Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 287
Aptamer sequence: AGCAGCACAGAGGTCAGATGAGGCCTGGTGATCGTGCCCAGGCCATATGAGCAAGGAACCCCTATGCGTGCTACCGTGAA
Target unique ID: P0C573
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_278 | A-9 | Protein | HBEAG_HBVD3 | 22.9 nM | 1× PBS buffer (10 mM sodium phosphate, 137 mM NaCl, and 4.5 mM KCl, pH 7.4), 7 mM MgCl2 added after refolding Validated against patent samples in blood serum | 32250595 |
Structure information of aptamer
| Aptamer Sequence: | AGCAGCACAGAGGTCAGATGAGGCCTGGTGATCGTGCCCAGGCCATATGAGCAAGGAACCCCTATGCGTGCTACCGTGAA |
| 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_278 | Description | A-9 |
| Aptamer chemistry | DNA | Length | 80 nt |
| GC content | 57.5% | Molecular weight | 25,012.80 Da |
| Molarity of 1 μg/μl solution | 39.98 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | AGCAGCACAGAGGTCAGATGAGGCCTGGTGATCGTGCCCAGGCCATATGAGCAAGGAACCCCTATGCGTGCTACCGTGAA | ||
| Applications | Binding assay for HBeAg | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P0C573 | Protein name | External core antigen (HBeAg) (Precore protein) (p25) |
| Gene name(s) | C | Organism | External core antigen (HBeAg) (Precore protein) (p25) |
| Status | reviewed in uniprot database | Length | 212 |
| Mass | 24,350 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | N/A |
| PDB ID(s) | N/A |
 |
Function | May regulate immune response to the intracellular capsid in acting as a T-cell tolerogen, by having an immunoregulatory effect which prevents destruction of infected cells by cytotoxic T-cells. |
Activity data
 |
Interaction ID | 287 |
| Target type | Protein | |
| Target unique ID | P0C573 | |
| Activity | 22.9 nM | |
| Binding Conditions/Buffer | 1× PBS buffer (10 mM sodium phosphate, 137 mM NaCl, and 4.5 mM KCl, pH 7.4), 7 mM MgCl2 added after refolding Validated against patent samples in blood serum |
|
| Assay | Determination of the dissociation constants (Kd) for aptamers A-9 and A-9S bound to HBeAg. Varying concentrations (0-8 nM) of HBeAg were incubated with 10 pM aptamer at room temperature for 1 h. The aptamer bound to the HBeAg protein was measured using the affinity real-time qPCR assay. A negative control of affinity assay was performed in parallel using an oligonucleotide sequence unable to bind to HBeAg (Table S1). Error bars represent one standard deviation from six analyses involving duplicate experiments |
|
| PubMed ID | 32250595 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_277 | DNA | TTTTTTGGTCAGATGAGGCCTGGTGATCGTGCCCAGGCCATATGAGCAAGGAACCCCTATGCGTGCT | |
| Apta_105 | DNA | AGCAGCACAGAGGTCAGATGATGCTCTAGGCGAAAGACTTGGCGTAGAACGACGGGAGGCCCTATGCGTGCTACCGTGAA | |
| Apta_106 | DNA | AGCAGCACAGAGGTCAGATGGAGCCAGGAGTCGGCCTACAGAAGATTCTGATGTACCTCACCTATGCGTGCTACCGTGAA | |
| Apta_105 | DNA | AGCAGCACAGAGGTCAGATGATGCTCTAGGCGAAAGACTTGGCGTAGAACGACGGGAGGCCCTATGCGTGCTACCGTGAA | |
| Apta_106 | DNA | AGCAGCACAGAGGTCAGATGGAGCCAGGAGTCGGCCTACAGAAGATTCTGATGTACCTCACCTATGCGTGCTACCGTGAA | |
| Apta_175 | DNA | AGCAGCACAGAGGTCAGATGAGGACTGTCGATAAGTATAATGGCAAGTAGCTCGATACATCCTATGCGTGCTACCGTGAA | |
| Apta_103 | DNA | AGCAGCACAGAGGTCAGATGCATCGCATTATTCGCGGCCGGCCAACGAGAGTATGTTTCTCCTATGCGTGCTACCGTGAA | |
| Apta_108 | DNA | AGCAGCACAGAGGTCAGATGCTTTGCCACGGCAACGTCCCAAAACTAATGGTAACTATACCCTATGCGTGCTACCGTGAA | |
| Apta_103 | DNA | AGCAGCACAGAGGTCAGATGCATCGCATTATTCGCGGCCGGCCAACGAGAGTATGTTTCTCCTATGCGTGCTACCGTGAA | |
| Apta_108 | DNA | AGCAGCACAGAGGTCAGATGCTTTGCCACGGCAACGTCCCAAAACTAATGGTAACTATACCCTATGCGTGCTACCGTGAA | |
| Apta_228 | DNA | AGCAGCACAGAGGTCAGATGCGGCGCGGGGTCTTTTACAAATAGTTGTCCTAGCCACGCCTATGCGTGCTACCGTGAA | |
| Apta_99 | DNA | AGCAGCACAGAGGTCAGATGTCGGGCGGTTCGGGACCTTGCTGCGACATATGCGTATTATCCTATGCGTGCTACCGTGAA | |
| Apta_100 | DNA | AGCAGCACAGAGGTCAGATGATTCAAGGGTAACACATCCAGGGGAACGGAATTGCAGCCCCCTATGCGTGCTACCGTGAA | |
| Apta_107 | DNA | AGCAGCACAGAGGTCAGATGTTCATTTCAGTTGACCGATAGCATTGAGCAATGATCTATTCCTATGCGTGCTACCGTGAA | |
| Apta_99 | DNA | AGCAGCACAGAGGTCAGATGTCGGGCGGTTCGGGACCTTGCTGCGACATATGCGTATTATCCTATGCGTGCTACCGTGAA | |
| Apta_100 | DNA | AGCAGCACAGAGGTCAGATGATTCAAGGGTAACACATCCAGGGGAACGGAATTGCAGCCCCCTATGCGTGCTACCGTGAA | |
| Apta_107 | DNA | AGCAGCACAGAGGTCAGATGTTCATTTCAGTTGACCGATAGCATTGAGCAATGATCTATTCCTATGCGTGCTACCGTGAA | |
| Apta_173 | DNA | AGCAGCACAGAGGTCAGATGGCAGGTTTCGACGTACAATGCTATGGAGGCTTTATGATCGCCTATGCGTGCTACCGTGAA | |
| Apta_174 | DNA | AGCAGCACAGAGGTCAGATGTCGGTCTTGTGTATACATACCCGTGTGTTTTCATCTCAGGCCTATGCGTGCTACCGTGAA | |
| Apta_177 | DNA | AGCAGCACAGAGGTCAGATGCCATAGGTGCCTGAATTGTCCCAAACATTCGCATGATCGACCTATGCGTGCTACCGTGAA |
DEV TOOL
 |
 |
 |
 |