Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 651
Aptamer sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC
Target unique ID: 3467
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_547 LGA11 Molecule Gentamicin 22.3 nM PBS with 10% (v/v) methanol 22793869
Structure information of aptamer
Aptamer Sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC
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_547 Description LGA11
Aptamer chemistry RNA Length 79 nt
GC content 57.0% Molecular weight 25,496.16 Da
Molarity of 1 μg/μl solution 39.22 μM Number of G-quadruplexes 2
G-Score 19 Function Aptasensor
Sequence GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC
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 580
Target type Molecule
Target unique ID 3081545
Activity 28.4 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 651
Target type Molecule
Target unique ID 3467
Activity 22.3 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 663
Target type Molecule
Target unique ID 6032
Activity 52.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 723
Target type Molecule
Target unique ID 8378
Activity 40.3 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869

No relevant experimental diagram

 Interaction ID 757
Target type Molecule
Target unique ID 165580
Activity 21.4 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 779
Target type Molecule
Target unique ID 19649
Activity 49.9 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 797
Target type Molecule
Target unique ID 36294
Activity 19.2 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_548 RNA GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC 73.42%
Apta_123 RNA GGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC 53.33%
Apta_984 RNA GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA 53.16%
Apta_1224 RNA GGAGGCGCCAACUGAAUGAAUGUUCUGGAUCUGCUAGAGACUAUCUGCUUCGGCAGCACUCUCCGUUAACAACACGUACAUCCGUAACUAGUCGCGUCAC 53.00%
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 52.63%
Apta_1221 RNA GGAGGCGCCAACUGAAUGAACGAGUUGAAAUGCGGAUCAAGUUACUGCUUCGGCAGUACCUAGUGGGAAAAGUUCUUGGGUCCGUAACUAGUCGCGUCAC 52.00%
Apta_352 RNA GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA 51.90%
Apta_854 RNA GGGAGCUCAGAAUAAACGCUCAAGGGUAGGGAUCGUUACCCCGACAUUUUAAUGGGCCGAUGUUUCGACAUGAGGCCCGGAUCCGGC 51.72%
Apta_720 RNA GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA 51.38%
Apta_398 RNA GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA 51.25%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 51.14%
Apta_561 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUGUGGAAACAGACGUGGCACAUGACUACGUCGAAACGGUAGCGAGAGCUC 51.11%
Apta_43 RNA GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC 51.09%
Apta_710 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACGAAACGGUAGCGAGAGCUC 51.06%
Apta_38 RNA GGUAGAUACGAUGGAUACCCCCUGUGGCCCGUCAACACAGGGGAAGUGGCAUGACGCGCAGCCA 50.63%
Apta_130 RNA GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA 50.63%
Apta_399 RNA GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA 50.63%
Apta_400 RNA GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA 50.63%
Apta_594 RNA GGGCUAUUGCUGGAGGGGCGCCACAUGAAAGUGGUGGUUGGGUGCGGUCGGCGAUAGCUC 50.63%
Apta_276 RNA GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC 50.59%

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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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