Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_346 | Rapt1 | Protein | TCDB_CLODI | 8.9 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: | GTACGTTCAGGAGCAGTGCGA |
| 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_346 | Description | Rapt1 |
| Aptamer chemistry | DNA | Length | 21 nt |
| GC content | 57.1% | Molecular weight | 6,751.16 Da |
| Molarity of 1 μg/μl solution | 148.12 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Aptasensor |
| Sequence | GTACGTTCAGGAGCAGTGCGA | ||
| 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 | 351 |
| Target type | Protein | |
| Target unique ID | P18177 | |
| Activity | 8.9 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_347 | DNA | AAAAAAAAAAAAGTACGTTCAGGAGCAGTGCGA | |
| Apta_545 | DNA | TTAGTTGGGGTTCAGTTGG | |
| Apta_1024 | DNA | GTCCAGGGTTCCAAGGTGCTTCGTGGAC | |
| Apta_701 | DNA | GTACTGGCGTTCGGGGGGTACCGCTGC | |
| Apta_629 | DNA | TGGGGGTTGAGGCTAAGCCGA | |
| Apta_1039 | DNA | GCCCGTCCGTATGGTGGGT | |
| Apta_125 | DNA | TGGTGGATGGCGCAGTCGGCGACAA | |
| Apta_324 | DNA | CAAACAATCAAACAGCAGTGGGGTG | |
| Apta_324 | DNA | CAAACAATCAAACAGCAGTGGGGTG | |
| Apta_504 | DNA | TTGCTCCTTATAGAGCCGTCCGAGC | |
| Apta_806 | DNA | GGTTGGATGTAAGGTTGGAGGGGGG | |
| Apta_1148 | DNA | CCGTCTTCCAGACAAGAGTGCAGGG | |
| Apta_700 | DNA | GCAGGGGCGTTCGGGGGGTACCGCTGC | |
| Apta_62 | DNA | AGTCCGTGGTAGGGCAGGTTGGGGTGACT | |
| Apta_186 | DNA | AGGAACGCTTTAGGTCTGAGATCTCGGAAT | |
| Apta_195 | DNA | AGGAAGGCTTTAGGGGTCTGAGATCTCGGAAT | |
| Apta_203 | DNA | GGAAGGCTTTAGGTCTGAGATCTCGG | |
| Apta_215 | DNA | AGGAAGGCTTTAGGTCCGAGATCTCGGAAT | |
| Apta_318 | DNA | CCCGTCTTCCAGACAAGAGTGCAGGG | |
| Apta_389 | DNA | GCCTGTGGTGTTGGGGCGGGTGCG |
DEV TOOL
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