Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1067
Aptamer sequence: GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA
Target unique ID: CRL-2299
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_984 | A15 | Cell | mouse endothelial cells（bEnd.3 [BEND3]） | 48.74 nM | 10 mmol/l HEPES, pH 7.4, 50 mmol/l NaCl, 1 mmol/l MgCl2, 1 mmol/l CaCl2, 0.01% bovine serum albumin | 23299833 |
Structure information of aptamer
| Aptamer Sequence: | GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA |
| 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_984 | Description | A15 |
| Aptamer chemistry | RNA | Length | 71 nt |
| GC content | 59.2% | Molecular weight | 22,911.55 Da |
| Molarity of 1 μg/μl solution | 43.65 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA | ||
| Applications | Binding to target tissue | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| ATCC ID | CRL-2299 | Cell name | mouse endothelial cells(bEnd.3 [BEND3]) |
| Category | Animal cells | Organism | Mus musculus, mouse |
| Product type | N/A | Cell type | endothelial cell |
| Morphology | endothelial | Tissue | Brain; Cerebral cortex |
| Disease | Endothelioma | Product format | Frozen |
| Antigen expression | ICAM-1 +; VCAM-1 +; MAdCAM-1 + | Genes expressed | Von Willebrand factor-; ICAM-1+; VCAM-1+; MAdCAM-1+ ; The expression of Peyer's Patch high endothelial receptor for lymphocytes, the mucosal vascular addressin (MAdCAM-1) and E-selectin can be induced on bEnd |
| Cell description | bEnd.3 [BEND3] are endothelial cells isolated from brain tissue derived from a mouse with endothelioma. Applications include neuroscience research. |
|
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| Application(s) | 3D cell culture; Neuroscience | ||
Activity data
 |
Interaction ID | 1067 |
| Target type | Cell | |
| Target unique ID | CRL-2299 | |
| Activity | 48.74 nM | |
| Binding Conditions/Buffer | 10 mmol/l HEPES, pH 7.4, 50 mmol/l NaCl, 1 mmol/l MgCl2, 1 mmol/l CaCl2, 0.01% bovine serum albumin |
|
| Assay | Equal amounts of aptamers (SCAP and A15) were peripherally injected in mice (n = 3-4) and after 4 hours, total RNA was isolated. Aptamer quantitation in brain, kidney, and liver was done using one-step qRT-PCR (5 μg of DNase-treated input RNA) by including 18S RNA as loading control |
|
| PubMed ID | 23299833 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_130 | RNA | GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA | |
| Apta_352 | RNA | GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA | |
| Apta_132 | RNA | GGGAGGACGAUGCGGCGUUUCCUCUGGUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_315 | RNA | GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA | |
| Apta_131 | RNA | GGGAGGACGAUGCGGUCCUGUCGUCUGUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_133 | RNA | GGGAGGACGAUGCGGUGAGUCGUUCCCUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_396 | RNA | GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_414 | RNA | GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_134 | RNA | GGGAGGACGAUGCGGGCCGUUGUUGUGUGCCGCCCCAGACGACUCGCCCGA | |
| Apta_135 | RNA | GGGAGGACGAUGCGGAUUCUGGUUACUGGCCGCCCCAGACGACUCGCCCGA | |
| Apta_398 | RNA | GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_467 | RNA | GGGAGGACGAUGCGGCAGUGCCCAACCGGAACAACAACCACCGGCGGCUCCUGCUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_399 | RNA | GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_415 | RNA | GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_305 | RNA | GGGAGGACGAUGCGGAUCGCCCUGAACCGGCCCAGCAGACUGCUGACGGCACGAUCCGCAUCGUCCUCCC | |
| Apta_129 | RNA | GGGAGGACGAUGCGGACACCGUUAAUCUGAGGCCCUGUCCUAUUCCUUCACGCCUCAGA | |
| Apta_397 | RNA | GGGAGGACGAUGCGGAUACCAGGAUCACAUCCUGAGGAACCCCGGCUCCCAACCUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_400 | RNA | GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_548 | RNA | GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC | |
| Apta_276 | RNA | GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC |
DEV TOOL
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