Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 909
Aptamer sequence: GGGATACCAGCTTATTCAATTTGATTCCATCTTCCTGGACTGTCGAAAATTCAGTATCGGGAGGTTACGTATTTGGTTTATAGATAGTAAGTGCAATCT
Target unique ID: 43895
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_823 | Ⅰ-1 | Cell | Escherichia coli(E.coli)O157:H7 | 110 nM | 30 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1.5 mM MgCl2, 2 mM dithiothreitol, and 1% BSA | 22166202 |
Structure information of aptamer
| Aptamer Sequence: | GGGATACCAGCTTATTCAATTTGATTCCATCTTCCTGGACTGTCGAAAATTCAGTATCGGGAGGTTACGTATTTGGTTTATAGATAGTAAGTGCAATCT |
| 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_823 | Description | Ⅰ-1 |
| Aptamer chemistry | DNA | Length | 99 nt |
| GC content | 38.4% | Molecular weight | 30,597.61 Da |
| Molarity of 1 μg/μl solution | 32.68 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Target recognition |
| Sequence | GGGATACCAGCTTATTCAATTTGATTCCATCTTCCTGGACTGTCGAAAATTCAGTATCGGGAGGTTACGTATTTGGTTTATAGATAGTAAGTGCAATCT | ||
| Applications | Diagnostic ligand against the pathogen-related food borne illness | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| ATCC ID | 43895 | Cell name | Escherichia coli(E.coli) O157:H7 |
| Category | Bacteria | Organism | N/A |
| Product type | N/A | 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 | Produces Shiga-like toxins I and II. Quality control strain for Difco products. |
|
|
| Application(s) | Media testing; Quality control | ||
Activity data
 |
Interaction ID | 909 |
| Target type | Cell | |
| Target unique ID | 43895 | |
| Activity | 110 nM | |
| Binding Conditions/Buffer | 30 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1.5 mM MgCl2, 2 mM dithiothreitol, and 1% BSA |
|
| Assay | Comparison of binding ability of RNA aptamer I-1 and its truncated aptamers to O157:H7 strain versus K12 strain. Binding capacity of each aptamer or library RNA to a specific strain is presented as relative fluorescence units to the sample without any RNA (SAHRP) |
|
| PubMed ID | 22166202 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_450 | DNA | ATACCAGCTTATTCAATTACATGTCCTGAAGGGGAATAATATACAGCTTTGGGTGGGTAGATAGTAAGTGCAATCT | |
| Apta_1016 | DNA | ATACCAGCTTATTCAATTTCTTCGCCAGTGCCAGGATCTCAGTTGGCGGTTCATTAGCTGGGTTGGTCGAAGATAGTAAGTGCAATCT | |
| Apta_626 | DNA | ATACCAGCTTATTCAATTGGTGGTAGGATGGGCTCGATCGAGGTCTTCAGTCGGCTCGGTTTAGTTTATGTTCTCCTGTAGATAGTAAGTGCAATCT | |
| Apta_727 | DNA | ATACCAGCTTATTCAATTAGTCACACTTAGAGTTCTAACTGCTGCGCCGCCGGGAAAATACTGTACGGTTAGATAGTAAGTGCAATCT | |
| Apta_807 | DNA | GGGTCTTCCTGGACTGTCGAAAATTCAGTATCGGGAGGTTACGTATTTGGTTTATAGATAGTAA | |
| Apta_1015 | DNA | ATACCAGCTTATTCAATTGACCCGTTTCGTTCCCTCTGGGAAGTTTAGCCCAGTTGCCTGGGCGATACCAAGATAGTAAGTGCAATCT | |
| Apta_626 | DNA | ATACCAGCTTATTCAATTGGTGGTAGGATGGGCTCGATCGAGGTCTTCAGTCGGCTCGGTTTAGTTTATGTTCTCCTGTAGATAGTAAGTGCAATCT | |
| Apta_349 | DNA | ATACCAGCTTATTCAATTAGACGAGTTTTATTCATTTTCCATGTCGTAGCTTACCGTGAGATAGTAAGTGCAATCT | |
| Apta_452 | DNA | ATACCAGCTTATTCAATTGAAGAGTATAAAAAGAGTGATTATCTTTTGTAGGTTTTTTAGATAGTAAGTGCAATCT | |
| Apta_792 | DNA | ATACCAGCTTATTCAATTCCCAAATTGCCACCACTTACAGCATGATAACATACTACATCTTTTCATCAAGATAGTAAGTGCAATCT | |
| Apta_354 | DNA | ATACCAGCTTATTCAATTCTATACTCCACTTTGCTATTTCTCGGTTCCTTCACGCGCCGATCGCAGGCTGATGAATTGAGATAGTAAGTGCAATCT | |
| Apta_627 | DNA | ATACCAGCTTATTCAATTATGCGGGGATGAGGCTTGATCTGTGGCTCTGATCCATGATCAGTCGTCTTACGTGCGGTCCAGATAGTAAGTGCAATCT | |
| Apta_805 | DNA | ATACCAGCTTATTCAATTAGGCGGTGCATTGTGGTTGGTAGTATACATGAGGTTTGGTTGAGACTAGTCGCAAGATATAGATAGTAAGTGCAATCT | |
| Apta_627 | DNA | ATACCAGCTTATTCAATTATGCGGGGATGAGGCTTGATCTGTGGCTCTGATCCATGATCAGTCGTCTTACGTGCGGTCCAGATAGTAAGTGCAATCT | |
| Apta_451 | DNA | ATACCAGCTTATTCAATTGAGTAAGAGTGCACTATGTTTTACGAGCCGTTTCCTCGGCAGATAGTAAGTGCAATCT | |
| Apta_628 | DNA | ATACCAGCTTATTCAATTAGCCCGGTATTGAGGTCGATCTCTTATCCTATGGCTTGTCCCCCATGGCTCGGTTATATCCAGATAGTAAGTGCAATCT | |
| Apta_628 | DNA | ATACCAGCTTATTCAATTAGCCCGGTATTGAGGTCGATCTCTTATCCTATGGCTTGTCCCCCATGGCTCGGTTATATCCAGATAGTAAGTGCAATCT | |
| Apta_625 | DNA | ATACCAGCTTATTCAATTCAGGGCGGTATGAGGCTCGATCAAGGTCGGAGCGAGAATTTTTTCGCGGAGTCGGCTGGATCAGATAGTAAGTGCAATCT | |
| Apta_884 | DNA | ATACCAGCTTATTCAATTTGCACCACTTATTGTTACTAATCTGAGATAGTAAGTGCAATCT | |
| Apta_625 | DNA | ATACCAGCTTATTCAATTCAGGGCGGTATGAGGCTCGATCAAGGTCGGAGCGAGAATTTTTTCGCGGAGTCGGCTGGATCAGATAGTAAGTGCAATCT |
DEV TOOL
 |
 |
 |
 |