Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 848
Aptamer sequence: AGCAGAGTTCACGACCCGATAAGGGGAAAATACATTTCGGATCTCCGTTGTCGCCCTGGTACCGAGTTACATACCAATCGTCGCAG
Target unique ID: HTB-30
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_765 | sk5 | Cell | SK-BR-3 cell | 3.47 nM | PBS (pH 7.4), 5 mM MgCl2, 4.5 g/L glucose, 0.1 mg/mL yeast tRNA, 1 mg/mL BSA | 30555580 |
Structure information of aptamer
| Aptamer Sequence: | AGCAGAGTTCACGACCCGATAAGGGGAAAATACATTTCGGATCTCCGTTGTCGCCCTGGTACCGAGTTACATACCAATCGTCGCAG |
| 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_765 | Description | sk5 |
| Aptamer chemistry | DNA | Length | 86 nt |
| GC content | 51.2% | Molecular weight | 26,485.97 Da |
| Molarity of 1 μg/μl solution | 37.76 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Aptasensor |
| Sequence | AGCAGAGTTCACGACCCGATAAGGGGAAAATACATTTCGGATCTCCGTTGTCGCCCTGGTACCGAGTTACATACCAATCGTCGCAG | ||
| Applications | Probe for molecular subtyping of breast cancer | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| ATCC ID | HTB-30 | Cell name | SK-BR-3 cell |
| Category | Human cells | Organism | Homo sapiens, human |
| Product type | N/A | Cell type | N/A |
| Morphology | epithelial | Tissue | Breast; Mammary gland |
| Disease | Adenocarcinoma | Product format | Frozen |
| Antigen expression | Blood Type A; Rh+; HLA A11, Bw22(+/-), B40, B18 | Genes expressed | N/A |
| Cell description | SK-BR-3 [SKBR3] cells were isolated in 1970 from pleural effusion cells of a 43-year-old, White, female adenocarcinoma patient with blood type A+ who had been treated with radiation, steroids, cytoxan, and 5-fluorouracil. Use these cells in your breast cancer research. |
|
|
| Application(s) | 3D cell culture | ||
Activity data
 |
Interaction ID | 848 |
| Target type | Cell | |
| Target unique ID | HTB-30 | |
| Activity | 3.47 nM | |
| Binding Conditions/Buffer | PBS (pH 7.4), 5 mM MgCl2, 4.5 g/L glucose, 0.1 mg/mL yeast tRNA, 1 mg/mL BSA |
|
| Assay | Dissociation constants (Kd) of the selected aptamers |
|
| PubMed ID | 30555580 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_763 | DNA | AGCAGAGTTCACGACCCGATAAGGGGAAAACACATTTCGGATCTCCGTTGTCGCCCTGGTACCGAGTTACATACCAATCGTCGCAG | |
| Apta_764 | DNA | AGCAGAGTTCACGACCCGATAAGGGGAAAATACATTTCGGATCTCCGTTGTCGCCCTGATACCGAGTTACATACCAATCGTCGCAG | |
| Apta_761 | DNA | AGCAGAGTTCACGACCCGATAAGGGGAAAACACATTTCGGATCTCCGTTGTCGCCCTGATACCGAGTTACATACCAATCGTCGCAG | |
| Apta_760 | DNA | AGCAGAGTTCACGACCCGATAAGGGCGATGCCGATCCCTGTGGCCGTAGGGGCAGTCCCGCTAGAGTTACATACCAATCGTCGCAG | |
| Apta_762 | DNA | AGCAGAGTTCACGACCCGATAAGGGCGATGCCGATCCCTGTGGCCGTAGGGACAGTCCCGCTAGAGTTACATACCAATCGTCGCAG | |
| Apta_140 | DNA | GGCAGGAAGACAAACACGATGGGGGGGTATGATTTGATGTGGTTGTTGCATGATCGTGGTCTGTGGTGCTGT | |
| Apta_233 | DNA | AGCAGCACAGAGGTCAGATGTGAAACATAGCATATTTACTTATGTCGCCTTGCCGGTTCCTATGCGTGCTACCGTGAA | |
| Apta_401 | DNA | ATCCAGAGTGACGCAGCAGATAAGTAGGTATCCGTTTGAAAAACTTTTCTGACCGTCCGACTATGGACACGGTGGCTTAGT | |
| Apta_628 | DNA | ATACCAGCTTATTCAATTAGCCCGGTATTGAGGTCGATCTCTTATCCTATGGCTTGTCCCCCATGGCTCGGTTATATCCAGATAGTAAGTGCAATCT | |
| Apta_628 | DNA | ATACCAGCTTATTCAATTAGCCCGGTATTGAGGTCGATCTCTTATCCTATGGCTTGTCCCCCATGGCTCGGTTATATCCAGATAGTAAGTGCAATCT | |
| Apta_810 | DNA | ACAGCATCCCCATGTGAACAATCGCATTGTGATTGTTACGGTTTCCGCCTCATGGACGTGCTG | |
| Apta_550 | DNA | GGTAATACGACTCACTATAGGGAGATACCAGCTTATTCAATTTTACAGAACAACCAACGTCGCTCCGGGTACTTCTTCATCGAGATAGTAAGTGCAATCT | |
| Apta_583 | DNA | GTACCAGCTTATTCAATTGCGAGCAGGGTCAATGGAATTAATGATCAATTGACAGACGCAAGTCTCCTGCGGTCCTGTGTTGAGATAGTATGTTCATCAG | |
| Apta_584 | DNA | GTACCAGCTTATTCAATTACACGGACAGAGGGTAGCGGCTCTGCGCATTGAGTTGCTGCGGGCTGAAGCGCGGTACATGGGAGATAGTATGTTCATCAG | |
| Apta_369 | DNA | GGCTGTTGTGAGCCTCCTCCCAGAGGGAAGACTTTAGGTTCGGTTCACGTCCCGCTTATTCTTACTCCC | |
| Apta_461 | DNA | CGCTCGGCTTCACGAGATTCGTGTCGTTGTGTCCTGTACCCGCCTTGACCAGTCACTCTAGAGCATCCGGACTG | |
| Apta_774 | DNA | GAATTCAGTCGGACAGCGAGGAAAATTTCGTTATTTTCGTTTCCGGGAACTCGGGCATTTAGAGATGGACGAATATCGTCTCCC | |
| Apta_1004 | DNA | ATAGGAGTCGACCGACCAGACCCGACCTCTCTTTCACTGTGACACAATGGTGCGTCTACATCTAGACTC | |
| Apta_934 | DNA | GACGCTTACTCAGGTGTGACTCGTGAACCCACCTCAGGGCATCTTACATTTCTTCTAAGTTGTTACCATGTTTCGAAGGACGCAGATGAAGTCTC | |
| Apta_860 | DNA | CACGGATCCTGACAAGGATGTGTGCGTTGTCGAGACCTGCGACCGGAACACTACACTGTGTGGGATGGATTTCTTTACAGTTGTGTGCAGCTCCGTCCGACTCTTCCTAGCTATGGTTCGATCAAGA |
DEV TOOL
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