Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 628
Aptamer sequence: GGGCUAUUGCUGGAGGGGCGCCACAUGAAAGUGGUGGUUGGGUGCGGUCGGCGAUAGCUC
Target unique ID: 136591209
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_594 | DMHBI-binding aptamer | Molecule | 3,5-Dimethoxy-4-hydroxybenzylidene imidazolinone | 512 nM | 40 mM HEPES pH 7.4 (or 40 mM Bicine pH 8.0), 125 mM KCl, 5 mM MgCl2, and 5% DMSO | 21798953 |
Structure information of aptamer
| Aptamer Sequence: | GGGCUAUUGCUGGAGGGGCGCCACAUGAAAGUGGUGGUUGGGUGCGGUCGGCGAUAGCUC |
| 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_594 | Description | DMHBI-binding aptamer |
| Aptamer chemistry | RNA | Length | 60 nt |
| GC content | 63.3% | Molecular weight | 19,558.59 Da |
| Molarity of 1 μg/μl solution | 51.13 μM | Number of G-quadruplexes | 2 |
| G-Score | 20 | Function | Live-cell imaging |
| Sequence | GGGCUAUUGCUGGAGGGGCGCCACAUGAAAGUGGUGGUUGGGUGCGGUCGGCGAUAGCUC | ||
| Applications | Imaged in living cells | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| PubChem ID | 136591209 | Molecular name | 3,5-Dimethoxy-4-hydroxybenzylidene imidazolinone |
| Molecular formula | C12H12N2O4 | Molecular weight | 248.23 |
| IUPAC name | 4-[(4-hydroxy-3,5-dimethoxyphenyl)methylidene]-1H-imidazol-5-one | InChIKey | YYHQRYROONCAML-UHFFFAOYSA-N |
| LogP | 0.908 | Topological polar surface area | 80.15 |
| Hydrogen bond acceptor | 5 | Hydrogen bond donor | 2 |
Synonym(s): SCHEMBL16111649; 3,5-dimethoxy-4-hydroxybenzylidene imidazolinone
Activity data
 |
Interaction ID | 628 |
| Target type | Molecule | |
| Target unique ID | 136591209 | |
| Activity | 512 nM | |
| Binding Conditions/Buffer | 40 mM HEPES pH 7.4 (or 40 mM Bicine pH 8.0), 125 mM KCl, 5 mM MgCl2, and 5% DMSO |
|
| Assay | 13-2 enhances the fluorescence of DMHBI. Solutions containing DMHBI, 13-2 RNA, DMHBI with 13-2 RNA, or DMHBI with total HeLa cell RNA were photographed under illumination with 365 nm light |
|
| PubMed ID | 21798953 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_718 | RNA | GGGUUGUGAGCUCCCGGCUCGCAUUGUGAGGUGGAGGGGGACGUGCUGCAGGUCGACGCAUGCGCCG | |
| Apta_130 | RNA | GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA | |
| Apta_1168 | RNA | GCGACUACGGUGAGGGUCGGGUCCAGUAGCUUCGGCUACUGUUGAGUAGAGUGUGGGCUCCGUAGUCGC | |
| Apta_256 | RNA | GGGCGCUAAGUCCUCGCUCAUGCGCGUCCCAUGGGGUAUAGAGGGGUCGAAGUGGACGCGCGACUCGGAUCCU | |
| Apta_1124 | RNA | GGGCGAAUUCGGGUUGGAUAGUAGGCGCAUAUGGCAUCUUCGUGGUUGUGUAUUGCCCUUUAGUGAGGGUUAAUU | |
| Apta_496 | RNA | GGGCUAGCUGAUCGUACCCAGUAGCGUGGCAUGGGGUGCCUAGUCGGGCGAUACUAACAGCUAACACCC | |
| Apta_416 | RNA | GGACCUCGGCGAAAGCCGGUAACGCCACAAGUCGGAGGGUAAGAUCUGACAGGAACUGGGUGACGGAGGUUAGGUGC | |
| Apta_521 | RNA | GGGUUGGGAAGAAACUGUGGCACUUCGGUGCCAGCAACCC | |
| Apta_1166 | RNA | GAUGUAACUGAAUGAAAUGGUGAAGGACGGGUCCAGUAGGCUGC | |
| Apta_575 | RNA | AGAGCUUGACGGUCCCGAGAGUCGAGCCCAAGCUGACACUGGACCUUUGCGGACCACGUGUUGAUCGUCG | |
| Apta_500 | RNA | GGGAGAAAGGGAAGCUUGAGGUGCUAUGGAGUGGAGGAGUUGAAGGUGUCGGGGUUGGCAGAAGAAGGCGAGCGUACGGAUCCAUC | |
| Apta_613 | RNA | GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC | |
| Apta_566 | RNA | GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCCUGCGAUGCAGAAAGGUGCUGACGACACAUCGAAACGGUAGCGAGAGCUC | |
| Apta_576 | RNA | GGCACCAAAGCUGAAGUAGCGGGAUAACUCAAAUUACUUUAGGUGUAUGAAGGUGAAACUAGCAAUGAA | |
| Apta_984 | RNA | GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA | |
| Apta_696 | RNA | GAGUGCGCCCAUUGAUAAGAGCGUAGGUUCAACGGAGUCGUAGUCGUUCUCAAGUUGACGGUGCAUUAGAGUCCU | |
| Apta_547 | RNA | GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC | |
| Apta_157 | RNA | GGGUUCACUGCAGACUUGACGAAGCUUACAAACAAGAGCAAAAAGGGAGUUGACGUAGACUGUGCGGAAUGGAUCCACAUCUACGAAUUC | |
| Apta_172 | RNA | GGAGACAUCCCUCUUGUUGGUGGUGCCGUGUGGAUGUCUC | |
| Apta_244 | RNA | GCUUCCGGAGAGAAGGGUCAAAGUUGUGCGGGAGUGUGUUGUGG |
DEV TOOL
 |
 |
 |
 |