Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1011
Aptamer sequence: ATCCAGAGTGACGCAGCACGAGCCAGACATCTCACACCTGTTGCATATACATTTTGCATGGACACGGTGGCTTAGT
Target unique ID: Other-33
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_921 | PP3 | Other | Glycosylated Hemagglutinin of Vaccinia Virus-Infected Cells | 3.24 nM | 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco’s PBS (Sigma), BSA (1 mg/mL from Fisher) with t-RNA (0.1 mg/mL) | 20873781 |
Structure information of aptamer
| Aptamer Sequence: | ATCCAGAGTGACGCAGCACGAGCCAGACATCTCACACCTGTTGCATATACATTTTGCATGGACACGGTGGCTTAGT |
| 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_921 | Description | PP3 |
| Aptamer chemistry | DNA | Length | 76 nt |
| GC content | 50.0% | Molecular weight | 23,386.99 Da |
| Molarity of 1 μg/μl solution | 42.76 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Target recognition |
| Sequence | ATCCAGAGTGACGCAGCACGAGCCAGACATCTCACACCTGTTGCATATACATTTTGCATGGACACGGTGGCTTAGT | ||
| Applications | Recognize proteins expressed on the surface of VV-infected cells | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Target ID | Other-33 | Name | Glycosylated Hemagglutinin of Vaccinia Virus-Infected Cells |
Activity data
 |
Interaction ID | 1011 |
| Target type | Other | |
| Target unique ID | Other-33 | |
| Activity | 3.24 nM | |
| Binding Conditions/Buffer | 4.5 g/L glucose and 5 mM MgCl2 in Dulbecco’s PBS (Sigma), BSA (1 mg/mL from Fisher) with t-RNA (0.1 mg/mL) |
|
| Assay | The interaction between myc-His-tagged HA and the aptamer is reduced in the presence of glycosylation inhibitors. CV-1 cells infected in the presence of 5 μg/mL tunicamycin or monensin that are N-linked and O-linked glycosylation inhibitors, respectively |
|
| PubMed ID | 20873781 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_923 | DNA | ATCCAGAGTGACGCAGCATCGACCTCTGTGCGAGCGGGTTGCATATATATTTTGCATGGACACGGTGGCTTAGT | |
| Apta_922 | DNA | ATCCAGAGTGACGCAGCACACCGTTTGTATTCTGCATTGTTTTGCATTCTACATGGACACGGTGGCTTAGT | |
| Apta_1293 | DNA | ATCCAGAGTGACGCAGCATGCCCTAGTTACTACTACTCTTTTTAGCAAACGCCCTCGCTTTGGACACGGTGGCTTAGT | |
| Apta_725 | DNA | ATCCAGAGTGACGCAGCATGCTCATCCACGATTCTGGCGAATTTAGTGCCTGTCTTTTTCTCTTGGACACGGTGGCTTAGT | |
| Apta_785 | DNA | ATCCAGAGTGACGCAGCATGAATCTTTTCTTTTGGTTTTGATATTTATAGTTGGTGAATGGACACGGTGGCTTAGT | |
| Apta_784 | DNA | ATCCAGAGTGACGCAGCATTTTGACGCTTTATCCTTTTCTTATGGCGGGATAGTTTCGTGGACACGGTGGCTTAGT | |
| Apta_794 | DNA | ATCCAGAGTGACGCAGCAAGGAGATTCGAGGGGGAAGGTTTGTTATAGGGGTTAATGGACACGGTGGCTTAGT | |
| Apta_920 | DNA | ATCCAGAGTGACGCAGCACGGCACTCACTCTTTGTTAAGTGGTCTGCTTCTTAACCTTCATCGACACGGTGGCTTA | |
| Apta_1088 | DNA | ATCCAGAGTGACGCAGCATCGAGTGGCTTGTTTGTAATGTAGGGTTCCGGTCGTGGGTTGGACACGGTGGCTTAGT | |
| Apta_401 | DNA | ATCCAGAGTGACGCAGCAGATAAGTAGGTATCCGTTTGAAAAACTTTTCTGACCGTCCGACTATGGACACGGTGGCTTAGT | |
| Apta_786 | DNA | ATCCAGAGTGACGCAGCATTTGTATCCTATTTTGTTTATGTAATTGTCGTTGATCATGTGGACACGGTGGCTTAGT | |
| Apta_1089 | DNA | ATCCAGAGTGACGCAGCAATTACCGATGGCTTGTTTGTAATGTAGGGTTCCGTCGGATTGGACACGGTGGCTTAGT | |
| Apta_1090 | DNA | ATCCAGAGTGACGCAGCAGGGCTTGGGTTGGGAATAAGGATGTGGGAGGCGGCGAACATGGACACGGTGGCTTAGT | |
| Apta_787 | DNA | ATCCAGAGTGACGCAGCATTTGTTTAATATGTTTTTTAATTCCCCTTGTGGTGTGTTGTGGACACGGTGGCTTAGT | |
| Apta_1112 | DNA | ATCCAGAGTGACGCAGCAGGGCACATTGTTCACACACAGATCACATTACGGAAAACACAACTACACGAAATGTCGTTGGTGGCCC | |
| Apta_902 | DNA | ATACGGGAGCCAACACCACCAACATTATCAGAGTATGTTACTTATAGTGGTGGCAGAGCAGGTGTGACGGAT | |
| Apta_792 | DNA | ATACCAGCTTATTCAATTCCCAAATTGCCACCACTTACAGCATGATAACATACTACATCTTTTCATCAAGATAGTAAGTGCAATCT | |
| Apta_288 | DNA | ATCCAGAGTGACGCAGCATTTCATCGGGTCCAAAAGGGGCTGCTCGGGATTGCGGATATGGACACGT | |
| Apta_726 | DNA | TACCAGTGCGATGCTCAGGCCGATGTCAACTTTTTCTAACTCACTGGTTTTGCCTGACGCATTCGGTTGAC | |
| Apta_738 | DNA | ATCGTCTGCTCCGTCCAATACCTGCATATACACTTTGCATGTGGTTTGGTGTGAGGTCGTGC |
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