Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_347 | Rapt2 | Protein | TCDB_CLODI | 5.0 nM | 20 mM Tris-HCl, 100 mM NaCl, 5 mM KCl and 10 mM MgCl2, 1 mM DTT, 0.05% Tween-20, pH 7.5 | 32155319 |
Structure information of aptamer
| Aptamer Sequence: | AAAAAAAAAAAAGTACGTTCAGGAGCAGTGCGA |
| 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_347 | Description | Rapt2 |
| Aptamer chemistry | DNA | Length | 33 nt |
| GC content | 36.4% | Molecular weight | 10,509.64 Da |
| Molarity of 1 μg/μl solution | 95.15 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Aptasensor |
| Sequence | AAAAAAAAAAAAGTACGTTCAGGAGCAGTGCGA | ||
| Applications | Binding to toxin B protein | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P18177 | Protein name | Toxin B (EC 3.4.22.-) [Cleaved into: Glucosyltransferase TcdB (EC 2.4.1.-)] |
| Gene name(s) | tcdB toxB | Organism | Toxin B (EC 3.4.22.-) [Cleaved into: Glucosyltransferase TcdB (EC 2.4.1.-)] |
| Status | reviewed in uniprot database | Length | 2366 |
| Mass | 269,712 | Activity regulation | Protease activity is activated upon binding to 1D-myo-inositol hexakisphosphate (InsP6), which induces conformational reorganization |
| Involvement in disease | N/A | Catalytic activity | Reaction=L-threonyl-[protein] + UDP-alpha-D-glucose = 3-O-(alpha-D-glucosyl)-L-threonyl-[protein] + H(+) + UDP |
| PDB ID(s) | 2BVL;2BVM;4NC2;4NP4;5UQM;5UQN;5UQT;6AR6;6C0B;6OQ5;6OQ6;6OQ7;6OQ8;7LOU;7LOV;7ML7;7N8X;7N95;7N97;7N9Q;7N9R;7N9S;7N9Y;7S0Y; |
 |
Function | Precursor of a cytotoxin that targets and disrupts the colonic epithelium, inducing the host inflammatory and innate immune responses and resulting in diarrhea and pseudomembranous colitis. |
Activity data
|
No relevant experimental diagram |
Interaction ID | 352 |
| Target type | Protein | |
| Target unique ID | P18177 | |
| Activity | 5.0 nM | |
| Binding Conditions/Buffer | 20 mM Tris-HCl, 100 mM NaCl, 5 mM KCl and 10 mM MgCl2, 1 mM DTT, 0.05% Tween-20, pH 7.5 |
|
| Assay | N/A |
|
| PubMed ID | 32155319 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_346 | DNA | GTACGTTCAGGAGCAGTGCGA | |
| Apta_1260 | DNA | GAAAGGGACGTTCCAAGTTCGTATAAGCAGTCCTGTGCGT | |
| Apta_162 | DNA | CCGTACATACTACGTACGTACGTGAACAGAGGCAGAG | |
| Apta_261 | DNA | TAAACCCCAAAACAGTGCAACTAGGTGTAGGTCCCGTGGT | |
| Apta_324 | DNA | CAAACAATCAAACAGCAGTGGGGTG | |
| Apta_324 | DNA | CAAACAATCAAACAGCAGTGGGGTG | |
| Apta_257 | DNA | GGCAGAAGAAATATCGAAACCCAGAATGGTCGGCCAGGCG | |
| Apta_474 | DNA | CAAAAAGATAGGTGGATTTTTCCCCGGATCGGTTTGTATG | |
| Apta_506 | DNA | AAGCGCGCGAGACTACGTTTGTAGGGATACCGATGTCG | |
| Apta_586 | DNA | GGGAGACAAGGAAAATCCTTCAATGAAGTGGGTCGACA | |
| Apta_1191 | DNA | TAATACTACCAACTTCTTTGCCTGGCGTAAGTAACAGTCA | |
| Apta_644 | DNA | TCAATCTAACCATGCATGCAGTTTAGGCAGGATTCGTTATCGCAA | |
| Apta_834 | DNA | CGCAATACCAAAGTGGCGAGAGCGCTGTCTTGAGTGAGTGGTTGG | |
| Apta_649 | DNA | GCACACCGATGGCGGTCCTGTTTAGGGGGTGTGCGTG | |
| Apta_322 | DNA | GAAGTGAAAATGACAGAACACAACA | |
| Apta_322 | DNA | GAAGTGAAAATGACAGAACACAACA | |
| Apta_345 | DNA | ACAGTAACCGCGTGAGGTCGA | |
| Apta_419 | DNA | ATCAGGGCTAAAGAGTGCAGAGTTACTTAG | |
| Apta_630 | DNA | GACCAGGGCAAACGGTAGGGAGTGGTC | |
| Apta_1139 | DNA | AATAGGGTAAAAAAAAAAAGTTGGTCCTATG |
DEV TOOL
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