Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1031
Aptamer sequence: TAGGGAAGAGAAGGACATATGATACTGGCCTTGACACCCTGTTGTGGCTTGATGACAATAACATTGACTAGTACATGACCACTTGA
Target unique ID: BAA-2128
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_948 | EF508 | Cell | Enterococcus faecalis | 37 nM | 10 mM of Tris–EDTA bufer (pH 8.5) | 33262379 |
Structure information of aptamer
| Aptamer Sequence: | TAGGGAAGAGAAGGACATATGATACTGGCCTTGACACCCTGTTGTGGCTTGATGACAATAACATTGACTAGTACATGACCACTTGA |
| 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_948 | Description | EF508 |
| Aptamer chemistry | DNA | Length | 86 nt |
| GC content | 43.0% | Molecular weight | 26,627.10 Da |
| Molarity of 1 μg/μl solution | 37.56 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Target recognition |
| Sequence | TAGGGAAGAGAAGGACATATGATACTGGCCTTGACACCCTGTTGTGGCTTGATGACAATAACATTGACTAGTACATGACCACTTGA | ||
| Applications | Aptamer EF508 exhibited high binding afnity to E. faecalis cells (KD-value: 37 nM) and successfully discriminated E. faecalis from 20 diferent Enterococcus and non-Enterococcusspp | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| ATCC ID | BAA-2128 | Cell name | Enterococcus faecalis |
| Category | Bacteria | Organism | N/A |
| Product type | Drug-resistant bacterium | Cell type | N/A |
| Morphology | N/A | Tissue | N/A |
| Disease | N/A | Product format | Freeze-dried |
| Antigen expression | N/A | Genes expressed | N/A |
| Cell description | N/A |
|
|
| Application(s) | Antimicrobial resistance research; Drug development | ||
Activity data
 |
Interaction ID | 1031 |
| Target type | Cell | |
| Target unique ID | BAA-2128 | |
| Activity | 37 nM | |
| Binding Conditions/Buffer | 10 mM of Tris–EDTA bufer (pH 8.5) |
|
| Assay | Binding saturation curve of aptamer EF508 to E. faecalis cells. Cells were incubated with increasing concentrations of aptamer (0, 1, 3, 10, 30, 100 and 300?nM) and measured by qPCR. Data points represent the mean of three biological replicates. A non-linear regression curve was ftted to the data using SigmaPlot version 14.0. Te dissociation constant (KD) is shown as the mean ± SD |
|
| PubMed ID | 33262379 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_236 | DNA | AGCAGCACAGAGGTCAGATGAGATGGTTGACCGGTTGATGTGATTAAGGAGACGTCGATTCCTATGCGTGCTACCGTGAA | |
| Apta_99 | DNA | AGCAGCACAGAGGTCAGATGTCGGGCGGTTCGGGACCTTGCTGCGACATATGCGTATTATCCTATGCGTGCTACCGTGAA | |
| Apta_99 | DNA | AGCAGCACAGAGGTCAGATGTCGGGCGGTTCGGGACCTTGCTGCGACATATGCGTATTATCCTATGCGTGCTACCGTGAA | |
| Apta_107 | DNA | AGCAGCACAGAGGTCAGATGTTCATTTCAGTTGACCGATAGCATTGAGCAATGATCTATTCCTATGCGTGCTACCGTGAA | |
| Apta_107 | DNA | AGCAGCACAGAGGTCAGATGTTCATTTCAGTTGACCGATAGCATTGAGCAATGATCTATTCCTATGCGTGCTACCGTGAA | |
| Apta_495 | DNA | GGGAATGGATCCACATCTACGTATTACTGCTGGTGACGAGGGCTAGACGACGTACCTTCACTGCAGACTTGACGAAGCTT | |
| Apta_502 | DNA | GGGAGACAAGAATAAACGCTCAAATGGACTTTTGAATGTGGCAACAAATTCGACAGGAGGCTCACAACAGGC | |
| Apta_101 | DNA | AGCAGCACAGAGGTCAGATGTGTTAGGCTGGGACACGTATTACACTTACCGTAAATATTTCCTATGCGTGCTACCGTGAA | |
| Apta_104 | DNA | AGCAGCACAGAGGTCAGATGCAAACCACAGCCTGAGTGGTTAGCGTATGTCATTTACGGACCTATGCGTGCTACCGTGAA | |
| Apta_104 | DNA | AGCAGCACAGAGGTCAGATGCAAACCACAGCCTGAGTGGTTAGCGTATGTCATTTACGGACCTATGCGTGCTACCGTGAA | |
| Apta_101 | DNA | AGCAGCACAGAGGTCAGATGTGTTAGGCTGGGACACGTATTACACTTACCGTAAATATTTCCTATGCGTGCTACCGTGAA | |
| Apta_175 | DNA | AGCAGCACAGAGGTCAGATGAGGACTGTCGATAAGTATAATGGCAAGTAGCTCGATACATCCTATGCGTGCTACCGTGAA | |
| Apta_232 | DNA | AGCAGCACAGAGGTCAGATGCTATGAGCAGATCCGATAGAAAGTTAATGCCCTAGAACATCCTATGCGTGCTACCGTGAA | |
| Apta_234 | DNA | AGCAGCACAGAGGTCAGATGAAATTTTGCACTTACTTGACGTTTCCTCGATAGCCACAAGCCTATGCGTGCTACCGTGAA | |
| Apta_278 | DNA | AGCAGCACAGAGGTCAGATGAGGCCTGGTGATCGTGCCCAGGCCATATGAGCAAGGAACCCCTATGCGTGCTACCGTGAA | |
| Apta_790 | DNA | GGGAGACAAGAATAAACGCTCAAGAAGTGAAAATGACAGAACACAACATTCGACAGGAGGCTCACAACAGGC | |
| Apta_920 | DNA | ATCCAGAGTGACGCAGCACGGCACTCACTCTTTGTTAAGTGGTCTGCTTCTTAACCTTCATCGACACGGTGGCTTA | |
| Apta_140 | DNA | GGCAGGAAGACAAACACGATGGGGGGGTATGATTTGATGTGGTTGTTGCATGATCGTGGTCTGTGGTGCTGT | |
| Apta_173 | DNA | AGCAGCACAGAGGTCAGATGGCAGGTTTCGACGTACAATGCTATGGAGGCTTTATGATCGCCTATGCGTGCTACCGTGAA | |
| Apta_174 | DNA | AGCAGCACAGAGGTCAGATGTCGGTCTTGTGTATACATACCCGTGTGTTTTCATCTCAGGCCTATGCGTGCTACCGTGAA |
DEV TOOL
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