Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_629 | ky2 | Molecule | Bekanamycin | 84.5 nM | 20 mM Tris-HCl, 50 mM NaCl, 5 mM KCl, 5 mM MgCl2, pH 8.0 | 21530479 |
Structure information of aptamer
| Aptamer Sequence: | TGGGGGTTGAGGCTAAGCCGA |
| 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_629 | Description | ky2 |
| Aptamer chemistry | DNA | Length | 21 nt |
| GC content | 61.9% | Molecular weight | 6,567.24 Da |
| Molarity of 1 μg/μl solution | 152.27 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Aptasensor |
| Sequence | TGGGGGTTGAGGCTAAGCCGA | ||
| Applications | Detection of kanamycin | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| PubChem ID | 439318 | Molecular name | Bekanamycin |
| Molecular formula | C18H37N5O10 | Molecular weight | 483.5 |
| IUPAC name | (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxyoxane-3,4-diol | InChIKey | SKKLOUVUUNMCJE-FQSMHNGLSA-N |
| LogP | -7.325 | Topological polar surface area | 288.4 |
| Hydrogen bond acceptor | 15 | Hydrogen bond donor | 11 |
Synonym(s): bekanamycin; Kanamycin B; 4696-76-8; Aminodeoxykanamycin; Nebramycin V; nebramycin factor 5; 2'-Amino-2'-deoxykanamycin; Klebcil; UNII-15JT14C3GI; Bekanamycin [INN]; NK 1006; 15JT14C3GI; CHEBI:28098; Bekanamycin (INN); NK-1006; (1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside; (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-(((1R,2S,3S,4R,6S)-4,6-diamino-3-(((2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)-2-hydroxycyclohexyl)oxy)tetrahydro-2H-pyran-3,4-diol; (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxyoxane-3,4-diol; Becanamicina; Bekanamycine; Bekanamycinum; (1R,2S,3S,4R,6S)-4,6-diamino-3-(3-amino-3-deoxy-alpha-D-glucopyranosyloxy)-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside; O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1->4)-O-(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl-(1->6))-2-deoxy-D-streptamine; Bekanamycine [INN-French]; Bekanamycinum [INN-Latin]; Becanamicina [INN-Spanish]; NCGC00096063-01; 9CS; EINECS 225-170-5; BRN 0061646; Spectrum_001112; Kanamycin B; Bekanamycin; Spectrum2_000640; Spectrum3_000619; Spectrum4_001831; Spectrum5_000621; DSSTox_CID_3185; CHEMBL176; DSSTox_RID_76911; DSSTox_GSID_23185; BSPBio_002158; KBioGR_002528; KBioSS_001592; SCHEMBL158426; SPBio_000640; MEGxm0_000486; DTXSID8023185; ACon0_001346; KBio2_001592; KBio2_004160; KBio2_006728; KBio3_001658; HY-B1174; Tox21_113194; BDBM50368267; ZINC53132258; CS-4772; DB13673; SDCCGMLS-0066707.P001; NCGC00178790-01; CAS-4696-76-8; SBI-0052603.P002; C00825; D07497; AB00053732_02; A924196; Antibiotic derived from Streptomyces kanamyceticus; Kanamycin B, Antibiotic for Culture Media Use Only; Q3637540; W-106082; UNII-NQJ13I4Z9U component SKKLOUVUUNMCJE-FQSMHNGLSA-N; UNII-RUC37XUP2P component SKKLOUVUUNMCJE-FQSMHNGLSA-N; Antibiotic derived from Streptomyces kanamyceticus. Kanamycin B; (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-2-hydroxy-cyclohexoxy]tetrahydropyran-3,4-diol; D-Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1-4)-O-(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl-(1-6))-2-deoxy-
Activity data
 |
Interaction ID | 670 |
| Target type | Molecule | |
| Target unique ID | 439318 | |
| Activity | 84.5 nM | |
| Binding Conditions/Buffer | 20 mM Tris-HCl, 50 mM NaCl, 5 mM KCl, 5 mM MgCl2, pH 8.0 |
|
| Assay | A620/A520 ratio and color of the AuNP solution versus kanamycin concentration |
|
| PubMed ID | 21530479 | |
 |
Interaction ID | 799 |
| Target type | Molecule | |
| Target unique ID | 36294 | |
| Activity | 103 nM | |
| Binding Conditions/Buffer | 20 mM Tris-HCl, 50 mM NaCl, 5 mM KCl, 5 mM MgCl2, pH 8.0 |
|
| Assay | A620/A520 ratio and color of the AuNP solution versus kanamycin concentration |
|
| PubMed ID | 21530479 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_18 | DNA | TGGGGGGTTGGACGGGCGGGGCTGC | |
| Apta_8 | DNA | TGTGGGGGTGGACGGGCCGGGTAGA | |
| Apta_23 | DNA | TGTGGGGGTGGACGGGCCGAGTACG | |
| Apta_24 | DNA | TGTGGGGATGGATGGGCCGGGCTGC | |
| Apta_203 | DNA | GGAAGGCTTTAGGTCTGAGATCTCGG | |
| Apta_184 | DNA | AGGAAGGCTTTAGGTCTGAGATCTCGGAAT | |
| Apta_147 | DNA | TGCGGTTGTAGTACTCGTGGCCG | |
| Apta_15 | DNA | TGAGGGGGGGGGAGGGCGGGGCTGC | |
| Apta_19 | DNA | TGAGGGGGGGGGAGGTCGGGCCTGC | |
| Apta_25 | DNA | TGTGGGGGTGGTTGGGCGGGGCTGC | |
| Apta_27 | DNA | AGGGGGAGGGGTGGGGCCGGGCAGA | |
| Apta_125 | DNA | TGGTGGATGGCGCAGTCGGCGACAA | |
| Apta_196 | DNA | AGGAAGGCTTTAGGTCTGAGATCTC | |
| Apta_700 | DNA | GCAGGGGCGTTCGGGGGGTACCGCTGC | |
| Apta_193 | DNA | AGGAAGGCTTTAGGGTCTGAGATCTCGGAAT | |
| Apta_1147 | DNA | GGGGACTAGAGGACTTGTGCGGCC | |
| Apta_205 | DNA | TTAAGGCTTTAGGTCTGAGATCTCTT | |
| Apta_186 | DNA | AGGAACGCTTTAGGTCTGAGATCTCGGAAT | |
| Apta_192 | DNA | AGGAAGGCTTTAGCTCTGAGATCTCGGAAT | |
| Apta_214 | DNA | AGGAAGGCTTTAGGTTTCCTAAAGCCTTCC |
DEV TOOL
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