Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 324
Aptamer sequence: GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA
Target unique ID: P15209
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_315 | C4-3 | Protein | NTRK2_MOUSE | 2 nM | 0.901 mM CaCl2, 0.493 mM MgCl2, 2.67 mM KCl, 1.47 mM KH2PO4 , 137.93 mM NaCl and 8.06 mM Na2HPO4 | 22752556 |
Structure information of aptamer
| Aptamer Sequence: | GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA |
| 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_315 | Description | C4-3 |
| Aptamer chemistry | RNA | Length | 51 nt |
| GC content | 64.7% | Molecular weight | 16,670.76 Da |
| Molarity of 1 μg/μl solution | 59.99 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA | ||
| Applications | Identification of aptamer-based agonists for a variety of cell-surface signaling receptors | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P15209 | Protein name | BDNF/NT-3 growth factors receptor (EC 2.7.10.1) (GP145-TrkB/GP95-TrkB) (Trk-B) (Neurotrophic tyrosine kinase receptor type 2) (TrkB tyrosine kinase) |
| Gene name(s) | Ntrk2 Trkb | Organism | BDNF/NT-3 growth factors receptor (EC 2.7.10.1) (GP145-TrkB/GP95-TrkB) (Trk-B) (Neurotrophic tyrosine kinase receptor type 2) (TrkB tyrosine kinase) |
| Status | reviewed in uniprot database | Length | 821 |
| Mass | 92,133 | Activity regulation | The formation of active receptors dimers able to fully transduce the ligand-mediated signal, may be negatively regulated by the formation of inactive heterodimers with the non-catalytic isoforms |
| Involvement in disease | N/A | Catalytic activity | Reaction=ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein] |
| PDB ID(s) | N/A |
 |
Function | Receptor tyrosine kinase involved in the development and the maturation of the central and the peripheral nervous systems through regulation of neuron survival, proliferation, migration, differentiation, and synapse formation and plasticity. |
Activity data
 |
Interaction ID | 324 |
| Target type | Protein | |
| Target unique ID | P15209 | |
| Activity | 2 nM | |
| Binding Conditions/Buffer | 0.901 mM CaCl2, 0.493 mM MgCl2, 2.67 mM KCl, 1.47 mM KH2PO4 , 137.93 mM NaCl and 8.06 mM Na2HPO4 |
|
| Assay | C4-3 is specifically internalized by TrkB-expressing HEK cells. TrkB-expressing or TrkB-negative HEK cells were incubated with 100 nM FAM-labeled C4-3 or control RNA for 1 h at 37 °C. Surface-bound RNA was stripped from the cells with a salt/acid wash, and then cells were fixed with formaldehyde, permeabilized, and labeled with anti-FAM and fluorescent secondary antibodies. A, TrkB-expressing HEK cells incubated with C4-3. B, HEK cells incubated with C4-3. C, TrkB-expressing HEK cells incubated with control RNA. Note evidence of C4-3 immunoreactivity signal within TrkB-expressing HEK cells [punctate (e.g., see arrows) and diffuse fluorescence in A] and signal absence in cells lacking TrkB (B). Signal detected with control RNA in TrkB-expressing HEK cells (C) provides a measure of nonspecific uptake of RNA molecules of the size of C4-3 in these cells |
|
| PubMed ID | 22752556 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_131 | RNA | GGGAGGACGAUGCGGUCCUGUCGUCUGUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_132 | RNA | GGGAGGACGAUGCGGCGUUUCCUCUGGUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_133 | RNA | GGGAGGACGAUGCGGUGAGUCGUUCCCUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_134 | RNA | GGGAGGACGAUGCGGGCCGUUGUUGUGUGCCGCCCCAGACGACUCGCCCGA | |
| Apta_135 | RNA | GGGAGGACGAUGCGGAUUCUGGUUACUGGCCGCCCCAGACGACUCGCCCGA | |
| Apta_130 | RNA | GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA | |
| Apta_352 | RNA | GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA | |
| Apta_984 | RNA | GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA | |
| Apta_129 | RNA | GGGAGGACGAUGCGGACACCGUUAAUCUGAGGCCCUGUCCUAUUCCUUCACGCCUCAGA | |
| Apta_305 | RNA | GGGAGGACGAUGCGGAUCGCCCUGAACCGGCCCAGCAGACUGCUGACGGCACGAUCCGCAUCGUCCUCCC | |
| Apta_399 | RNA | GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_400 | RNA | GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_396 | RNA | GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_397 | RNA | GGGAGGACGAUGCGGAUACCAGGAUCACAUCCUGAGGAACCCCGGCUCCCAACCUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_414 | RNA | GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_415 | RNA | GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_398 | RNA | GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_660 | RNA | UGGGAGGAGUGCUGCUCUCCAGGCACUCUUGUUGCUCGGA | |
| Apta_467 | RNA | GGGAGGACGAUGCGGCAGUGCCCAACCGGAACAACAACCACCGGCGGCUCCUGCUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_230 | RNA | GGGAGGACGAUGCGGGCGUGAAUGGUGUUGUGAGG |
DEV TOOL
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