Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 868
Aptamer sequence: ATCCAGAGTGACGCAGCATTTTGACGCTTTATCCTTTTCTTATGGCGGGATAGTTTCGTGGACACGGTGGCTTAGT
Target unique ID: CRL-3413
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_784 | U2 | Cell | U87-EGFRvIII cells | 3.37 nM | 0.45 g of glucose, 10 mg yeast tRNA, 5 mg salmon sperm DNA, 0.1 g BSA and 0.5 ml of 1 M MgCl2 in 100 ml of 1X phosphate-buffered saline [PBS] | 24603483 |
Structure information of aptamer
| Aptamer Sequence: | ATCCAGAGTGACGCAGCATTTTGACGCTTTATCCTTTTCTTATGGCGGGATAGTTTCGTGGACACGGTGGCTTAGT |
| 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_784 | Description | U2 |
| Aptamer chemistry | DNA | Length | 76 nt |
| GC content | 47.4% | Molecular weight | 23,483.01 Da |
| Molarity of 1 μg/μl solution | 42.58 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Live-cell imaging |
| Sequence | ATCCAGAGTGACGCAGCATTTTGACGCTTTATCCTTTTCTTATGGCGGGATAGTTTCGTGGACACGGTGGCTTAGT | ||
| Applications | Molecular Imaging of Glioblastoma In Vivo | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| ATCC ID | CRL-3413 | Cell name | U87-EGFRvIII cells |
| Category | Human cells | Organism | Homo sapiens, human |
| Product type | N/A | Cell type | N/A |
| Morphology | bright smooth spheres | Tissue | Brain |
| Disease | Glioblastoma | Product format | Frozen |
| Antigen expression | N/A | Genes expressed | N/A |
| Cell description | N/A |
|
|
| Application(s) | 3D cell culture; Cancer research; Neuroscience | ||
Activity data
 |
Interaction ID | 868 |
| Target type | Cell | |
| Target unique ID | CRL-3413 | |
| Activity | 3.37 nM | |
| Binding Conditions/Buffer | 0.45 g of glucose, 10 mg yeast tRNA, 5 mg salmon sperm DNA, 0.1 g BSA and 0.5 ml of 1 M MgCl2 in 100 ml of 1X phosphate-buffered saline [PBS] |
|
| Assay | Good specificity and high affinity of selected aptamers to U87-EGFRvIII cells |
|
| PubMed ID | 24603483 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_786 | DNA | ATCCAGAGTGACGCAGCATTTGTATCCTATTTTGTTTATGTAATTGTCGTTGATCATGTGGACACGGTGGCTTAGT | |
| Apta_785 | DNA | ATCCAGAGTGACGCAGCATGAATCTTTTCTTTTGGTTTTGATATTTATAGTTGGTGAATGGACACGGTGGCTTAGT | |
| Apta_787 | DNA | ATCCAGAGTGACGCAGCATTTGTTTAATATGTTTTTTAATTCCCCTTGTGGTGTGTTGTGGACACGGTGGCTTAGT | |
| Apta_923 | DNA | ATCCAGAGTGACGCAGCATCGACCTCTGTGCGAGCGGGTTGCATATATATTTTGCATGGACACGGTGGCTTAGT | |
| Apta_1089 | DNA | ATCCAGAGTGACGCAGCAATTACCGATGGCTTGTTTGTAATGTAGGGTTCCGTCGGATTGGACACGGTGGCTTAGT | |
| Apta_725 | DNA | ATCCAGAGTGACGCAGCATGCTCATCCACGATTCTGGCGAATTTAGTGCCTGTCTTTTTCTCTTGGACACGGTGGCTTAGT | |
| Apta_922 | DNA | ATCCAGAGTGACGCAGCACACCGTTTGTATTCTGCATTGTTTTGCATTCTACATGGACACGGTGGCTTAGT | |
| Apta_1088 | DNA | ATCCAGAGTGACGCAGCATCGAGTGGCTTGTTTGTAATGTAGGGTTCCGGTCGTGGGTTGGACACGGTGGCTTAGT | |
| Apta_921 | DNA | ATCCAGAGTGACGCAGCACGAGCCAGACATCTCACACCTGTTGCATATACATTTTGCATGGACACGGTGGCTTAGT | |
| Apta_1293 | DNA | ATCCAGAGTGACGCAGCATGCCCTAGTTACTACTACTCTTTTTAGCAAACGCCCTCGCTTTGGACACGGTGGCTTAGT | |
| Apta_794 | DNA | ATCCAGAGTGACGCAGCAAGGAGATTCGAGGGGGAAGGTTTGTTATAGGGGTTAATGGACACGGTGGCTTAGT | |
| Apta_401 | DNA | ATCCAGAGTGACGCAGCAGATAAGTAGGTATCCGTTTGAAAAACTTTTCTGACCGTCCGACTATGGACACGGTGGCTTAGT | |
| Apta_920 | DNA | ATCCAGAGTGACGCAGCACGGCACTCACTCTTTGTTAAGTGGTCTGCTTCTTAACCTTCATCGACACGGTGGCTTA | |
| Apta_1090 | DNA | ATCCAGAGTGACGCAGCAGGGCTTGGGTTGGGAATAAGGATGTGGGAGGCGGCGAACATGGACACGGTGGCTTAGT | |
| Apta_288 | DNA | ATCCAGAGTGACGCAGCATTTCATCGGGTCCAAAAGGGGCTGCTCGGGATTGCGGATATGGACACGT | |
| Apta_1180 | DNA | GAATTCAGTCGGACAGCGCAATTGTGGTTCTTACCCTATCCCTTGTGTTTGGCGTTCGTTGCGATGGACGAATATCGTCTCCC | |
| Apta_734 | DNA | TCCTCGATGCACCAGTTCACCTTATTTGCTTCTTCTCTCTGTTCTGACTGGGTGCTGAGGA | |
| Apta_349 | DNA | ATACCAGCTTATTCAATTAGACGAGTTTTATTCATTTTCCATGTCGTAGCTTACCGTGAGATAGTAAGTGCAATCT | |
| Apta_535 | DNA | ATCCGTCACACCTGCTCTTGGGGTTATTACTCGTGAGATTGGGAATAGGTTACATGGTGTTGGCTCCCGTAT | |
| Apta_656 | DNA | GCACACCGATGGCGGTCCTGTTTTACGGTAGCTTATATGCAGGGGGTGTGCGTGGGGAGGTGCGGTTGC |
DEV TOOL
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