Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 724
Aptamer sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
Target unique ID: 8378
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_548 LS13 Molecule Neomycin 37 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 8378 Molecular name Neomycin
Molecular formula C23H46N6O13 Molecular weight 614.6
IUPAC name (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2R,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol InChIKey PGBHMTALBVVCIT-VCIWKGPPSA-N
LogP -8.895 Topological polar surface area 353.11
Hydrogen bond acceptor 19 Hydrogen bond donor 13

Synonym(s):
neomycin; Framycetin; NEOMYCIN B; Mycifradin; Soframycin; Actiline; Fradiomycin; Neomas; Fradiomycin B; Fradiomycinum; Framicetina; Framycetine; Framycetinum; Caswell No. 595; 119-04-0; NEOMYCIN SULFATE; 1404-04-2; USAF CB-19; CCRIS 5462; HSDB 3242; Soframycine; UNII-4BOC774388; Neo-Rx; Antibiotique; Enterfram; Nivemycin; Actilin; Framygen; Myacyne; Neolate; CHEBI:7508; Vonamycin powder V; (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside; (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2R,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol; Neomcin; Neomycin solution; Neomin; 4BOC774388; Neomicina [DCIT]; Framycetinum [INN-Latin]; Neomicina; Neomycin sulphate; Neomycine; Neomycinum; PIMAVECORT; Neomycine [INN-French]; Neomycinum [INN-Latin]; Framycetine [INN-French]; NMY; Framicetina [INN-Spanish]; Framycetin [INN:BAN:DCF]; Bycomycin; Jernadex; Framycetin (INN); Neomycin [INN:BAN]; EINECS 204-292-2; EINECS 215-766-3; EPA Pesticide Chemical Code 006303; BRN 0101621; Mycerin; Antibiotic 956; (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2R,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxy-tetrahydropyran-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]oxy-3-hydroxy-cyclohexoxy]tetrahydropyran-3,4-diol; C23H46N6O13; NEOMYCINB; Antibiotic produced by Streptomyces decaris. Neomycin B; Prestwick3_000158; KDR Kinase Inhibitor, 3; BDBM19; SCHEMBL3279; ANTIBIOTIQUE EF 185; BSPBio_000296; GTPL709; 4-18-00-07476 (Beilstein Handbook Reference); D-Streptamine, O-2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl-(1-4)-O-(O-2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl-(1-3)-beta-D-ribofuranosyl-(1-5))-2-deoxy-; BPBio1_000326; CHEMBL184618; DTXSID2023359; HMS2089P15; ZINC71928291; AKOS024284361; CS-6390; DB00452; NCGC00179612-01; D-Streptamine, O-2,6-diamino-2,6-dideoxy-.beta.-L-idopyranosyl-(1.->3)-O-.beta.-D-ribofuranosyl-(1->5)]-O-[2,6-diamino-2,6-dideoxy-.alpha.-D-glucopyranosyl-(1->4)]-2-deoxy; HY-17624; AB00443887; C01737; D05140; 30384-EP2272825A2; 30384-EP2272838A1; 30384-EP2277898A2; 30384-EP2287165A2; 30384-EP2287166A2; 30384-EP2292620A2; 30384-EP2295401A2; 30384-EP2295402A2; 30384-EP2298776A1; 30384-EP2305662A1; 30384-EP2305695A2; 30384-EP2305696A2; 30384-EP2305697A2; 30384-EP2305698A2; 30384-EP2311464A1; AB00443887-03; MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN; J-004060; Q4492348; BRD-K71013094-065-01-2; UNII-I16QD7X297 component PGBHMTALBVVCIT-VCIWKGPPSA-N; (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2-{[(2S,3R,4S,5R)-4-{[(2R,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxycyclohexyl]oxy}oxane-3,4-diol; (2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(2R,3S,4R,5S)-5-{[(1R,2R,3S,5R,6S)-3,5-diamino-2-{[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-6-hydroxycyclohexyl]oxy}-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}oxane-3,4-diol; 11004-65-2; 6-(2-{(4S,2R,3R,5R)-4-[(5S,6S,2R,3R,4R)-3-amino-6-(aminomethyl)-4,5-dihydroxy( 2H-3,4,5,6-tetrahydropyran-2-yloxy)]-3-hydroxy-5-(hydroxymethyl)oxolan-2-yloxy }(3S,6S,1R,2R,4R)-4,6-diamino-3-hydroxycyclohexyloxy)(3S,2R,4R,5R,6R)-5-amino- 2-(aminomethyl)-2H; WURCS=2.0/3,3,2/[a222h-1b_1-4][a2122h-1a_1-5_2*N_6*N][a2121h-1b_1-5_2*N_6*N]/1-2-3/a1n2-b1n1*1OC^RC^RO*2/4C^SC^RCC^S$3/10N/8N/7O_a3-c1

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%

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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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