Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_706 | Clone 73-min | Molecule | Sulforhodamine B | 190 nM | 0.1 M KCl, 5 mM MgCl2, 10 mM Na-HEPES (pH 7.4). | 9831529 |
Structure information of aptamer
| Aptamer Sequence: | CCGGCCAAGGGTGGGAGGGAGGGGGCCGG |
| 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_706 | Description | Clone 73-min |
| Aptamer chemistry | DNA | Length | 29 nt |
| GC content | 82.8% | Molecular weight | 9,155.85 Da |
| Molarity of 1 μg/μl solution | 109.22 μM | Number of G-quadruplexes | 3 |
| G-Score | 64 | Function | Targeted binding |
| Sequence | CCGGCCAAGGGTGGGAGGGAGGGGGCCGG | ||
| Applications | Recognizing the fluorophore sulforhodamine B | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| PubChem ID | 65191 | Molecular name | Sulforhodamine B |
| Molecular formula | C27H30N2O7S2 | Molecular weight | 558.7 |
| IUPAC name | 2-[3-(diethylamino)-6-diethylazaniumylidenexanthen-9-yl]-5-sulfobenzenesulfonate | InChIKey | IOOMXAQUNPWDLL-UHFFFAOYSA-N |
| LogP | 4.014 | Topological polar surface area | 130.96 |
| Hydrogen bond acceptor | 7 | Hydrogen bond donor | 1 |
Synonym(s): Sulforhodamine B; Lissamine rhodamine B; 2609-88-3; Sulforhodamine B, acid form; Kiton Rhodamine B; Xanthylium, 3,6-bis(diethylamino)-9-(2,4-disulfophenyl)-, inner salt; SULFORHODAMINEB; Kayaku Acid Rhodamine BH; Food Color Red No. 106; 2-[3-(diethylamino)-6-diethylazaniumylidenexanthen-9-yl]-5-sulfobenzenesulfonate; 3520-42-1; sulforhodamine-B; Sulfo-Rhodamine-B; EINECS 220-025-2; Xanthylium, 3,6-bis(diethylamino)-9-(2,4-disulfophenyl)-, hydroxide, inner salt; Hydrogen 3,6-bis(diethylamino)-9-(2,4-disulphonatophenyl)xanthylium; SCHEMBL18483; CHEMBL4302011; AKOS024370868; MCULE-3642131160; 3520-42-1 (SODIUM SALT); E79436; Q2452042; Sulforhodamine B, acid form, laser grade, Dye content 95 %; [6-(diethylamino)-9-(2,4-disulfophenyl)xanthen-3-ylidene]-diethyl-ammonium; 2-(3,6-BIS(DIETHYLAMINO)XANTHYLIUM-9-YL)-5-SULFOBENZENESULFONATE; [6-(Diethylamino)-9-(2,4-disulfophenyl)-3H-xanthen-3-ylidene]diethylammonium, 8CI; 2-(6-(diethylamino)-3-(diethyliminio)-3H-xanthen-9-yl)-5-sulfobenzenesulfonate; 3,6-Bis(diethylamino)-9-(2,4-disulfophenyl)xanthylium hydroxide inner salt, 9CI; N-(6-(Diethylamino)-9-(2,4-disulfophenyl)-3H- xanthen-3-ylidene)-N-ethylethanaminium, hydroxide, inner salt, sodium salt
Activity data
|
No relevant experimental diagram |
Interaction ID | 781 |
| Target type | Molecule | |
| Target unique ID | 65191 | |
| Activity | 190 nM | |
| Binding Conditions/Buffer | 0.1 M KCl, 5 mM MgCl2, 10 mM Na-HEPES (pH 7.4). |
|
| Assay | N/A |
|
| PubMed ID | 9831529 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_831 | DNA | CCGCCCAGCGGGGGTAGGGCCGGACGTAGGAGGAGCTGCG | |
| Apta_880 | DNA | GCCGCACAATCGGGTTGGGCAGGGAGGGCACGTGTGGCGC | |
| Apta_1188 | DNA | CGGGCGGGGCGTGGGGTGTTGGAGTGGAGGGCGGGGCGGC | |
| Apta_218 | RNA | AGCCGCGAGGGGAGGGAUAGGGUAGGGCGCGGCU | |
| Apta_262 | DNA | ACGGACTCGCAAAAGGTGGAACAGGAGTGGGCCCCGCGGC | |
| Apta_862 | DNA | TGTGCCAAAGAGAGTGGTGGGGGGGTGGGCGGAACTCGCG | |
| Apta_926 | RNA | UCGGCAGCGGUUAGAGAGGUGGUGUGCGGG | |
| Apta_10 | DNA | GGGGGGGGTGGCTGGGCGGGGTGGG | |
| Apta_12 | DNA | TGAGGGGGTGGGTGGGACGGGTTGG | |
| Apta_13 | DNA | AGGGGGGGGGGAGGGGTCGGGGTGG | |
| Apta_15 | DNA | TGAGGGGGGGGGAGGGCGGGGCTGC | |
| Apta_18 | DNA | TGGGGGGTTGGACGGGCGGGGCTGC | |
| Apta_19 | DNA | TGAGGGGGGGGGAGGTCGGGCCTGC | |
| Apta_20 | DNA | AGAGGGGGGGGTGGGGGTGGCCTGC | |
| Apta_30 | DNA | AGAGGGGGGGGTGGAGGGGGCTAGA | |
| Apta_1194 | DNA | GGGAGAGGTGGGAGCGGGGCCAGGG | |
| Apta_75 | DNA | CACTGGTAGGTTGGTGTGGTTGGGGCCAGTG | |
| Apta_46 | DNA | CGGGTGGGAGTTGTGGGGGGGGGTGGGAGGGTT | |
| Apta_869 | DNA | ACTAGGACGCTTGGGAGGGGGGGTGGGGTGTCCGGTCGCG | |
| Apta_675 | DNA | ACTGTCCGTCGGGTTTAGGGTGGCGTTCGG |
DEV TOOL
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