Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 53
Aptamer sequence: UCCCUGGCCCAAGAUCCUAAUAAAGUUUUUUCGGACCGGAGCGAAACCACUAUCCUCUUAAGCAAUCUGU
Target unique ID: P00646
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_53 | F2-1 | Protein | CEA3_ECOLX | 14 nM | 10 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 30 mM NH4Cl | 15023071 |
Structure information of aptamer
| Aptamer Sequence: | UCCCUGGCCCAAGAUCCUAAUAAAGUUUUUUCGGACCGGAGCGAAACCACUAUCCUCUUAAGCAAUCUGU |
| 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_53 | Description | F2-1 |
| Aptamer chemistry | RNA | Length | 70 nt |
| GC content | 45.7% | Molecular weight | 22,256.20 Da |
| Molarity of 1 μg/μl solution | 44.93 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Target recognition |
| Sequence | UCCCUGGCCCAAGAUCCUAAUAAAGUUUUUUCGGACCGGAGCGAAACCACUAUCCUCUUAAGCAAUCUGU | ||
| 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 | 53 |
| Target type | Protein | |
| Target unique ID | P00646 | |
| Activity | 14 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_425 | RNA | UGCCGCCAUAUCACACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG | |
| Apta_426 | RNA | UGCCGCUAUAAUGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG | |
| Apta_295 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAAAGCUAUCGCCCAAUUCGCAGUGAUAUCCUUUAAGAUAGUAAGUGCAAUCU | |
| Apta_623 | RNA | GGGAAUGGAUCCACAUCUACGAAUUCACCGCGGGGUUGCGGACCGGGAGCUCCAGCUUCACUGCAGACUUGACGAAGCUU | |
| Apta_424 | RNA | UGCUAGUAUAUCGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG | |
| Apta_624 | RNA | GGGAAUGGAUCCACAUCUACGAAUUCGAAUUGCCGUAAUUUCCCGUGGAGCGAUGCUUCACUGCAGACUUGACGAAGCUU | |
| Apta_707 | RNA | GGCCUAAAACAUACCAGAUUUCGAUCUGGAGAGGUGAAGAAUUCGACCACCUAGGCCGGU | |
| Apta_1222 | RNA | GGAGGCGCCAACUGAAUGAAACCGUGCUAAGGAGUUGGACUCCGCUGCUUCGGCAGAGCGAUAUAGUGCCAGCUGAUACAUCCGUAACUAGUCGCGUCAC | |
| Apta_380 | RNA | GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG | |
| Apta_296 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAAACCUGGUCUCUCUGUCAGCAAAGACUAUGTUGAGAUAGUAAGUGCAAUCU | |
| Apta_270 | RNA | CUGUCGAACAUGCUGAGGGUAACGUACUGGCAAGCUCACCUCAGCGUAGCUAa | |
| Apta_1249 | RNA | AAUCGGCCCAAUUUUACCUUCGGACUUCAGUAUCUAGUGUGGCUUUAAAUCAUAGC | |
| Apta_430 | RNA | GGGAUAUCCUCGAGCAUAAGAAACAAGAUAGAUCCUGAAACUGUUUUAAGGUUGGCCGAUCUUCUGCUCGAGAAUGCAUGAAGCGUUCCAUAUUUUU | |
| Apta_297 | RNA | AUACCAGCUUAUUCAAUUGCCUGAGUAGCUGGGUCCGUCCCCACACAUUACCAUUUGUAGAUAGUAAGUGCAAUCU | |
| Apta_300 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAACUGCUGCAUCGUCUCCCACGUAUUACACAUGAAGAUAGUAAGUGCAAUCU | |
| Apta_382 | RNA | GGCGUGACCUGAUGAGUCACGCAGACGCUAGCGAAUUGGUUCCUCGAAAGGGGAAAGCGUUAUUAAGAAACCAAAAUGUGUUACGAAACGUUCCC | |
| Apta_129 | RNA | GGGAGGACGAUGCGGACACCGUUAAUCUGAGGCCCUGUCCUAUUCCUUCACGCCUCAGA | |
| Apta_316 | DNA | CCGCCCAAATCCCTAAGAGAAGACTGTAATGACATCAAACCAGACACACTACACACGCA | |
| Apta_1224 | RNA | GGAGGCGCCAACUGAAUGAAUGUUCUGGAUCUGCUAGAGACUAUCUGCUUCGGCAGCACUCUCCGUUAACAACACGUACAUCCGUAACUAGUCGCGUCAC | |
| Apta_895 | RNA | ACCGAGUCCAGAAGCUUGUAGUACUACCGCAACGUUGGCGUUCGGCGUUGGCCGCGUCAUCGCUAGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC |
DEV TOOL
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