Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 754
Aptamer sequence: CGACGCGCGTTGGTGGTGGATGGTGTGTTACACGTGTTGT
Target unique ID: 54675779
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_691 No. 4 Molecule Oxytetracycline 9.61 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: CGACGCGCGTTGGTGGTGGATGGTGTGTTACACGTGTTGT
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_691 Description No. 4
Aptamer chemistry DNA Length 40 nt
GC content 57.5% Molecular weight 12,476.97 Da
Molarity of 1 μg/μl solution 80.15 μM Number of G-quadruplexes 2
G-Score 20 Function Targeted binding
Sequence CGACGCGCGTTGGTGGTGGATGGTGTGTTACACGTGTTGT
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 754
Target type Molecule
Target unique ID 54675779
Activity 9.61 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_1261 DNA GGGCGGACGCTAGGTGGTGATGCTGTGCTACACGTGTTGT 77.50%
Apta_1257 DNA CGACGCACAGTCGCTGGTGCGTACCTGGTTGCCGTTGTGT 65.00%
Apta_1237 DNA GGGGTTGTGTGGGGAGTTTGTCCTGTTGTG 62.50%
Apta_65 DNA CTACCGTGGTAGGGAAGGTTGGAGTGTAG 60.00%
Apta_1205 DNA GGCAGGTGGTGTTGGTTGGTTGTGCGTGGAGTTGG 60.00%
Apta_795 DNA CGCAGCAAGGAGATTCGAGGGGGAAGGTTTGTTATAGGGGTTAATGGA 58.33%
Apta_940 DNA TGTGCGGGGGAGGGGAGTGGCGCTGTTGGTGCGGGTATAGCGCGTGGTGT 58.00%
Apta_941 DNA CGGGTGCCTTAAAGTGTAGGTGGGAGGGGGATGATTATGTACGATCAAGT 58.00%
Apta_255 DNA TAGCGATACTGCGTGGGTTGGGGCGGGTAGGGCCAGCAGTCTCGT 57.78%
Apta_750 DNA ATGCGAACAGGTGGGTGGGTTGGGTGGATTGTTCGGCTTCTTGAT 57.78%
Apta_845 DNA CCAAACGCGCTGGTTTGGAATGCTTAGAGTTTGATCGATGCCTAA 57.78%
Apta_41 DNA CGGTCGCTCCGTGTGGCTTGGGTTGGGTGTGGCAGTGAC 57.50%
Apta_75 DNA CACTGGTAGGTTGGTGTGGTTGGGGCCAGTG 57.50%
Apta_146 DNA GGTGCGGTTCGTGCGGTTGTAGTACTCGTGGCCG 57.50%
Apta_350 DNA GGTGGTGGTGGTTGTGGTGGTGGTGG 57.50%
Apta_1085 DNA TGGGGTGGTGGTGTGGGTGGGGGTTTGTTC 57.50%
Apta_1150 DNA CTAAGCAGGAAGGTATGGATTGGTTGCATTAG 57.50%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 57.50%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 57.50%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 57.50%