Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 285
Aptamer sequence: GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC
Target unique ID: P0A7I0
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_276 | classⅡ-1 | Protein | RF1_ECOLI | 30 nM | Elution Buffer (250 mM imidazole) | 17188871 |
Structure information of aptamer
| Aptamer Sequence: | GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC |
| 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_276 | Description | classⅡ-1 |
| Aptamer chemistry | RNA | Length | 85 nt |
| GC content | 52.9% | Molecular weight | 27,459.08 Da |
| Molarity of 1 μg/μl solution | 36.42 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC | ||
| Applications | Enhanced the amber suppression efficiency in the presence of an anticodonadjusted (CUA) suppressor tRNA without practically damaging the protein translation machinery of the cell-free extract of E.coli, as confirmed by the translation of amber-mutated (gfpamber141 or gfpamber178) and wild-type (gfpwild) genes of GFP | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P0A7I0 | Protein name | Peptide chain release factor RF1 (RF-1) |
| Gene name(s) | prfA sueB uar b1211 JW1202 | Organism | Peptide chain release factor RF1 (RF-1) |
| Status | reviewed in uniprot database | Length | 360 |
| Mass | 40,517 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | N/A |
| PDB ID(s) | 2B3T;5J30;5J3C;5J4D;5O2R;6GWT;6GXM;6GXN;6GXO;6ORL; |
 |
Function | Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. |
Activity data
 |
Interaction ID | 285 |
| Target type | Protein | |
| Target unique ID | P0A7I0 | |
| Activity | 30 nM | |
| Binding Conditions/Buffer | Elution Buffer (250 mM imidazole) |
|
| Assay | Overlay of SPR sensorgrams showing the specific affinity of class II-1 aptamer for E. coli RF-1. Various concentrations of E. coli RF-1 (10–100 nM) or E. coli RF-2 (100 nM) were injected (total 60 lL, 180 s) at a flow rate of 20 lL/min over a sensor chip SA precoated with class II-1-bio aptamer. The arrow indicates the end of injection |
|
| PubMed ID | 17188871 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_874 | RNA | GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACAGAAGGACGUCGAAACGGUAGCGAGAGCUC | |
| Apta_984 | RNA | GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA | |
| Apta_1225 | RNA | GGAGGCGCCAACUGAAUGAAAGAGGUAACGAAAGAUGAUUGUGCCUGCUUCGGCAGUACAACUUCUCGGAUAAAUGAUUAUCCGUAACUAGUCGCGUCAC | |
| Apta_724 | RNA | GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC | |
| Apta_893 | RNA | ACCGAGUCCAGAAGCUUGUAGUACUUAUGUCCCAUCGAACGCAGUGUAUCUUGCACCGACUCUCUGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC | |
| Apta_1221 | RNA | GGAGGCGCCAACUGAAUGAACGAGUUGAAAUGCGGAUCAAGUUACUGCUUCGGCAGUACCUAGUGGGAAAAGUUCUUGGGUCCGUAACUAGUCGCGUCAC | |
| Apta_1222 | RNA | GGAGGCGCCAACUGAAUGAAACCGUGCUAAGGAGUUGGACUCCGCUGCUUCGGCAGAGCGAUAUAGUGCCAGCUGAUACAUCCGUAACUAGUCGCGUCAC | |
| Apta_499 | RNA | GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC | |
| Apta_1290 | RNA | GCGCGAGAAACGGUCACUAGAAUAGUGGGCCGUCAUGCUAACGCCUCUUUCGGUGUUGGGGAAUAUUGGCCAAUCGAGU | |
| Apta_909 | RNA | GGGAAUUCGAGCUCGGUACCUUUACCGUAAGGCCUGUCUUCGUUUGACAGCGGCUUGUUGACCCUCCACUUUGUACCUGCUGCCAACUGCAGGCAUGCAAGCUUGG | |
| Apta_55 | RNA | GACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGAGGGCUCGGACUCUGAUUGCCUCCCCGCACC | |
| Apta_156 | RNA | GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU | |
| Apta_314 | RNA | GGUUACCAGCCUUCACUGCUCCCGGACGCGUCUGUAUCCGCUACCCGCCGCACCACGGUCGGUCACAC | |
| Apta_575 | RNA | AGAGCUUGACGGUCCCGAGAGUCGAGCCCAAGCUGACACUGGACCUUUGCGGACCACGUGUUGAUCGUCG | |
| Apta_645 | RNA | CUGGACGACGGGGACGCCACUGGACUAGGUAAGCCAGGACCGUACGUCGGGAGCCGUCAGAAUA | |
| Apta_936 | RNA | GGAGCUCAGCCUUCACUGCGAUCACCGUGUCGGUGGCUAGUCGAUGUAUCCCGAUCACCAUUGGGGGCAAGUUUAGACAGGCACCACGGUCGGAUCCAC | |
| Apta_720 | RNA | GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA | |
| Apta_816 | RNA | GGGUUCACUGCAGACUUGACGAAGCUUGAGAGAUGCCCCCUGAUGUGCAUUCUUGUUGUGUUGCGGCAAUGGAUCCACAUCUACGAAUUC | |
| Apta_433 | RNA | GGGAGACAAGAAUAAACGCUCAACGUUCAGUAUAACAGUCCGAGUCUAACACACAAUGGGACACUGAAUUCGACAGGAGGCUCACAACAGGC | |
| Apta_1224 | RNA | GGAGGCGCCAACUGAAUGAAUGUUCUGGAUCUGCUAGAGACUAUCUGCUUCGGCAGCACUCUCCGUUAACAACACGUACAUCCGUAACUAGUCGCGUCAC |
DEV TOOL
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