Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1227
Aptamer sequence: GAUGUAACUGAAUGAAAUGGUGAAGGACGGGUCCAGUAGGCUGC
Target unique ID: 101889712
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_1166 | Spinach2 | Molecule | (5z)-5-(3,5-Difluoro-4-Hydroxybenzylidene)-2-Methyl-3-(2,2,2-Trifluoroethyl)-3,5-Dihydro-4h-Imidazol-4-One | 560 nM | 40 mM HEPES pH 7.4, 125 mM KCl and 5 mM MgCl2 | 24393009 |
Structure information of aptamer
| Aptamer Sequence: | GAUGUAACUGAAUGAAAUGGUGAAGGACGGGUCCAGUAGGCUGC |
| 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_1166 | Description | Spinach2 |
| Aptamer chemistry | RNA | Length | 44 nt |
| GC content | 50.0% | Molecular weight | 14,327.58 Da |
| Molarity of 1 μg/μl solution | 69.80 μM | Number of G-quadruplexes | 2 |
| G-Score | 18 | Function | Live-cell imaging |
| Sequence | GAUGUAACUGAAUGAAAUGGUGAAGGACGGGUCCAGUAGGCUGC | ||
| Applications | Dynamic localizations | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| PubChem ID | 101889712 | Molecular name | (5z)-5-(3,5-Difluoro-4-Hydroxybenzylidene)-2-Methyl-3-(2,2,2-Trifluoroethyl)-3,5-Dihydro-4h-Imidazol-4-One |
| Molecular formula | C13H9F5N2O2 | Molecular weight | 320.21 |
| IUPAC name | (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-methyl-3-(2,2,2-trifluoroethyl)imidazol-4-one | InChIKey | AWYCLBWNRONMQC-WMZJFQQLSA-N |
| LogP | 2.834 | Topological polar surface area | 52.9 |
| Hydrogen bond acceptor | 3 | Hydrogen bond donor | 1 |
Synonym(s): DFHBI 1T; DFHBI-1T; 1539318-36-9; (5Z)-5-[(3,5-Difluoro-4-hydroxyphenyl)methylene]-3,5-dihydro-2-methyl-3-(2,2,2-trifluoroethyl)-4H-imidazol-4-one; (5z)-5-(3,5-Difluoro-4-Hydroxybenzylidene)-2-Methyl-3-(2,2,2-Trifluoroethyl)-3,5-Dihydro-4h-Imidazol-4-One; (Z)-5-(3,5-Difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one; SCHEMBL16714224; ZINC98208365; AKOS027470226; HY-110251; CS-0033116; Q27453430; (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-methyl-3-(2,2,2-trifluoroethyl)imidazol-4-one; 4-[(Z)-3,5-Difluoro-4-hydroxybenzylidene]-2-methyl-1-(2,2,2-trifluoroethyl)-1H-imidazole-5(4H)-one
Activity data
 |
Interaction ID | 1226 |
| Target type | Molecule | |
| Target unique ID | 70808995 | |
| Activity | 530 nM | |
| Binding Conditions/Buffer | 20 mM HEPES pH 7.4, 100 mM KCl and 100 µM MgCl2 |
|
| Assay | Emission spectra of Spinach and Spinach2 |
|
| PubMed ID | 24162923 | |
 |
Interaction ID | 1227 |
| Target type | Molecule | |
| Target unique ID | 101889712 | |
| Activity | 560 nM | |
| Binding Conditions/Buffer | 40 mM HEPES pH 7.4, 125 mM KCl and 5 mM MgCl2 |
|
| Assay | Emission spectra of Spinach and Spinach2 |
|
| PubMed ID | 24393009 | |
 |
Interaction ID | 1228 |
| Target type | Molecule | |
| Target unique ID | 129080921 | |
| Activity | 1300 nM | |
| Binding Conditions/Buffer | 40 mM HEPES pH 7.4, 125 mM KCl and 5 mM MgCl2 |
|
| Assay | Emission spectra of Spinach and Spinach2 |
|
| PubMed ID | 24393009 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_927 | RNA | UUACAAUGAGGUGGGACGCGGGUUGUGGUG | |
| Apta_1167 | RNA | GGCGCGAGGAAGGAGGUCUGAGGAGGUCACUGCGCC | |
| Apta_447 | RNA | ACGCUCAACGAGCCAGGAACAUCGACGUCAGCAAACGCGAGCGCAACCAGUAACACC | |
| Apta_242 | RNA | GCUUCCAGGAAGAGAAGUGUCAUGUGAUCAGUCCUGGUGGGUGG | |
| Apta_293 | RNA | CGGCCACAGAAUGAAAAACCUCAUCGAUGUUGCAUAGUUG | |
| Apta_379 | RNA | UACGACACGAUUGGGACGUGUCUAUGGGAC | |
| Apta_521 | RNA | GGGUUGGGAAGAAACUGUGGCACUUCGGUGCCAGCAACCC | |
| Apta_269 | RNA | AACGCUCAACGUCAGAAGGCAACGUAUAGGCAAGCACACUUCGACAUGAGGC | |
| Apta_594 | RNA | GGGCUAUUGCUGGAGGGGCGCCACAUGAAAGUGGUGGUUGGGUGCGGUCGGCGAUAGCUC | |
| Apta_718 | RNA | GGGUUGUGAGCUCCCGGCUCGCAUUGUGAGGUGGAGGGGGACGUGCUGCAGGUCGACGCAUGCGCCG | |
| Apta_51 | RNA | GCCUUAGUAACGUGCUUUGAUGUCGAUUCGACAGGAGGC | |
| Apta_55 | RNA | GACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGAGGGCUCGGACUCUGAUUGCCUCCCCGCACC | |
| Apta_89 | RNA | AAUAACCUUAAUGCGACGUUGGUUCGUCAACAUGG | |
| Apta_90 | RNA | ACAACCUAAAUGCGACGUUGGGUCAAAAACGUGAA | |
| Apta_94 | RNA | AUGACAGGAUGCAGAGCUCCACUGUCUAGUGUUUA | |
| Apta_155 | RNA | GACCCAGGGCCGGGACGCAAAGCAGCCAAAACAGACGGCCCCAGUCAGGGAGUU | |
| Apta_402 | RNA | GCCUGUAAGGUGGUCGGUGUGGCGAGUGUGUUAGGAGAGAUUGC | |
| Apta_599 | RNA | GUCUCUGUGUGCGCCAGAGAACACUGGGGCAGAUAUGGGCCAGCACAGAAUGAGGCCC | |
| Apta_606 | RNA | CGGUUGGAUGGGUGUUGGUGGUUUGUUGAGUCCAGGCGGC | |
| Apta_633 | RNA | GGCAUCGGAAAGUGGGUUGAUGUAAGUAACAGGCGAUGCC |
DEV TOOL
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