Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 845
Aptamer sequence: AGCAGAGTTCACGACCCGATAAGGGCGATGCCGATCCCTGTGGCCGTAGGGACAGTCCCGCTAGAGTTACATACCAATCGTCGCAG
Target unique ID: HTB-30
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_762 | sk2 | Cell | SK-BR-3 cell | 1.69 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: | AGCAGAGTTCACGACCCGATAAGGGCGATGCCGATCCCTGTGGCCGTAGGGACAGTCCCGCTAGAGTTACATACCAATCGTCGCAG |
| 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_762 | Description | sk2 |
| Aptamer chemistry | DNA | Length | 86 nt |
| GC content | 58.1% | Molecular weight | 26,537.97 Da |
| Molarity of 1 μg/μl solution | 37.68 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Aptasensor |
| Sequence | AGCAGAGTTCACGACCCGATAAGGGCGATGCCGATCCCTGTGGCCGTAGGGACAGTCCCGCTAGAGTTACATACCAATCGTCGCAG | ||
| 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 | 845 |
| Target type | Cell | |
| Target unique ID | HTB-30 | |
| Activity | 1.69 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_760 | DNA | AGCAGAGTTCACGACCCGATAAGGGCGATGCCGATCCCTGTGGCCGTAGGGGCAGTCCCGCTAGAGTTACATACCAATCGTCGCAG | |
| Apta_761 | DNA | AGCAGAGTTCACGACCCGATAAGGGGAAAACACATTTCGGATCTCCGTTGTCGCCCTGATACCGAGTTACATACCAATCGTCGCAG | |
| Apta_763 | DNA | AGCAGAGTTCACGACCCGATAAGGGGAAAACACATTTCGGATCTCCGTTGTCGCCCTGGTACCGAGTTACATACCAATCGTCGCAG | |
| Apta_764 | DNA | AGCAGAGTTCACGACCCGATAAGGGGAAAATACATTTCGGATCTCCGTTGTCGCCCTGATACCGAGTTACATACCAATCGTCGCAG | |
| Apta_765 | DNA | AGCAGAGTTCACGACCCGATAAGGGGAAAATACATTTCGGATCTCCGTTGTCGCCCTGGTACCGAGTTACATACCAATCGTCGCAG | |
| Apta_461 | DNA | CGCTCGGCTTCACGAGATTCGTGTCGTTGTGTCCTGTACCCGCCTTGACCAGTCACTCTAGAGCATCCGGACTG | |
| Apta_511 | DNA | ATCCGTCACACCTGCTCTCAGGGGATCACATTCTTGACGGTGTGATACAGTGCCTGGTGTTGGCTCCCGTAT | |
| Apta_772 | DNA | GAATTCAGTCGGACAGCGCGGTGTTGGTGGTGGGGTGGTTTGGGAATCTGTTCGGCTGGAGATGGACGAATATCGTCTCCC | |
| Apta_465 | DNA | AGCTGACACAGCAGGTTGGTGGGGGTGGCTTCCAGTTGGGTTGACAATACGTAGGGACACGAAGTCCAACCACGAGTCGAGCAATCTCGAAAT | |
| Apta_278 | DNA | AGCAGCACAGAGGTCAGATGAGGCCTGGTGATCGTGCCCAGGCCATATGAGCAAGGAACCCCTATGCGTGCTACCGTGAA | |
| Apta_979 | DNA | ATGAGTAGTGCGGAGGGATGTGAATACTGACGCGGTCATAGTCGCTGTTGTACCATTGA | |
| Apta_991 | DNA | AGCAGTGAAGAGGCGAGAGATTTATGAGGGTAGCGTCCACATATGCCAGGATCGTGTTG | |
| Apta_1000 | DNA | ATAGGAGTCGACCGACCAGAACCGTTCCCATACTTCTCCAGCGATACTTAGTGCGTCTACATCTAGACTC | |
| Apta_1004 | DNA | ATAGGAGTCGACCGACCAGACCCGACCTCTCTTTCACTGTGACACAATGGTGCGTCTACATCTAGACTC | |
| Apta_1010 | DNA | ATAGGAGTCGACCGACCAGACCGACCCTCGTCGTACCAACTGATGACCTAGTGGCGTCTACATCTAGACTC | |
| Apta_1178 | DNA | AGCGTCGAATACCACTACAGGGGATGCGAAGTTCCGCGGTCGAGTATATGATACATCCATCTAATGGAGCTCGTGGTCAG | |
| Apta_628 | DNA | ATACCAGCTTATTCAATTAGCCCGGTATTGAGGTCGATCTCTTATCCTATGGCTTGTCCCCCATGGCTCGGTTATATCCAGATAGTAAGTGCAATCT | |
| Apta_628 | DNA | ATACCAGCTTATTCAATTAGCCCGGTATTGAGGTCGATCTCTTATCCTATGGCTTGTCCCCCATGGCTCGGTTATATCCAGATAGTAAGTGCAATCT | |
| Apta_584 | DNA | GTACCAGCTTATTCAATTACACGGACAGAGGGTAGCGGCTCTGCGCATTGAGTTGCTGCGGGCTGAAGCGCGGTACATGGGAGATAGTATGTTCATCAG | |
| Apta_99 | DNA | AGCAGCACAGAGGTCAGATGTCGGGCGGTTCGGGACCTTGCTGCGACATATGCGTATTATCCTATGCGTGCTACCGTGAA |
DEV TOOL
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