Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 652
Aptamer sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
Target unique ID: 3467
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_548 LS13 Molecule Gentamicin 26.7 nM PBS with 10% (v/v) methanol 22793869
Structure information of aptamer
Aptamer Sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
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_548 Description LS13
Aptamer chemistry RNA Length 79 nt
GC content 46.8% Molecular weight 25,394.90 Da
Molarity of 1 μg/μl solution 39.38 μM Number of G-quadruplexes 2
G-Score 17 Function Aptasensor
Sequence GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
Applications Detection of antibiotics
Target information
Type Detail Type Detail
PubChem ID 3467 Molecular name Gentamicin
Molecular formula C21H43N5O7 Molecular weight 477.6
IUPAC name 2-[4,6-diamino-3-[3-amino-6-[1-(methylamino)ethyl]oxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol InChIKey CEAZRRDELHUEMR-UHFFFAOYSA-N
LogP -3.327 Topological polar surface area 199.73
Hydrogen bond acceptor 12 Hydrogen bond donor 8

Synonym(s):
gentamicin; Gentavet; Gentamicins; GENTAMYCIN; Gentamicin sulphate sterile; Gentacycol; 1403-66-3; Gentamycin C1; Cidomycin; Gentamicinum; Gentamycinum; Refobacin; Garasol; Refobacin TM; 2-[4,6-diamino-3-[3-amino-6-[1-(methylamino)ethyl]oxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol; Gentamicina; Gentamicine; Gentocin; Gentamycin-creme; Gentamycins; Gentamicine [INN-French]; Gentamicinum [INN-Latin]; Gentamycin-creme [German]; Gentamicina [INN-Spanish]; Oksitselanim; Centicin; Lyramycin; Septigen; Gentamicin (TN); Gentamicin (BAN); Gentamicin [INN]; HSDB 3087; Gentamicin [INN:BAN]; EINECS 215-765-8; 4,6-diamino-3-{[3-deoxy-4-c-methyl-3-(methylamino)pentopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,3,4,6,7-pentadeoxy-6-(methylamino)heptopyranoside; SCHEMBL537630; CHEMBL329592; GTPL2427; SCHEMBL19996168; STL454325; AKOS015961211; DB00798; J4.074F; 2-[4,6-diamino-3-[3-amino-6-(1-methylaminoethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-5-methyl-4-methylaminooxane-3,5-diol; AC-13386; FT-0626646; FT-0668965; D08013; 123871-EP2292088A1; 123871-EP2295422A2; 123871-EP2295439A1; Q422482

Activity data
Interaction ID 581
Target type Molecule
Target unique ID 3081545
Activity 35.9 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 652
Target type Molecule
Target unique ID 3467
Activity 26.7 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 664
Target type Molecule
Target unique ID 6032
Activity 69.9 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 724
Target type Molecule
Target unique ID 8378
Activity 37 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 758
Target type Molecule
Target unique ID 165580
Activity 19.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 780
Target type Molecule
Target unique ID 19649
Activity 19.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 798
Target type Molecule
Target unique ID 36294
Activity 24.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_547 RNA GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC 73.42%
Apta_43 RNA GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC 59.78%
Apta_984 RNA GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA 54.43%
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 52.63%
Apta_720 RNA GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA 52.29%
Apta_1223 RNA GGAGGCGCCAACUGAAUGAAAGGUUACGCUUCAACGCCGUGCAGCUGCUUCGGCAGGCUUGUGAGUACAUGGCCCAUUGAUCCGUAACUAGUCGCGUCAC 52.00%
Apta_576 RNA GGCACCAAAGCUGAAGUAGCGGGAUAACUCAAAUUACUUUAGGUGUAUGAAGGUGAAACUAGCAAUGAA 51.90%
Apta_410 RNA GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG 51.76%
Apta_414 RNA GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA 51.25%
Apta_500 RNA GGGAGAAAGGGAAGCUUGAGGUGCUAUGGAGUGGAGGAGUUGAAGGUGUCGGGGUUGGCAGAAGAAGGCGAGCGUACGGAUCCAUC 51.16%
Apta_1225 RNA GGAGGCGCCAACUGAAUGAAAGAGGUAACGAAAGAUGAUUGUGCCUGCUUCGGCAGUACAACUUCUCGGAUAAAUGAUUAUCCGUAACUAGUCGCGUCAC 51.00%
Apta_129 RNA GGGAGGACGAUGCGGACACCGUUAAUCUGAGGCCCUGUCCUAUUCCUUCACGCCUCAGA 50.63%
Apta_130 RNA GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA 50.63%
Apta_352 RNA GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA 50.63%
Apta_1100 RNA GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU 50.63%
Apta_123 RNA GGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC 50.00%
Apta_137 RNA GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC 50.00%
Apta_432 RNA GGGAGACAAGAAUAAACGCUCAAGGCAUUUCUGCUAGUCUGGUUGUAAGAUAUUCAACACGUGAGUUUCGACAGGAGGCUCACAACAGGC 50.00%
Apta_562 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUUAGGGCCAAGUGUGGUGAAAGACACACUCGAAACGGUAGCGAGAGCUC 50.00%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 50.00%

ABOUT

AptaDB is an online database we developed to integrate comprehensive information about aptamer.
The detail of this database is described here:

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