Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_126 | VR20 | Protein | TNFA_HUMAN | 8.7 nM | PBS, 0.005% (v/v) Tween-20 | 23046187 |
Structure information of aptamer
| Aptamer Sequence: | TCCTCATATAGAGTGCGGGGCGTGT |
| 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_126 | Description | VR20 |
| Aptamer chemistry | DNA | Length | 25 nt |
| GC content | 56.0% | Molecular weight | 7,968.92 Da |
| Molarity of 1 μg/μl solution | 125.49 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | TCCTCATATAGAGTGCGGGGCGTGT | ||
| Applications | Binding specififically to TNFa | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P01375 | Protein name | Tumor necrosis factor (Cachectin) (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) [Cleaved into: Tumor necrosis factor, membrane form (N-terminal fragment) (NTF); Intracellular domain 1 (ICD1); Intracellular domain 2 (ICD2); C-domain 1; C-domain 2; Tumor necrosis factor, soluble form] |
| Gene name(s) | TNF TNFA TNFSF2 | Organism | Tumor necrosis factor (Cachectin) (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) [Cleaved into: Tumor necrosis factor, membrane form (N-terminal fragment) (NTF); Intracellular domain 1 (ICD1); Intracellular domain 2 (ICD2); C-domain 1; C-domain 2; Tumor necrosis factor, soluble form] |
| Status | reviewed in uniprot database | Length | 233 |
| Mass | 25,644 | Activity regulation | N/A |
| Involvement in disease | Psoriatic arthritis (PSORAS) | Catalytic activity | N/A |
| PDB ID(s) | 1A8M;1TNF;2AZ5;2E7A;2TUN;2ZJC;2ZPX;3ALQ;3IT8;3L9J;3WD5;4G3Y;4TSV;4TWT;4Y6O;5M2I;5M2J;5M2M;5MU8;5TSW;5UUI;5WUX;5YOY;6OOY;6OOZ;6OP0;6RMJ;6X81;6X82;6X83;6X85;6X86;7ASY;7AT7;7ATB;7JRA;7KP9;7KPA;7KPB; |
 |
Function | Cytokine that binds to TNFRSF1A/TNFR1 and TNFRSF1B/TNFBR. |
Activity data
 |
Interaction ID | 127 |
| Target type | Protein | |
| Target unique ID | P01375 | |
| Activity | 8.7 nM | |
| Binding Conditions/Buffer | PBS, 0.005% (v/v) Tween-20 |
|
| Assay | Binding curves of immobilized aptamer VR20 associated with increasing concentrations of TNFα |
|
| PubMed ID | 23046187 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_320 | DNA | GCACTCTGTGGGGGTGGACGGGCCGGGT | |
| Apta_517 | DNA | ACCTTCGGGGAGTATTGCGGAGGAAGGT | |
| Apta_671 | DNA | GCATCTGATCGGGTGTGGGTGGCGTAAAGG | |
| Apta_673 | DNA | GCAGTCCTAGATCGGGTGTGGCTGGCTTGG | |
| Apta_676 | DNA | TCAGTCCCGATCAGGTGTGGGTGGCATTGG | |
| Apta_682 | DNA | CCTTGTAGATCGGGTGTGGTTTGGCGTAGG | |
| Apta_504 | DNA | TTGCTCCTTATAGAGCCGTCCGAGC | |
| Apta_463 | DNA | GTTCTCATGCACACTTATAGCGGGGGGATCCAGTACT | |
| Apta_679 | DNA | CAGGTGGCAGATCGGGTGTGGGTGGCCTGG | |
| Apta_681 | DNA | CCTGACGATCGGGTGTGGGTTGGCTTGAGG | |
| Apta_1065 | DNA | CCTCGCTATGATGGAGTGCGTTTAGATCAGGGAACGGGTT | |
| Apta_18 | DNA | TGGGGGGTTGGACGGGCGGGGCTGC | |
| Apta_24 | DNA | TGTGGGGATGGATGGGCCGGGCTGC | |
| Apta_147 | DNA | TGCGGTTGTAGTACTCGTGGCCG | |
| Apta_546 | DNA | CACGGCATGGTGGGCGTCGTG | |
| Apta_66 | DNA | TACCGTGGTAGGGAAGGTTGGAGTGTA | |
| Apta_62 | DNA | AGTCCGTGGTAGGGCAGGTTGGGGTGACT | |
| Apta_63 | DNA | GACCCGTGGTAGGGTAGGATGGGGTGGTC | |
| Apta_70 | DNA | AGGTCGTAGGTTGGTGTGGTTGGGGCGACCT | |
| Apta_72 | DNA | AGTCAGTAGGTTGGTGTGGTTGGGGCTGACT |
DEV TOOL
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