Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1230
Aptamer sequence: GCGACUACGGUGAGGGUCGGGUCCAGUAGCUUCGGCUACUGUUGAGUAGAGUGUGGGCUCCGUAGUCGC
Target unique ID: 70808995
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_1168 | iSpinach | Molecule | Dfhbi | N/A | 2 mM of each NTP, 25 mM MgCl2, 40 mM Tris-HCl pH 8.0, 5 mM DTT, 1 mM Spermidine | 28939697 |
Structure information of aptamer
| Aptamer Sequence: | GCGACUACGGUGAGGGUCGGGUCCAGUAGCUUCGGCUACUGUUGAGUAGAGUGUGGGCUCCGUAGUCGC |
| 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_1168 | Description | iSpinach |
| Aptamer chemistry | RNA | Length | 69 nt |
| GC content | 60.9% | Molecular weight | 22,333.19 Da |
| Molarity of 1 μg/μl solution | 44.78 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Live-cell imaging |
| Sequence | GCGACUACGGUGAGGGUCGGGUCCAGUAGCUUCGGCUACUGUUGAGUAGAGUGUGGGCUCCGUAGUCGC | ||
| Applications | Dynamic localizations | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| PubChem ID | 70808995 | Molecular name | Dfhbi |
| Molecular formula | C12H10F2N2O2 | Molecular weight | 252.22 |
| IUPAC name | (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2,3-dimethylimidazol-4-one | InChIKey | ZDDIJYXDUBFLID-YHYXMXQVSA-N |
| LogP | 1.902 | Topological polar surface area | 52.9 |
| Hydrogen bond acceptor | 3 | Hydrogen bond donor | 1 |
Synonym(s): DFHBI; 1241390-29-3; (5z)-5-(3,5-Difluoro-4-Hydroxybenzylidene)-2,3-Dimethyl-3,5-Dihydro-4h-Imidazol-4-One; 4-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-1,2-dimethyl-4,5-dihydro-1H-imidazol-5-one; 5 (Z)-5-[(3,5-Difluoro-4-hydroxyphenyl)methylene]-3,5-dihydro-2,3-dimethyl-4H-Imidazol-4-one; SCHEMBL12960487; ZINC98208407; AKOS027470225; HY-110250; CS-0033115; Q27453616; (5Z)-5-[(3,5-DIFLUORO-4-HYDROXYPHENYL)METHYLIDENE]-2,3-DIMETHYLIMIDAZOL-4-ONE; (z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1h-imidazol-5(4h)-one; (Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one; 4-(3,5-Difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazole-5(4H)-one; 4-[(Z)-3,5-Difluoro-4-hydroxybenzylidene]-1,2-dimethyl-1H-imidazole-5(4H)-one; (5Z)-5-[(3,5-Difluoro-4-hydroxyphenyl)methylene]-3,5-dihydro-2,3-dimethyl-4H-imidazol-4-one
Activity data
 |
Interaction ID | 1230 |
| Target type | Molecule | |
| Target unique ID | 70808995 | |
| Activity | N/A | |
| Binding Conditions/Buffer | 2 mM of each NTP, 25 mM MgCl2, 40 mM Tris-HCl pH 8.0, 5 mM DTT, 1 mM Spermidine |
|
| Assay | Transcription efficiency of the genes coding for iSpinach and its D5 variants |
|
| PubMed ID | 28939697 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_59 | RNA | GGACCUCGGCGAAAGCUAACGUCUCAUGGCUAAAUUGCCAUGUUGCUACAAAUGAUAUGACUAGAGAGGUUAGGUGCCUCGUGAUGUCCAGUCGC | |
| Apta_1221 | RNA | GGAGGCGCCAACUGAAUGAACGAGUUGAAAUGCGGAUCAAGUUACUGCUUCGGCAGUACCUAGUGGGAAAAGUUCUUGGGUCCGUAACUAGUCGCGUCAC | |
| Apta_594 | RNA | GGGCUAUUGCUGGAGGGGCGCCACAUGAAAGUGGUGGUUGGGUGCGGUCGGCGAUAGCUC | |
| Apta_312 | RNA | GGGAAAAGAGACGGCCGGCGCCAUAGCCGAGAUCCGAGGUGUUGCCGAGAA | |
| Apta_613 | RNA | GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC | |
| Apta_380 | RNA | GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG | |
| Apta_793 | RNA | GGGAGAGAACAAUGACCUGCGGUGCCAAGCCGUCGGGUUAUGUUGAUCUCCUCAAGGACGAGUGCAUUGCAUCACGUCAGUAG | |
| Apta_410 | RNA | GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG | |
| Apta_415 | RNA | GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_244 | RNA | GCUUCCGGAGAGAAGGGUCAAAGUUGUGCGGGAGUGUGUUGUGG | |
| Apta_402 | RNA | GCCUGUAAGGUGGUCGGUGUGGCGAGUGUGUUAGGAGAGAUUGC | |
| Apta_453 | RNA | GGGCUAGCUGAUCGUACCAGUAGCGUGGCCUGGGGGGCCUAGUCGUGCGAUACUAACAGCUAACACCC | |
| Apta_305 | RNA | GGGAGGACGAUGCGGAUCGCCCUGAACCGGCCCAGCAGACUGCUGACGGCACGAUCCGCAUCGUCCUCCC | |
| Apta_575 | RNA | AGAGCUUGACGGUCCCGAGAGUCGAGCCCAAGCUGACACUGGACCUUUGCGGACCACGUGUUGAUCGUCG | |
| Apta_612 | RNA | GGGCGACCCUGAUGAGCCUUAGGAUAUGCUUCGGCAGAAGGACGUCGAAACGGUGAAAGCCGUAGGUUGCCC | |
| Apta_396 | RNA | GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_397 | RNA | GGGAGGACGAUGCGGAUACCAGGAUCACAUCCUGAGGAACCCCGGCUCCCAACCUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_398 | RNA | GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_414 | RNA | GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_467 | RNA | GGGAGGACGAUGCGGCAGUGCCCAACCGGAACAACAACCACCGGCGGCUCCUGCUCAGACGACUCGCUGAGGAUCCGAGA |
DEV TOOL
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