Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 43
Aptamer sequence: GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC
Target unique ID: O95786
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_43 | CL9 | Protein | DDX58_HUMAN | 37.2 nM | 1X PBS with 1 mM MgCl2 | 22127865 |
Structure information of aptamer
| Aptamer Sequence: | GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC |
| 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_43 | Description | CL9 |
| Aptamer chemistry | RNA | Length | 92 nt |
| GC content | 50.0% | Molecular weight | 29,424.39 Da |
| Molarity of 1 μg/μl solution | 33.99 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC | ||
| Applications | To be an antiviral agent that specifically boosts the RIG-I-dependent signaling cascade | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | O95786 | Protein name | Antiviral innate immune response receptor RIG-I (ATP-dependent RNA helicase DDX58) (EC 3.6.4.13) (DEAD box protein 58) (RIG-I-like receptor 1) (RLR-1) (Retinoic acid-inducible gene 1 protein) (RIG-1) (Retinoic acid-inducible gene I protein) (RIG-I) |
| Gene name(s) | DDX58 | Organism | Antiviral innate immune response receptor RIG-I (ATP-dependent RNA helicase DDX58) (EC 3.6.4.13) (DEAD box protein 58) (RIG-I-like receptor 1) (RLR-1) (Retinoic acid-inducible gene 1 protein) (RIG-1) (Retinoic acid-inducible gene I protein) (RIG-I) |
| Status | reviewed in uniprot database | Length | 925 |
| Mass | 106,600 | Activity regulation | N/A |
| Involvement in disease | Singleton-Merten syndrome 2 (SGMRT2) | Catalytic activity | Reaction=ATP + H2O = ADP + H(+) + phosphate |
| PDB ID(s) | 2LWD;2LWE;2QFB;2QFD;2RMJ;2YKG;3LRN;3LRR;3NCU;3OG8;3ZD6;3ZD7;4AY2;4BPB;4NQK;4ON9;4P4H;5E3H;5F98;5F9F;5F9H;6GPG;6KYV;7BAH;7BAI;7JL1;7JL3;7MK1; |
 |
Function | Innate immune receptor that senses cytoplasmic viral nucleic acids and activates a downstream signaling cascade leading to the production of type I interferons and pro-inflammatory cytokines. |
Activity data
 |
Interaction ID | 43 |
| Target type | Protein | |
| Target unique ID | O95786 | |
| Activity | 37.2 nM | |
| Binding Conditions/Buffer | 1X PBS with 1 mM MgCl2 |
|
| Assay | The binding affinity (Kd) of AP-treated CL9 aptamer to full length RIG-I measured by filter assay |
|
| PubMed ID | 22127865 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_885 | RNA | GGGAGAGCGGAAGCGUGCUGGGCCUGGUUGCUGUAAAAAUAGACACGAAUCUGCCGACCAUAACCCAGAGGUCGAUGGAUCCCCCC | |
| Apta_410 | RNA | GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG | |
| Apta_548 | RNA | GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC | |
| Apta_396 | RNA | GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_352 | RNA | GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA | |
| Apta_415 | RNA | GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_467 | RNA | GGGAGGACGAUGCGGCAGUGCCCAACCGGAACAACAACCACCGGCGGCUCCUGCUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_305 | RNA | GGGAGGACGAUGCGGAUCGCCCUGAACCGGCCCAGCAGACUGCUGACGGCACGAUCCGCAUCGUCCUCCC | |
| Apta_414 | RNA | GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_398 | RNA | GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_460 | RNA | GGAUGGCAGCGGAGAGUUGCUUGGAAUGCGUUAUAGUCUCUUAGGUGUGUACAGCCCACACCACUCUCC | |
| Apta_547 | RNA | GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC | |
| Apta_720 | RNA | GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA | |
| Apta_169 | RNA | GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUUCGACAUGAGACUCACAACAGUUCCCUUUAGUGAGGGUUAAUU | |
| Apta_170 | RNA | GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCC | |
| Apta_400 | RNA | GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_793 | RNA | GGGAGAGAACAAUGACCUGCGGUGCCAAGCCGUCGGGUUAUGUUGAUCUCCUCAAGGACGAGUGCAUUGCAUCACGUCAGUAG | |
| Apta_984 | RNA | GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA | |
| Apta_874 | RNA | GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACAGAAGGACGUCGAAACGGUAGCGAGAGCUC | |
| Apta_413 | RNA | GUGAGACCAGCCGAGUGGUGUCUGGCUAUUCACUGGAGCGUGGGUGGAACCCCUGCGCACUCGUUUGGCUGUCCGGGCCUUCGGGCCGGGAUUAUCUCU |
DEV TOOL
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