Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 342
Aptamer sequence: GGGAGGAUAUUUUCUCAGACCGUAAGUACCGAAUGUGCUUUUGGCCGAUUUUUGGCCCCUGCAGUUGCAGCAUCGUGAACUAGGAUCCGGG
Target unique ID: P16088
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_337 | F1a | Protein | POL_FIVPE | 1.9 nM | 50 mM Tris-HCl (pH 7.7), 200 mM potassium acetate, and 10 mM dithiothreitol | 8639644 |
Structure information of aptamer
| Aptamer Sequence: | GGGAGGAUAUUUUCUCAGACCGUAAGUACCGAAUGUGCUUUUGGCCGAUUUUUGGCCCCUGCAGUUGCAGCAUCGUGAACUAGGAUCCGGG |
| 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_337 | Description | F1a |
| Aptamer chemistry | RNA | Length | 91 nt |
| GC content | 51.6% | Molecular weight | 29,488.18 Da |
| Molarity of 1 μg/μl solution | 33.91 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | GGGAGGAUAUUUUCUCAGACCGUAAGUACCGAAUGUGCUUUUGGCCGAUUUUUGGCCCCUGCAGUUGCAGCAUCGUGAACUAGGAUCCGGG | ||
| Applications | Potent inhibitor of the RNA-dependent DNA polymerase activity of both the recombinant and the virion-derived FIV reverse transcriptase | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P16088 | Protein name | Pol polyprotein [Cleaved into: Protease (Retropepsin) (EC 3.4.23.-); Reverse transcriptase/ribonuclease H (RT) (EC 2.7.7.49) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2); Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) (EC 3.6.1.23); Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)] |
| Gene name(s) | pol | Organism | Pol polyprotein [Cleaved into: Protease (Retropepsin) (EC 3.4.23.-); Reverse transcriptase/ribonuclease H (RT) (EC 2.7.7.49) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2); Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) (EC 3.6.1.23); Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)] |
| Status | reviewed in uniprot database | Length | 1124 |
| Mass | 127,494 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | Reaction=Endohydrolysis of RNA in RNA/DNA hybrids |
| PDB ID(s) | 1B11;1DUT;1F7D;1F7K;1F7N;1F7O;1F7P;1F7Q;1F7R;1FIV;2FIV;2HAH;3FIV;3OGP;3OGQ;4FIV;4MQ3;4PA1;5FIV;6FIV; |
 |
Function | During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. |
Activity data
|
No relevant experimental diagram |
Interaction ID | 342 |
| Target type | Protein | |
| Target unique ID | P16088 | |
| Activity | 1.9 nM | |
| Binding Conditions/Buffer | 50 mM Tris-HCl (pH 7.7), 200 mM potassium acetate, and 10 mM dithiothreitol |
|
| Assay | N/A |
|
| PubMed ID | 8639644 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_720 | RNA | GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA | |
| Apta_909 | RNA | GGGAAUUCGAGCUCGGUACCUUUACCGUAAGGCCUGUCUUCGUUUGACAGCGGCUUGUUGACCCUCCACUUUGUACCUGCUGCCAACUGCAGGCAUGCAAGCUUGG | |
| Apta_396 | RNA | GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_414 | RNA | GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_724 | RNA | GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC | |
| Apta_380 | RNA | GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG | |
| Apta_854 | RNA | GGGAGCUCAGAAUAAACGCUCAAGGGUAGGGAUCGUUACCCCGACAUUUUAAUGGGCCGAUGUUUCGACAUGAGGCCCGGAUCCGGC | |
| Apta_376 | RNA | GGGAGCUCAGCCUUCACUGCACUCCGGCUGGUGGACGCGGUACGAGCAAUUUGUACCGGAUGGAUGUUCGGGCAGCGGUGUGGCAGGGAUGAGCGGCACCACGGUCGGAUCCAC | |
| Apta_171 | RNA | GGGAGCUCAGAAUAAACGCUCAACCAGUCUUGUGGCUUUGAAAGAGAGGAGUGUUCGACAUGAGGCCCGGAUCCGGC | |
| Apta_256 | RNA | GGGCGCUAAGUCCUCGCUCAUGCGCGUCCCAUGGGGUAUAGAGGGGUCGAAGUGGACGCGCGACUCGGAUCCU | |
| Apta_399 | RNA | GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_415 | RNA | GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_429 | RNA | GCAUGCAGUGUCUAUUCUCGAGUAGCGAUCGUUGAAGGGGUAUAAGGUUGGCAGAUCGCUAGCAUGCAACUGACUCGGAUAAGCA | |
| Apta_984 | RNA | GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA | |
| Apta_1100 | RNA | GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU | |
| Apta_130 | RNA | GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA | |
| Apta_170 | RNA | GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCC | |
| Apta_276 | RNA | GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC | |
| Apta_398 | RNA | GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_547 | RNA | GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC |
DEV TOOL
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