Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1136
Aptamer sequence: GGCTGGTCCGCTGGGAACAAGGGCGGGAGGGAGGGTGTGGGTGCGACAAGCGGACCAGCC
Target unique ID: P17763
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_1082 | AptD2 | Protein | POLG_DEN1W | 104 pM | 20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM MgCl2 and 2.7 mM KCl | 34169309 |
Structure information of aptamer
| Aptamer Sequence: | GGCTGGTCCGCTGGGAACAAGGGCGGGAGGGAGGGTGTGGGTGCGACAAGCGGACCAGCC |
| 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_1082 | Description | AptD2 |
| Aptamer chemistry | DNA | Length | 60 nt |
| GC content | 71.7% | Molecular weight | 18,844.01 Da |
| Molarity of 1 μg/μl solution | 53.07 μM | Number of G-quadruplexes | 3 |
| G-Score | 64 | Function | Target detection |
| Sequence | GGCTGGTCCGCTGGGAACAAGGGCGGGAGGGAGGGTGTGGGTGCGACAAGCGGACCAGCC | ||
| Applications | Detection of dengue NS1 protein | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P17763 | Protein name | Genome polyprotein [Cleaved into: Capsid protein C (Capsid protein) (Core protein); Protein prM (Precursor membrane protein); Peptide pr (Peptide precursor); Small envelope protein M (Matrix protein); Envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Serine protease subunit NS2B (Flavivirin protease NS2B regulatory subunit) (Non-structural protein 2B); Serine protease NS3 (EC 3.4.21.91) (EC 3.6.1.15) (EC 3.6.4.13) (Flavivirin protease NS3 catalytic subunit) (Non-structural protein 3); Non-structural protein 4A (NS4A); Peptide 2k; Non-structural protein 4B (NS4B); RNA-directed RNA polymerase NS5 (EC 2.1.1.56) (EC 2.1.1.57) (EC 2.7.7.48) (Non-structural protein 5)] |
| Gene name(s) | N/A | Organism | Genome polyprotein [Cleaved into: Capsid protein C (Capsid protein) (Core protein); Protein prM (Precursor membrane protein); Peptide pr (Peptide precursor); Small envelope protein M (Matrix protein); Envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Serine protease subunit NS2B (Flavivirin protease NS2B regulatory subunit) (Non-structural protein 2B); Serine protease NS3 (EC 3.4.21.91) (EC 3.6.1.15) (EC 3.6.4.13) (Flavivirin protease NS3 catalytic subunit) (Non-structural protein 3); Non-structural protein 4A (NS4A); Peptide 2k; Non-structural protein 4B (NS4B); RNA-directed RNA polymerase NS5 (EC 2.1.1.56) (EC 2.1.1.57) (EC 2.7.7.48) (Non-structural protein 5)] |
| Status | reviewed in uniprot database | Length | 3392 |
| Mass | 378,702 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | Reaction=Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala |
| PDB ID(s) | 3J8D;3L6P;3LKW;4AL8;4GSX;4GT0;4LCY;4OIG;5VIC;5WJL;5WKF;7DWT;7DWU; |
 |
Function | Plays a role in virus budding by binding to the cell membrane and gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. |
Activity data
 |
Interaction ID | 1136 |
| Target type | Protein | |
| Target unique ID | P17763 | |
| Activity | 104 pM | |
| Binding Conditions/Buffer | 20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM MgCl2 and 2.7 mM KCl |
|
| Assay | Binding analysis of the UB-DNA aptamers to each DEN-NS1 by a Biacore T200 SPR system |
|
| PubMed ID | 34169309 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_864 | DNA | CTCCTCTGACTGTAACCACGACTAGGACGCTTGGGAGGGGGGGTGGGGTGTCCGGTCGCGGCATAGGTAGTCCAGAAGCC | |
| Apta_33 | DNA | GCGGTAAACTGCGTCCGAAGGGGCTGCAGTGACCCGAATGGGTCCGCCGCGAAGCG | |
| Apta_485 | DNA | TGTCGTTGGGGGGGTAGGGAAGGGTGAAACGACAAGCCAGAAGTT | |
| Apta_745 | DNA | GGTTGCATGCCGTGGGGAGGGGGGTGGGTTTTATAGCGTACTCAG | |
| Apta_1011 | DNA | GCTGTGTGACTCCTGCAATGGTAGCGGGTAGGGGAGGGAGGGTGAATGGAGGATGTTCATGGCAGCTGTATCTTGTCTCC | |
| Apta_616 | DNA | GGTGCGGGTAGGGATGAGGGCGGGTCGGGTTGAGTGTGAGCTTAGGGGtGGCGGATCTAC | |
| Apta_865 | DNA | CTCCTCTGACTGTAACCACGTGTGCCAAAGAGAGTGGTGGGGGGGTGGGCGGAACTCGCGGCATAGGTAGTCCAGAAGCC | |
| Apta_708 | DNA | CGTACGGAATTCGCTAGCGGGCGGGGGTGCTGGGGGAATGGAGTGCTGCGTGCTGCGGGGATCCGAGCTCCACGTG | |
| Apta_589 | DNA | GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG | |
| Apta_1119 | DNA | GGGAATGGATCCACATCTACGAATTCGGTTGTGAAGATTGGGAGCGTCGTGGCTACTTCACTGCAGACTTGACGAAGCTT | |
| Apta_589 | DNA | GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG | |
| Apta_771 | DNA | GAATTCCGTCGGACAGCGGTATGCATGGGAGGTTCTGGAGGGGGTGGGTTGGCGTGCGTTCCAGATGGACGAATATCGTCTCCC | |
| Apta_4 | DNA | CCTGCCTTTGGAACCGACCGCCAGGCCGAGGAAAGGCACCGACAGC | |
| Apta_68 | DNA | AGATGCCTGTCGAGCATGCTGTGAATAGGTAGGGTCGGATGGGCTACGGTGTAGCTAAACTGCTTTGTCGACGGG | |
| Apta_77 | DNA | GGTGTGGGCGACATGGGGGTTGGTGGTGTAGGAGCGCCAT | |
| Apta_751 | DNA | GGTCGCAGATGGATTAAGTATGTGGGTGGGGGGGTGGAAGTTAAT | |
| Apta_870 | DNA | CCGGGGAATCTAGGGGAGGGCGGGTGGGTCAATTGAGCCG | |
| Apta_1071 | DNA | TTGAAGTGACTCCGCACTGGGTGGGTGGGAGGGTCGTGCGGCTGGTCATAGCAGGGT | |
| Apta_1189 | DNA | GCGGGCGGGGGGAGGGCGGCCGTGGGCTGCGAGTGGGAGG | |
| Apta_1190 | DNA | TTCAGGGCGGGGTAAACGGGAGGTGGGGGGGGCTTGGGAC |
DEV TOOL
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