Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 416
Aptamer sequence: GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG
Target unique ID: P59595
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_410 | aptamer 1 | Protein | NCAP_SARS | 1.65 nM | 30 mM Tris-HCl, pH 7.5, 150 mM NaCl, 10 mM MgCl2, 2mM DTT, 1%BSA | 19684916 |
Structure information of aptamer
| Aptamer Sequence: | GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG |
| 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_410 | Description | aptamer 1 |
| Aptamer chemistry | RNA | Length | 85 nt |
| GC content | 58.8% | Molecular weight | 27,476.22 Da |
| Molarity of 1 μg/μl solution | 36.40 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Aptasensor |
| Sequence | GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG | ||
| Applications | These aptamer-antibody hybrid immunoassays may be useful for rapid, sensitive detection of SARS-CoV N protein | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P59595 | Protein name | Nucleoprotein (Nucleocapsid protein) (NC) (Protein N) |
| Gene name(s) | N 9a | Organism | Nucleoprotein (Nucleocapsid protein) (NC) (Protein N) |
| Status | reviewed in uniprot database | Length | 422 |
| Mass | 46,025 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | N/A |
| PDB ID(s) | 1SSK;1X7Q;2CJR;2GIB;2JW8;2OFZ;2OG3;3I6L;6IEX;7LG0; |
 |
Function | Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. |
Activity data
 |
Interaction ID | 416 |
| Target type | Protein | |
| Target unique ID | P59595 | |
| Activity | 1.65 nM | |
| Binding Conditions/Buffer | 30 mM Tris-HCl, pH 7.5, 150 mM NaCl, 10 mM MgCl2, 2mM DTT, 1%BSA |
|
| Assay | Detection of the SARS-CoV N protein by an aptamer-based chemiluminescence immunosorbent assay. Serially diluted N protein was captured by aptamer 1 bound to a streptavidin-coated 96-well plate via hybridization between oligo(A)16 tagged to the 30-end of the aptamer and biotinylated oligo(dT)16. Captured N protein was detected using polyclonal anti-N antibody and alkaline phosphatase-conjugated secondary antibody. The luminescence intensities and standard deviations are from triplicate experiments |
|
| PubMed ID | 19684916 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_43 | RNA | GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC | |
| Apta_885 | RNA | GGGAGAGCGGAAGCGUGCUGGGCCUGGUUGCUGUAAAAAUAGACACGAAUCUGCCGACCAUAACCCAGAGGUCGAUGGAUCCCCCC | |
| Apta_396 | RNA | GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_909 | RNA | GGGAAUUCGAGCUCGGUACCUUUACCGUAAGGCCUGUCUUCGUUUGACAGCGGCUUGUUGACCCUCCACUUUGUACCUGCUGCCAACUGCAGGCAUGCAAGCUUGG | |
| Apta_893 | RNA | ACCGAGUCCAGAAGCUUGUAGUACUUAUGUCCCAUCGAACGCAGUGUAUCUUGCACCGACUCUCUGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC | |
| Apta_130 | RNA | GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA | |
| Apta_499 | RNA | GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC | |
| Apta_895 | RNA | ACCGAGUCCAGAAGCUUGUAGUACUACCGCAACGUUGGCGUUCGGCGUUGGCCGCGUCAUCGCUAGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC | |
| Apta_352 | RNA | GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA | |
| Apta_398 | RNA | GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_414 | RNA | GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_415 | RNA | GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_612 | RNA | GGGCGACCCUGAUGAGCCUUAGGAUAUGCUUCGGCAGAAGGACGUCGAAACGGUGAAAGCCGUAGGUUGCCC | |
| Apta_793 | RNA | GGGAGAGAACAAUGACCUGCGGUGCCAAGCCGUCGGGUUAUGUUGAUCUCCUCAAGGACGAGUGCAUUGCAUCACGUCAGUAG | |
| Apta_1055 | RNA | CAAGCUUGCGGGUUGGCUUGUAACAAGAUCGCUACGUGUUGAACUCUGCAACACUGGUCGGAUAGCGUAAACGGG | |
| Apta_1168 | RNA | GCGACUACGGUGAGGGUCGGGUCCAGUAGCUUCGGCUACUGUUGAGUAGAGUGUGGGCUCCGUAGUCGC | |
| Apta_376 | RNA | GGGAGCUCAGCCUUCACUGCACUCCGGCUGGUGGACGCGGUACGAGCAAUUUGUACCGGAUGGAUGUUCGGGCAGCGGUGUGGCAGGGAUGAGCGGCACCACGGUCGGAUCCAC | |
| Apta_724 | RNA | GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC | |
| Apta_551 | RNA | GGAUGUCCAGUCGCUUGCAAUGCCCUUUUAGACCCUGAUGAGCGGUGCUAGUUAGUUGCAGUUUCGGUUGUUACGCGAAACGGUGAAAGCCGUAGGUCU | |
| Apta_399 | RNA | GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA |
DEV TOOL
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