Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 155
Aptamer sequence: GCAATGGTACGGTACTTCCGCGGTCCGGGGTGGGTGGGTGGTGGGGGGTGCGGGGGGGCGGCCGCAAAAGTGCACGCTACTTTGCTAA
Target unique ID: P03134
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_151 | NS1-aptamer | Protein | NS1_MUMIP | 18.91 nM | 50 mM Tris/Cl (pH 8.0), 150 mM NaCl, 1.5 mM MgCl2, 2 mM DTT and 1% (w/v) BSA | 24055449 |
Structure information of aptamer
| Aptamer Sequence: | GCAATGGTACGGTACTTCCGCGGTCCGGGGTGGGTGGGTGGTGGGGGGTGCGGGGGGGCGGCCGCAAAAGTGCACGCTACTTTGCTAA |
| 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_151 | Description | NS1-aptamer |
| Aptamer chemistry | DNA | Length | 88 nt |
| GC content | 67.0% | Molecular weight | 27,810.46 Da |
| Molarity of 1 μg/μl solution | 35.96 μM | Number of G-quadruplexes | 3 |
| G-Score | 64 | Function | Targeted therapy |
| Sequence | GCAATGGTACGGTACTTCCGCGGTCCGGGGTGGGTGGGTGGTGGGGGGTGCGGGGGGGCGGCCGCAAAAGTGCACGCTACTTTGCTAA | ||
| Applications | Induce IFN-b by suppressing the function of NS1 | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P03134 | Protein name | Initiator protein NS1 (NS1) (EC 3.1.21.-) (EC 3.6.4.12) (NCVP1) (Non-capsid protein NS-1) (Non-structural protein NS1) |
| Gene name(s) | NS1 | Organism | Initiator protein NS1 (NS1) (EC 3.1.21.-) (EC 3.6.4.12) (NCVP1) (Non-capsid protein NS-1) (Non-structural protein NS1) |
| Status | reviewed in uniprot database | Length | 672 |
| Mass | 76,249 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | Reaction=ATP + H2O = ADP + H(+) + phosphate |
| PDB ID(s) | 3WRN;3WRO;3WRQ;3WRR;3WRS;4PP4;4R94; |
 |
Function | Multifunctional protein which displays endonuclease and helicase activities required for initiating and directing viral DNA replication. |
Activity data
 |
Interaction ID | 155 |
| Target type | Protein | |
| Target unique ID | P03134 | |
| Activity | 18.91 nM | |
| Binding Conditions/Buffer | 50 mM Tris/Cl (pH 8.0), 150 mM NaCl, 1.5 mM MgCl2, 2 mM DTT and 1% (w/v) BSA |
|
| Assay | Affinity measurement of the selected aptamer specific to NS1 by ELISA. The immobilized 50-biotinylated aptamer was incubated with increasing concentrations of GST-tagged NS1. After addition of GST antibody-conjugated HRP, the amount of the NS1-aptamer complex was calculated and graphed as a function of NS1 concentration. The graph was fit to the Michaelis-Menten equation and the Kd was calculated (18.91 ± 3.95 nM) |
|
| PubMed ID | 24055449 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_409 | DNA | GCAATGGTACGGTACTTCCGGATGCGGAAACTGGCTAATTGGTGAGGCTGGGGCGGTCGTGCAGCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_408 | DNA | GCAATGGTACGGTACTTCCGTCATCAGCTTGTGATGTGGATGCGAACTGCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_994 | DNA | GCAATGGTACGGTACTTCCGGACAGTGCTGAAAACTGTGACCCCCCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_995 | DNA | GCAATGGTACGGTACTTCCCCACCCCACGCTGCTCCCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_951 | DNA | CACCTAATACGACTCACTATAGCGGATCCGAGGGGGTAGCGGGTGGGCCGGTGGATGCGGGGCGCCGGCGCCTGGCTCGAACAAGCTTGC | |
| Apta_832 | DNA | CCGGAGGTGGGTGAGGTCTGCGGCAGGCTGTGTGGGTGGACCGGAGGGGGGTGAGGTCTGCGGCAGGCTGTGTGGGTGGA | |
| Apta_81 | RNA | GCAAUGGUACGGUACUUCCAAGUGCGGGGGGGAGGUGGUGGUUCCAAAAGUGCACGCUACUUUGCUAA | |
| Apta_708 | DNA | CGTACGGAATTCGCTAGCGGGCGGGGGTGCTGGGGGAATGGAGTGCTGCGTGCTGCGGGGATCCGAGCTCCACGTG | |
| Apta_878 | DNA | TCGCACATTCCGCTTCTACCGGGGGGGTCGAGCTGAGTGGATGCGAATCTGTGGGTGGGCTTCGCACACACGGACTTAC | |
| Apta_953 | DNA | TCACCTCATACGACTCACTATAGCGGATCCGAGCCGGGGTGTTCTGTTGGCGGGGGCGGTGGGCGGGCTGGCTCGAACAAGCTTGC | |
| Apta_950 | DNA | CACCTAATACGACTCACTATAGCGGATCCGAAGGGGGCGCGAGGTGTAAGGGTGTGGGGTGGTGGGTGGGCCTGGCTCGAACAAGCTTGC | |
| Apta_589 | DNA | GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG | |
| Apta_771 | DNA | GAATTCCGTCGGACAGCGGTATGCATGGGAGGTTCTGGAGGGGGTGGGTTGGCGTGCGTTCCAGATGGACGAATATCGTCTCCC | |
| Apta_772 | DNA | GAATTCAGTCGGACAGCGCGGTGTTGGTGGTGGGGTGGTTTGGGAATCTGTTCGGCTGGAGATGGACGAATATCGTCTCCC | |
| Apta_775 | DNA | GAATTCAGTCGGACAGCGCGGTGTTGGTGGCGGGGGTGGTTGGGGGATTTGGCTGTCCTGAGTGATGGACGAATATCGTCTCCC | |
| Apta_837 | DNA | TGAGCCCAAGCCCTGGTATGTGATCGGTGACGAGGGTGCGGGGCGGGGGGTGAGGCACAGGGCAGGTCTACTTTGGGATC | |
| Apta_887 | DNA | ACGCTCGGATGCCACTACAGGGGGGTGGTCCTGAGGGTGGTGTGGTTGGTTTGGTTTCCTCATGGACGTGCTGGTGAC | |
| Apta_1011 | DNA | GCTGTGTGACTCCTGCAATGGTAGCGGGTAGGGGAGGGAGGGTGAATGGAGGATGTTCATGGCAGCTGTATCTTGTCTCC | |
| Apta_1090 | DNA | ATCCAGAGTGACGCAGCAGGGCTTGGGTTGGGAATAAGGATGTGGGAGGCGGCGAACATGGACACGGTGGCTTAGT | |
| Apta_589 | DNA | GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG |
DEV TOOL
 |
 |
 |
 |