Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_125 | VR11 | Protein | TNFA_HUMAN | 7.0 nM | PBS, 0.005% (v/v) Tween-20 | 23046187 |
Structure information of aptamer
| Aptamer Sequence: | TGGTGGATGGCGCAGTCGGCGACAA |
| 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_125 | Description | VR11 |
| Aptamer chemistry | DNA | Length | 25 nt |
| GC content | 64.0% | Molecular weight | 8,027.96 Da |
| Molarity of 1 μg/μl solution | 124.56 μM | Number of G-quadruplexes | 2 |
| G-Score | 17 | Function | Targeted binding |
| Sequence | TGGTGGATGGCGCAGTCGGCGACAA | ||
| 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 | 126 |
| Target type | Protein | |
| Target unique ID | P01375 | |
| Activity | 7.0 nM | |
| Binding Conditions/Buffer | PBS, 0.005% (v/v) Tween-20 |
|
| Assay | Binding curves of immobilized aptamer VR11 associated with increasing concentrations of TNFα |
|
| PubMed ID | 23046187 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_8 | DNA | TGTGGGGGTGGACGGGCCGGGTAGA | |
| Apta_9 | DNA | TGAGGGGGCGGCGGGGCCGGGCAGG | |
| Apta_27 | DNA | AGGGGGAGGGGTGGGGCCGGGCAGA | |
| Apta_629 | DNA | TGGGGGTTGAGGCTAAGCCGA | |
| Apta_497 | DNA | GTTCGATTGGATTGTGCCGGAAGTGCTGGCTCGAAC | |
| Apta_70 | DNA | AGGTCGTAGGTTGGTGTGGTTGGGGCGACCT | |
| Apta_75 | DNA | CACTGGTAGGTTGGTGTGGTTGGGGCCAGTG | |
| Apta_423 | DNA | TGGGAGCTGATGTCGCATGGGTTTTGATCACATGA | |
| Apta_1256 | DNA | GATCGGGTGTGGGTGGCGTAAAGGGAGCATCGGACA | |
| Apta_160 | DNA | CGGTGCAGTGGATACATGCCAGCCGTAGCCATCGTGGATA | |
| Apta_912 | DNA | TAGTATGGACTTGTCTTCTTGTCAGAGTCTGGCAGCACGT | |
| Apta_1014 | DNA | TGGGGGTTGGGTGGATAGGCTGGCGTCGGGGCAGGTCAGT | |
| Apta_18 | DNA | TGGGGGGTTGGACGGGCGGGGCTGC | |
| Apta_19 | DNA | TGAGGGGGGGGGAGGTCGGGCCTGC | |
| Apta_21 | DNA | TGTGGGGGAGGACGGGCGGGGATGC | |
| Apta_22 | DNA | TGTGGGGGTGGACTGGGTGGGTACC | |
| Apta_23 | DNA | TGTGGGGGTGGACGGGCCGAGTACG | |
| Apta_24 | DNA | TGTGGGGATGGATGGGCCGGGCTGC | |
| Apta_28 | DNA | AGTGGGGGGGGTGGAGCCGGGTAGA | |
| Apta_30 | DNA | AGAGGGGGGGGTGGAGGGGGCTAGA |
DEV TOOL
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