Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 54
Aptamer sequence: GUACAACACAUCAUUACGGCUGCUAUUGGCUCCAAGCGUCUUUCUCCCUGGUCAAUAGUCCAGCCACCACG
Target unique ID: P00646
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_54 | F3-1 | Protein | CEA3_ECOLX | 4 nM | 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 30 mM NH4Cl | 15023071 |
Structure information of aptamer
| Aptamer Sequence: | GUACAACACAUCAUUACGGCUGCUAUUGGCUCCAAGCGUCUUUCUCCCUGGUCAAUAGUCCAGCCACCACG |
| 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_54 | Description | F3-1 |
| Aptamer chemistry | RNA | Length | 71 nt |
| GC content | 52.1% | Molecular weight | 22,528.34 Da |
| Molarity of 1 μg/μl solution | 44.39 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Target recognition |
| Sequence | GUACAACACAUCAUUACGGCUGCUAUUGGCUCCAAGCGUCUUUCUCCCUGGUCAAUAGUCCAGCCACCACG | ||
| Applications | Recognition of colicin E3 | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P00646 | Protein name | Colicin-E3 (EC 3.1.-.-) (Colicin-E3 A chain) (Ribonuclease) |
| Gene name(s) | ceaC | Organism | Colicin-E3 (EC 3.1.-.-) (Colicin-E3 A chain) (Ribonuclease) |
| Status | reviewed in uniprot database | Length | 551 |
| Mass | 57,963 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | N/A |
| PDB ID(s) | 1E44;1JCH;1UJW;2B5U;4UDM;4V5K; |
 |
Function | Inactivates ribosomes by hydrolyzing 16S RNA in 30S ribosomes at a specific site. |
Activity data
 |
Interaction ID | 54 |
| Target type | Protein | |
| Target unique ID | P00646 | |
| Activity | 4 nM | |
| Binding Conditions/Buffer | 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 30 mM NH4Cl |
|
| Assay | Inhibition of the colicin E3 activity by the aptamers in poly(U)-dependent poly(Phe) synthesis. As a control, a randomly selected RNA fragment from the initial pool was used, with a Kd of 147 nM |
|
| PubMed ID | 15023071 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_300 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAACUGCUGCAUCGUCUCCCACGUAUUACACAUGAAGAUAGUAAGUGCAAUCU | |
| Apta_292 | RNA | CUACGAACUCAUGACACAAGGAUGCAAUCUCAUCCCGCCAGCCCACCGU | |
| Apta_294 | RNA | AUACCAGCUUAUUCAAUUGCCUGAUUAGCGGUAUCACGAUUACUUACCUUCGUUGCUGAGAUAGUAAGUGCAAUCU | |
| Apta_668 | RNA | GGAACCCAACUAGGCGUUUGAGGGGAUUCGGCCACGGUAACAACCCCUC | |
| Apta_766 | RNA | GGUUACCAGCCUUCACUGCGGACGGACAGAGAGUGCAACCUGCCGUGCCGCACCACGGUCGGUCACAC | |
| Apta_225 | RNA | GGGGCCACCAACGACAUUUAUCGAAUUGAUAACCUUACGCGAGAGCGUAGUUCGUUGAUAUAAAUAGUGCCCAUGGAUC | |
| Apta_137 | RNA | GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC | |
| Apta_295 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAAAGCUAUCGCCCAAUUCGCAGUGAUAUCCUUUAAGAUAGUAAGUGCAAUCU | |
| Apta_299 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAGACUGGAUAUACUCUUAAGCAUUUCUAUAAUCGAGAUAGUAAGUGCAAUCU | |
| Apta_432 | RNA | GGGAGACAAGAAUAAACGCUCAAGGCAUUUCUGCUAGUCUGGUUGUAAGAUAUUCAACACGUGAGUUUCGACAGGAGGCUCACAACAGGC | |
| Apta_816 | RNA | GGGUUCACUGCAGACUUGACGAAGCUUGAGAGAUGCCCCCUGAUGUGCAUUCUUGUUGUGUUGCGGCAAUGGAUCCACAUCUACGAAUUC | |
| Apta_276 | RNA | GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC | |
| Apta_723 | RNA | GGGAGCUCAGAAUAAACGCUCAAAUCCGUGGACAGGGCGUAAGCGCCUUCGACAUGAGACACGGAUCCUGCGACGAAUUCAGC | |
| Apta_793 | RNA | GGGAGAGAACAAUGACCUGCGGUGCCAAGCCGUCGGGUUAUGUUGAUCUCCUCAAGGACGAGUGCAUUGCAUCACGUCAGUAG | |
| Apta_1290 | RNA | GCGCGAGAAACGGUCACUAGAAUAGUGGGCCGUCAUGCUAACGCCUCUUUCGGUGUUGGGGAAUAUUGGCCAAUCGAGU | |
| Apta_2 | RNA | GGGCUUCUCUGGUUAGACCAGAUUUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCC | |
| Apta_132 | RNA | GGGAGGACGAUGCGGCGUUUCCUCUGGUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_133 | RNA | GGGAGGACGAUGCGGUGAGUCGUUCCCUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_453 | RNA | GGGCUAGCUGAUCGUACCAGUAGCGUGGCCUGGGGGGCCUAGUCGUGCGAUACUAACAGCUAACACCC | |
| Apta_1224 | RNA | GGAGGCGCCAACUGAAUGAAUGUUCUGGAUCUGCUAGAGACUAUCUGCUUCGGCAGCACUCUCCGUUAACAACACGUACAUCCGUAACUAGUCGCGUCAC |
DEV TOOL
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