Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 2
Aptamer sequence: GGGCUUCUCUGGUUAGACCAGAUUUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCC
Target unique ID: A6MI22
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_2 | TAR-1 | Protein | A6MI22_9HIV1 | 16 nM | 50 mM Tris-HCl (pH 7.8) and 50 mM KCl | 10886365 |
Structure information of aptamer
| Aptamer Sequence: | GGGCUUCUCUGGUUAGACCAGAUUUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCC |
| 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_2 | Description | TAR-1 |
| Aptamer chemistry | RNA | Length | 59 nt |
| GC content | 55.9% | Molecular weight | 18,943.21 Da |
| Molarity of 1 μg/μl solution | 52.79 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | GGGCUUCUCUGGUUAGACCAGAUUUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCC | ||
| Applications | Binding to target proteins | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | A6MI22 | Protein name | Protein Tat (Transactivating regulatory protein) |
| Gene name(s) | tat | Organism | Protein Tat (Transactivating regulatory protein) |
| Status | unreviewed in uniprot database | Length | 106 |
| Mass | 12,122 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | N/A |
| PDB ID(s) | N/A |
 |
Function | Extracellular circulating Tat can be endocytosed by surrounding uninfected cells via the binding to several surface receptors such as CD26, CXCR4, heparan sulfate proteoglycans (HSPG) or LDLR. |
Activity data
 |
Interaction ID | 2 |
| Target type | Protein | |
| Target unique ID | A6MI22 | |
| Activity | 16 nM | |
| Binding Conditions/Buffer | 50 mM Tris-HCl (pH 7.8) and 50 mM KCl |
|
| Assay | Determination of equilibrium dissociation constants (Kd) for binding of TAR-1 and of RNATat to CQ. Representative autoradiograms obtained from gel-shift assays for analysis of binding of TAR-1 and RNATat to CQ (A and B, respectively) |
|
| PubMed ID | 10886365 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_453 | RNA | GGGCUAGCUGAUCGUACCAGUAGCGUGGCCUGGGGGGCCUAGUCGUGCGAUACUAACAGCUAACACCC | |
| Apta_496 | RNA | GGGCUAGCUGAUCGUACCCAGUAGCGUGGCAUGGGGUGCCUAGUCGGGCGAUACUAACAGCUAACACCC | |
| Apta_521 | RNA | GGGUUGGGAAGAAACUGUGGCACUUCGGUGCCAGCAACCC | |
| Apta_612 | RNA | GGGCGACCCUGAUGAGCCUUAGGAUAUGCUUCGGCAGAAGGACGUCGAAACGGUGAAAGCCGUAGGUUGCCC | |
| Apta_599 | RNA | GUCUCUGUGUGCGCCAGAGAACACUGGGGCAGAUAUGGGCCAGCACAGAAUGAGGCCC | |
| Apta_599 | RNA | GUCUCUGUGUGCGCCAGAGAACACUGGGGCAGAUAUGGGCCAGCACAGAAUGAGGCCC | |
| Apta_399 | RNA | GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_623 | RNA | GGGAAUGGAUCCACAUCUACGAAUUCACCGCGGGGUUGCGGACCGGGAGCUCCAGCUUCACUGCAGACUUGACGAAGCUU | |
| Apta_51 | RNA | GCCUUAGUAACGUGCUUUGAUGUCGAUUCGACAGGAGGC | |
| Apta_136 | RNA | CGUGUCGUCCUGGUACGAUUUGGUAUAUAACCGUGGCUUUUCGACA | |
| Apta_365 | RNA | GGACCUAUGCAGUAGCCAGUGUGGACUGGGCUGCCCCCCC | |
| Apta_603 | RNA | CUUGUCUGAACAAUUUCGUCUGCCUUUGCGUUCCGACGGC | |
| Apta_633 | RNA | GGCAUCGGAAAGUGGGUUGAUGUAAGUAACAGGCGAUGCC | |
| Apta_703 | RNA | GGGCGGAUGAGACGCUUGGCGUGUGCUGUGGAGAGUCAUCCG | |
| Apta_856 | RNA | UGGGCCGGAGGUUAGCUUGCCCAUGGCAAGCAGGGCGCCACGGACCCA | |
| Apta_130 | RNA | GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA | |
| Apta_1124 | RNA | GGGCGAAUUCGGGUUGGAUAGUAGGCGCAUAUGGCAUCUUCGUGGUUGUGUAUUGCCCUUUAGUGAGGGUUAAUU | |
| Apta_1056 | RNA | GUCAUGUUGUGUUGUGGUCCAUCCUUUUCUACGCCAGUCGAGUCUGUAGCGUGGGAGUAAACUGAACGGUCAGACAGGA | |
| Apta_429 | RNA | GCAUGCAGUGUCUAUUCUCGAGUAGCGAUCGUUGAAGGGGUAUAAGGUUGGCAGAUCGCUAGCAUGCAACUGACUCGGAUAAGCA | |
| Apta_55 | RNA | GACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGAGGGCUCGGACUCUGAUUGCCUCCCCGCACC |
DEV TOOL
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