL-6R subunit alpha) (IL-6R-alpha) (IL-6RA) (IL-6R 1) (Membrane glycoprotein 80) (gp80) (CD antigen CD126) [Cleaved into: Soluble interleukin-6 receptor subunit alpha (sIL6R)] |
| Gene name(s) | IL6R | Organism | Interleukin-6 receptor subunit alpha (IL-6 receptor subunit alpha) (IL-6R subunit alpha) (IL-6R-alpha) (IL-6RA) (IL-6R 1) (Membrane glycoprotein 80) (gp80) (CD antigen CD126) [Cleaved into: Soluble interleukin-6 receptor subunit alpha (sIL6R)] |
| Status | reviewed in uniprot database | Length | 468 |
| Mass | 51,548 | Activity regulation | Classic and trans-signaling are both inhibited by tocilizumab, a humanized monoclonal antibody that blocks interleukin IL6R signaling |
| Involvement in disease | Hyper-IgE recurrent infection syndrome 5, autosomal recessive (HIES5) | Catalytic activity | N/A |
| PDB ID(s) | 1N26;1P9M;2ARW;5FUC;7DC8; |
 |
Function | Part of the receptor for interleukin 6. Binds to IL6 with low affinity, but does not transduce a signal. |
Activity data
 |
Interaction ID | 273 |
| Target type | Protein | |
| Target unique ID | P08887 | |
| Activity | 19.7 nM | |
| Binding Conditions/Buffer | 137 mM NaCl, 2.7 mM KCl, 6.5 mM Na2HPO4, and 3 mM MgCl2 at PH 7.5 |
|
| Assay | Aptamer AIR-3 binds the soluble IL-6 receptor (sIL-6R) with high affinity. Filter retention assays. Constant amounts (1 nM) of 32P-radioactively labeled aptamer AIR-3 (red diamonds) and RNA starting library R1 (black circles) were incubated with increasing amounts of sIL-6R (0–300 nM). Protein-bound RNA was visualized by autoradiography. Fractions of bound RNA molecules were plotted against the concentration of sIL-6R (logarithmic scale). Data points represent mean values of 10 independent measurements |
|
| PubMed ID | 22258147 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_388 | RNA | GCGGAAGCGUGCUGGGCUAGAAUAAUAAUAAGAAAACCAGUACUUUCGU | |
| Apta_237 | RNA | UUCAACGCUGUGAAGGGCUUAUACGAGCGGAUUACCC | |
| Apta_271 | RNA | CUGUCGAGCAUGCUCAGGGUAACGUAUAGUCAAGACACCUCAAGUGUAACU | |
| Apta_632 | RNA | GACGAGAAGGAGUGCUGGUUAUACUAGCGGUUAGGUCACUCGUC | |
| Apta_427 | RNA | GAAGCUUUCACACAACAAGGCCCGGGACUGUAUUAGGGAAAUUAGAGUACAGACAGUCGCCGUGGGUCGAAUUCCGCUCA | |
| Apta_601 | RNA | GGGAAUUCCGCGUGUGCGCCGCGGAAGAGGGAAUAUAGAGGCCAGCACAUAGUGAGGCCCUCCUCCC | |
| Apta_130 | RNA | GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA | |
| Apta_724 | RNA | GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC | |
| Apta_460 | RNA | GGAUGGCAGCGGAGAGUUGCUUGGAAUGCGUUAUAGUCUCUUAGGUGUGUACAGCCCACACCACUCUCC | |
| Apta_299 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAGACUGGAUAUACUCUUAAGCAUUUCUAUAAUCGAGAUAGUAAGUGCAAUCU | |
| Apta_1053 | RNA | GCCGCAAGUACGAGGGCGGCGCGCUCGACGCGGUUAGAUGAGUGUCGCCGUUUCCGAAGAUUGGCUACGCGGGG | |
| Apta_80 | RNA | GCAAUGGUACGGUACUUCCUUUGGAAGAUAGCUGGAGAACUAACCAAAAGUGCACGCUACUUUGCUAA | |
| Apta_136 | RNA | CGUGUCGUCCUGGUACGAUUUGGUAUAUAACCGUGGCUUUUCGACA | |
| Apta_660 | RNA | UGGGAGGAGUGCUGCUCUCCAGGCACUCUUGUUGCUCGGA | |
| Apta_859 | RNA | GGGAGUCUGAAGUCGGACUUGUUAUCAAUUCACUUCAGACU | |
| Apta_410 | RNA | GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG | |
| Apta_793 | RNA | GGGAGAGAACAAUGACCUGCGGUGCCAAGCCGUCGGGUUAUGUUGAUCUCCUCAAGGACGAGUGCAUUGCAUCACGUCAGUAG | |
| Apta_984 | RNA | GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA | |
| Apta_1168 | RNA | GCGACUACGGUGAGGGUCGGGUCCAGUAGCUUCGGCUACUGUUGAGUAGAGUGUGGGCUCCGUAGUCGC | |
| Apta_562 | RNA | GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUUAGGGCCAAGUGUGGUGAAAGACACACUCGAAACGGUAGCGAGAGCUC |
DEV TOOL
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