Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 55
Aptamer sequence: GACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGAGGGCUCGGACUCUGAUUGCCUCCCCGCACC
Target unique ID: P00646
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_55 | F4-1 | Protein | CEA3_ECOLX | 7 nM | 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 30 mM NH4Cl | 15023071 |
Structure information of aptamer
| Aptamer Sequence: | GACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGAGGGCUCGGACUCUGAUUGCCUCCCCGCACC |
| 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_55 | Description | F4-1 |
| Aptamer chemistry | RNA | Length | 70 nt |
| GC content | 52.9% | Molecular weight | 22,422.30 Da |
| Molarity of 1 μg/μl solution | 44.60 μM | Number of G-quadruplexes | 2 |
| G-Score | 20 | Function | Target recognition |
| Sequence | GACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGAGGGCUCGGACUCUGAUUGCCUCCCCGCACC | ||
| 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 | 55 |
| Target type | Protein | |
| Target unique ID | P00646 | |
| Activity | 7 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_1223 | RNA | GGAGGCGCCAACUGAAUGAAAGGUUACGCUUCAACGCCGUGCAGCUGCUUCGGCAGGCUUGUGAGUACAUGGCCCAUUGAUCCGUAACUAGUCGCGUCAC | |
| Apta_276 | RNA | GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC | |
| Apta_429 | RNA | GCAUGCAGUGUCUAUUCUCGAGUAGCGAUCGUUGAAGGGGUAUAAGGUUGGCAGAUCGCUAGCAUGCAACUGACUCGGAUAAGCA | |
| Apta_2 | RNA | GGGCUUCUCUGGUUAGACCAGAUUUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCC | |
| Apta_157 | RNA | GGGUUCACUGCAGACUUGACGAAGCUUACAAACAAGAGCAAAAAGGGAGUUGACGUAGACUGUGCGGAAUGGAUCCACAUCUACGAAUUC | |
| Apta_431 | RNA | CAGGCAUGCCUAGCUAAGCAGCCCAUGGCUUAUGCGCGGAAUAUUGGCUUCCGUUC | |
| Apta_460 | RNA | GGAUGGCAGCGGAGAGUUGCUUGGAAUGCGUUAUAGUCUCUUAGGUGUGUACAGCCCACACCACUCUCC | |
| Apta_707 | RNA | GGCCUAAAACAUACCAGAUUUCGAUCUGGAGAGGUGAAGAAUUCGACCACCUAGGCCGGU | |
| Apta_1053 | RNA | GCCGCAAGUACGAGGGCGGCGCGCUCGACGCGGUUAGAUGAGUGUCGCCGUUUCCGAAGAUUGGCUACGCGGGG | |
| Apta_1166 | RNA | GAUGUAACUGAAUGAAAUGGUGAAGGACGGGUCCAGUAGGCUGC | |
| Apta_1226 | RNA | GGAGGCGCCAACUGAAUGAAGGUGUAUUUCAGUUAAAGAACUUGCUGCUUCGGCAGCGUUCUGAGUUACUAGUCCAAUAAUCCGUAACUAGUCGCGUCAC | |
| Apta_720 | RNA | GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA | |
| Apta_59 | RNA | GGACCUCGGCGAAAGCUAACGUCUCAUGGCUAAAUUGCCAUGUUGCUACAAAUGAUAUGACUAGAGAGGUUAGGUGCCUCGUGAUGUCCAGUCGC | |
| Apta_724 | RNA | GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC | |
| Apta_886 | RNA | GGGAGACGAUAUUCGUCCAUUCGGGUGGCCCGUGUCUGAGCGGGGACGGCCACUUGAGCGCCGCUGUCCGACUGAAUUCUCGACC | |
| Apta_723 | RNA | GGGAGCUCAGAAUAAACGCUCAAAUCCGUGGACAGGGCGUAAGCGCCUUCGACAUGAGACACGGAUCCUGCGACGAAUUCAGC | |
| Apta_793 | RNA | GGGAGAGAACAAUGACCUGCGGUGCCAAGCCGUCGGGUUAUGUUGAUCUCCUCAAGGACGAGUGCAUUGCAUCACGUCAGUAG | |
| Apta_499 | RNA | GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC | |
| Apta_256 | RNA | GGGCGCUAAGUCCUCGCUCAUGCGCGUCCCAUGGGGUAUAGAGGGGUCGAAGUGGACGCGCGACUCGGAUCCU | |
| Apta_1222 | RNA | GGAGGCGCCAACUGAAUGAAACCGUGCUAAGGAGUUGGACUCCGCUGCUUCGGCAGAGCGAUAUAGUGCCAGCUGAUACAUCCGUAACUAGUCGCGUCAC |
DEV TOOL
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