Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 756
Aptamer sequence: CGAGTTGAGCCGGGCGCGGTACGGGTACTGGTATGTGTGG
Target unique ID: 54675779
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_693 No. 20 Molecule Oxytetracycline 56.84 nM 100 mM NaCl, 20 mM Tris-HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02 Tween 20, pH 7.6 17988875
Structure information of aptamer
Aptamer Sequence: CGAGTTGAGCCGGGCGCGGTACGGGTACTGGTATGTGTGG
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_693 Description No. 20
Aptamer chemistry DNA Length 40 nt
GC content 65.0% Molecular weight 12,520.99 Da
Molarity of 1 μg/μl solution 79.87 μM Number of G-quadruplexes 2
G-Score 21 Function Targeted binding
Sequence CGAGTTGAGCCGGGCGCGGTACGGGTACTGGTATGTGTGG
Applications Binding to oxytetracycline (OTC)
Target information
Type Detail Type Detail
PubChem ID 54675779 Molecular name Oxytetracycline
Molecular formula C22H24N2O9 Molecular weight 460.4
IUPAC name (4S,4aR,5S,5aR,6S,12aR)-4-(dimethylamino)-1,5,6,10,11,12a-hexahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide InChIKey OWFJMIVZYSDULZ-PXOLEDIWSA-N
LogP -1.4 Topological polar surface area 201.85
Hydrogen bond acceptor 10 Hydrogen bond donor 7

Synonym(s):
oxytetracycline; Terramycin; 79-57-2; Oxyterracine; Oxytetracyclin; Oxymycin; Terrafungine; Oxyterracin; Oxitetraciclina; Oxitetracyclin; Adamycin; Biostat; Geomycin; Ryomycin; Oxitetracyclinum; Oxytetracyclinum; Oxytetracycline (anhydrous); Oxyterracyne; Oxytetracycline anhydrous; Solkaciclina; Dabicycline; Fanterrin; Geotilin; Imperacin; Lenocycline; Oksisyklin; Proteroxyna; Riomitsin; Terramitsin; Ursocyclin; Ursocycline; Oxypam; Tarocyn; Tarosin; Teravit; Tetran; Antibiotic TM 25; Oxytetracycline amphoteric; 5-Hydroxytetracycline; Liquamycin LA 200; Biostat PA; Bisolvomycin; Oxysteclin; Oxymykoin; Vendarcin; Ossitetraciclina; Pennox 200; Oxytetracycline (Terramycin); Oxytetracycline [INN]; Berkmycen; Mycoshield TMQTHC 20; Oxytetracycline base; Dalimycin; Oxacycline; Unimycin; NSC-9169; Oxytetracycline calcium; Stevacin; Macocyn; Medamycin; Oxy-Kesso-tetra; 6153-64-6; UNII-SLF0D9077S; Mepatar; (4S,4aR,5S,5aR,6S,12aS)-4-(dimethylamino)-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide; OTC (antibiotic); MLS000069429; SLF0D9077S; Tetracycline, 5-hydroxy-; CHEBI:27701; Oxytetracycline (internal use); Stecsolin; Oxydon; TM 5; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-, (4S,4aR,5S,5aR,6S,12aS)-; Oxytetracid; E703; NCI-C56473; SMR000059000; Terramycin im; NSC 9169; Terramycin Q50; Q63393012; Ossitetraciclina [DCIT]; Oxytetracyclinum [INN-Latin]; Oxitetraciclina [INN-Spanish]; Terramicina Oftalmica; 79-57-2 (ANHYDROUS); Geomycin (Streptomyces vimosus); HSDB 3145; EINECS 201-212-8; LA 200; BRN 2714587; Embryostat; Galsenomycin; Oxitetracycline; SR-01000003006; Hydroxytetracyclinum; Oxytetracycline,(S); 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-, (4S-(4alpha,4aalpha,5alpha,5aalpha,6beta,12aalpha))-; 5-Hydroxy-Tetracycline; Spectrum_001055; Opera_ID_661; Prestwick0_000307; Prestwick1_000307; Prestwick2_000307; Prestwick3_000307; Spectrum2_000988; Spectrum3_000536; Spectrum4_000466; Spectrum5_001148; Oxytetracycline(Terramycin); SCHEMBL2899; CHEMBL1517; DSSTox_CID_14260; DSSTox_RID_79133; DSSTox_GSID_34260; BSPBio_000274; BSPBio_002151; KBioGR_000912; KBioSS_001535; 4-14-00-02633 (Beilstein Handbook Reference); DivK1c_000225; SCHEMBL560497; SPBio_001055; SPBio_002493; BPBio1_000302; CHEMBL461529; CHEMBL1401333; CHEMBL4280957; DTXSID1034260; NSC9169 (HCL); SCHEMBL13169109; SCHEMBL13782651; GTPL10919; KBio1_000225; KBio2_001535; KBio2_004103; KBio2_006671; KBio3_001651; 6153-64-6 (di-hydrate); NINDS_000225; BDBM241973; (4S,4aR,5S,5aR,6S,12aR)-4-(dimethylamino)-1,5,6,10,11,12a-hexahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide; HY-B0275; 2058-46-0 (mono-hydrochloride); Tox21_302380; LMPK07000005; MFCD00003700; s1773; ZINC95626782; AKOS015951277; AKOS015961254; ZINC100026355; ZINC100303028; CCG-269334; DB00595; MCULE-5398230579; CAS-79-57-2; IDI1_000225; NCGC00091268-04; NCGC00091268-05; NCGC00091268-06; NCGC00091268-07; NCGC00091268-08; NCGC00091268-09; NCGC00091268-11; NCGC00091268-12; NCGC00188956-01; NCGC00255168-01; AC-12777; AC-13466; S470; 7179-50-2 (calcium (1:1) salt); SBI-0051473.P003; SW196796-3; 3,5,6,10,12,12a-hexahydroxy-6-methyl-; C06624; E75911; Oxytetra Selective Supplement, for microbiology; AB00053514_04; AB00053514_05; AB01274728-01; AB01274728_02; 135740-EP2275422A1; 135740-EP2292608A1; 6153-65-7 (di-hydrochloride salt, di-hydrate); A839720; Q411646; (4S,4aR,5S,5aR,6S,12aS)-4-(dimethylamino)-; SR-01000003006-5; 1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene; Oxytetracycline, British Pharmacopoeia (BP) Reference Standard; Oxytetracycline, European Pharmacopoeia (EP) Reference Standard; (4S,4aR,5S,5aR,6S,12aS)-4-(dimethylamino)-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide

Activity data
Interaction ID 756
Target type Molecule
Target unique ID 54675779
Activity 56.84 nM
Binding Conditions/Buffer

100 mM NaCl, 20 mM Tris-HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02 Tween 20, pH 7.6

Assay

Binding of ssDNA aptamers to oxytetracycline (OTC) was performed by equilibrium dialysis as described in methods

PubMed ID 17988875
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_748 DNA AGCTTGAGGGTGGGCGGGTGGACGCGGTAGTGGTATATAGGTCGG 66.67%
Apta_641 DNA TTCAAGACGATGCCTGGCGCGAGTTACACACTTGCATGGAGCTGG 60.00%
Apta_12 DNA TGAGGGGGTGGGTGGGACGGGTTGG 57.50%
Apta_13 DNA AGGGGGGGGGGAGGGGTCGGGGTGG 57.50%
Apta_150 DNA CCGTAGGTTCGGGGCGGAGTGGTCCGGAAGGTGGCGTGG 57.50%
Apta_264 DNA GGCGTTGTCGGGCGCAGGTGTAGGCCTCGTGGTGGTGGGT 57.50%
Apta_390 DNA GGTGCGGCGGGACTAGTGGGTGTG 57.50%
Apta_681 DNA CCTGACGATCGGGTGTGGGTTGGCTTGAGG 57.50%
Apta_683 DNA GCAGTACGATCGGGGGTGGGTGGATGTAGG 57.50%
Apta_692 DNA ACGTTGACGCTGGTGCCCGCTTGTGGTGCGAGTGTTGTGT 57.50%
Apta_928 DNA GATTGAGTAGATAGTGGTTCTGTACGTAGTGAAAGAGTGG 57.50%
Apta_1195 DNA GGGGTTGGGGGGAGGCGGGGAATGGGGG 57.50%
Apta_1062 DNA GGGGTCTTGCAGGTCCCGTAGGAGGGGCCATTGGAGTGGGG 56.10%
Apta_14 DNA AGCGGGGGGGGCTGGGCTGGGTGGG 55.00%
Apta_16 DNA AGGGGGGGGGGACGGGACGGGTATA 55.00%
Apta_50 DNA AGTGGCGAGGGGGGTAGGTAAAGTATCCTTAGTGTGTTG 55.00%
Apta_65 DNA CTACCGTGGTAGGGAAGGTTGGAGTGTAG 55.00%
Apta_124 DNA GGTGGTGGGGGGGGTTGGTAGGGTGTCTTC 55.00%
Apta_148 DNA CCGTAGGTTCGGGGTCGGAGTGGTCCGGAAGGTGGCGTGG 55.00%
Apta_149 DNA CCGTAGGTTCGGGGTCGGAGTGGTCCGGAAGATGGCGTGG 55.00%