Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 639
Aptamer sequence: CUUCUUAAUCCUAAAGUCCCUGGUGUUUCUCUGCGUGGGG
Target unique ID: 54671203
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_605 VA 2 Molecule Doxycycline 115 nM 20 mM Tris at pH 7.5 with 100 mM NaCl, 2 mM MgCl2, 5 mM KCl and 1 mM CaCl2, RT 28634758
Structure information of aptamer
Aptamer Sequence: CUUCUUAAUCCUAAAGUCCCUGGUGUUUCUCUGCGUGGGG
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_605 Description VA 2
Aptamer chemistry RNA Length 40 nt
GC content 50.0% Molecular weight 12,680.43 Da
Molarity of 1 μg/μl solution 78.86 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Aptasensor
Sequence CUUCUUAAUCCUAAAGUCCCUGGUGUUUCUCUGCGUGGGG
Applications Binding to DOX
Target information
Type Detail Type Detail
PubChem ID 54671203 Molecular name Doxycycline
Molecular formula C22H24N2O8 Molecular weight 444.4
IUPAC name (4S,4aR,5S,5aR,6R,12aR)-4-(dimethylamino)-1,5,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide InChIKey SGKRLCUYIXIAHR-AKNGSSGZSA-N
LogP -0.504 Topological polar surface area 181.62
Hydrogen bond acceptor 9 Hydrogen bond donor 6

Synonym(s):
doxycycline; 564-25-0; Vibramycin; Doxytetracycline; Doxiciclina; Doxycyclinum; Doxycycline (anhydrous); Monodox; Oracea; Vibra-tabs; Doxycycline hyclate; 6alpha-Deoxy-5-oxytetracycline; 5-Hydroxy-alpha-6-deoxytetracycline; 6-alpha-Deoxy-5-oxytetracycline; Doxycyclin; alpha-6-Deoxy-5-hydroxytetracycline; BMY-28689; Liviatin; DOXY; Doxy-Caps; Vibravenos; UNII-334895S862; Deoxymykoin; Dossiciclina; Azudoxat; Doxitard; Doxivetin; Doxycen; Doxychel; Investin; Ronaxan; CHEBI:50845; Spanor; Doxy-Puren; alpha-Doxycycline; Doxy-Tabs; alpha-6-Deoxyoxytetracycline; MMV000011; (4S,4aR,5S,5aR,6R,12aR)-4-(dimethylamino)-1,5,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide; Doxycycline anhydrous; Supracyclin; Doxysol; Jenacyclin; 6-Deoxyoxytetracycline; Dossiciclina [DCIT]; Doxiciclina [Italian]; (4S,4aR,5S,5aR,6R,12aS)-4-(dimethylamino)-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide; 2-Naphthacenecarboxamide,4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S,4aR,5S,5aR,6R,12aS)-; Doxycyclinum [INN-Latin]; Doxycycline (internal use); Doxiciclina [INN-Spanish]; 334895S862; BU-3839T; 4-Epidoxycycline; Zenavod; DOXCYCLINE ANHYDROUS; Oxytetracycline, 6-deoxy-; Doxycycline (TN); Doxychel (TN); Vivox (*Hyclate); Doxycycline (INN); DMSC (*Fosfatex); NSC633557; HSDB 3071; Monodox (*monohydrate); BMY28689; BU 3839T; 24390-14-5; EINECS 209-271-1; BMY 28689; Vibramycin (*monohydrate); GS-3065 (*monohydrate); Doxirobe; Doxycycline [USAN:INN:BAN]; SR-01000075844; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S,4aR,5S,5aR,6R,12aS)-; Anhydrous doxycycline; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S-(4alpha,4aalpha,5alpha,5aalpha,6alpha,12aalpha))-; AB08 (*Fosfatex); Spectrum_000807; Spectrum2_000143; Spectrum3_000408; Spectrum4_000527; Spectrum5_000947; UPCMLD-DP021; CHEMBL1433; Lopac0_000405; SCHEMBL40930; SCHEMBL66828; BSPBio_001936; KBioGR_001133; KBioSS_001287; BIDD:GT0146; DivK1c_000345; SPBio_000246; CHEMBL436921; GTPL6464; SCHEMBL1176275; 4-Epioxytetracycline, 6-deoxy-; DTXSID0037653; SCHEMBL17826665; SCHEMBL19270298; SCHEMBL21753474; UPCMLD-DP021:001; BCBcMAP01_000024; KBio1_000345; KBio2_001287; KBio2_003855; KBio2_006423; KBio3_001156; DTXSID80992212; NINDS_000345; HMS2090E06; DOXYTETRACYCLINE; DOXYCYCLINE; HY-N0565; LMPK07000001; s5159; ZINC16052277; AKOS015900372; ZINC100056779; ZINC100302137; ZINC100611210; ZINC109562088; CCG-204498; DB00254; MCULE-4368118692; SDCCGSBI-0050391.P005; IDI1_000345; SMP1_000107; NCGC00161602-01; NCGC00161602-03; NCGC00161602-04; NCGC00161602-05; NCGC00161602-07; NCGC00161602-14; NCGC00188979-01; (4s,4ar,5s,5ar,6r,12as)-4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamide; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S,4aR,5S,5aR,6R,12aS); 2-Naphthacenecarboxamide, 4-alpha-S-(dimethylamino)-1,4,4a-alpha-5,5a-alpha,6,11,12a-octahydro-3,5-alpha,10,12,12a-alpha-pentahydroxy-6-alpha-methyl-1,11-dioxo-; AS-13499; I455; SBI-0050391.P004; CS-0009105; 1368-EP2269978A2; 1368-EP2269985A2; 1368-EP2269991A2; 1368-EP2284150A2; 1368-EP2284151A2; 1368-EP2284152A2; 1368-EP2284153A2; 1368-EP2284155A2; 1368-EP2284156A2; 1368-EP2284164A2; 1368-EP2287140A2; 1368-EP2287148A2; 1368-EP2287150A2; 1368-EP2289871A1; 1368-EP2295402A2; 1368-EP2295419A2; 1368-EP2298732A1; 1368-EP2301534A1; 1368-EP2301912A2; 1368-EP2301913A1; 1368-EP2301914A1; 1368-EP2301916A2; 1368-EP2305637A2; 1368-EP2305640A2; 1368-EP2308863A1; 1368-EP2311451A1; 1368-EP2311796A1; 1368-EP2311797A1; 1368-EP2311798A1; 1368-EP2311799A1; 1368-EP2316450A1; C06973; D07876; AB00053465-03; AB00053465_04; AB00053465_05; 564D250; A817263; Doxycycline, Antibiotic for Culture Media Use Only; Q422442; SR-01000075844-7; W-105517; SR-01000075844-18; (4S,4aR,5S,5aR,6R,12aS)-4-(DiMethylaMino)-3,5,10,12,12a-pentahydroxy-6-Methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxaMidehydrochloride; (4S,4aR,5S,5aR,6R,12aS)-4-(dimethylamino)-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide; 4-(Dimethylamino)-1,5,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-3,4,4a,5,5a,6,12,12a-octahydrotetracene-2-carboximidic acid; 7164-70-7

Activity data

No relevant experimental diagram

 Interaction ID 639
Target type Molecule
Target unique ID 54671203
Activity 115 nM
Binding Conditions/Buffer

20 mM Tris at pH 7.5 with 100 mM NaCl, 2 mM MgCl2, 5 mM KCl and 1 mM CaCl2, RT
Assay

N/A
PubMed ID 28634758
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_242 RNA GCUUCCAGGAAGAGAAGUGUCAUGUGAUCAGUCCUGGUGGGUGG 52.27%
Apta_270 RNA CUGUCGAACAUGCUGAGGGUAACGUACUGGCAAGCUCACCUCAGCGUAGCUAa 50.94%
Apta_89 RNA AAUAACCUUAAUGCGACGUUGGUUCGUCAACAUGG 50.00%
Apta_603 RNA CUUGUCUGAACAAUUUCGUCUGCCUUUGCGUUCCGACGGC 50.00%
Apta_243 RNA GCUUGAAGCUAGCAGUAAGACUAGCGCUACGGAUGGGUGUGCG 48.84%
Apta_716 RNA GGCGCUUCAUGCCGAAAGGCCCGUUGUAACGUC 47.50%
Apta_925 RNA GCUCGGCCAGGUCGCGGGUGGAUGUGAGGG 47.50%
Apta_304 RNA CGGCCGAUAGAAAGACUACUUGAGCCCUUAAAUGAGGUUAUGUGCGGCCG 46.00%
Apta_2 RNA GGGCUUCUCUGGUUAGACCAGAUUUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCC 45.76%
Apta_241 RNA GCUUGACGGAGAUCAAGGGCGAGUCUCAUACCAAGUUGAUGGGG 45.45%
Apta_244 RNA GCUUCCGGAGAGAAGGGUCAAAGUUGUGCGGGAGUGUGUUGUGG 45.45%
Apta_1055 RNA CAAGCUUGCGGGUUGGCUUGUAACAAGAUCGCUACGUGUUGAACUCUGCAACACUGGUCGGAUAGCGUAAACGGG 45.33%
Apta_1124 RNA GGGCGAAUUCGGGUUGGAUAGUAGGCGCAUAUGGCAUCUUCGUGGUUGUGUAUUGCCCUUUAGUGAGGGUUAAUU 45.33%
Apta_51 RNA GCCUUAGUAACGUGCUUUGAUGUCGAUUCGACAGGAGGC 45.00%
Apta_88 RNA AAUAACCUUAAUGCGACGUUGGUUUGUCAACAACG 45.00%
Apta_90 RNA ACAACCUAAAUGCGACGUUGGGUCAAAAACGUGAA 45.00%
Apta_93 RNA CUCCGCUAUCUAACGUAUGAUAGAAUGGAUGACUA 45.00%
Apta_594 RNA GGGCUAUUGCUGGAGGGGCGCCACAUGAAAGUGGUGGUUGGGUGCGGUCGGCGAUAGCUC 45.00%
Apta_634 RNA GGUCUUACGUCGUUCGCGACUAUUGGGAGACC 45.00%
Apta_707 RNA GGCCUAAAACAUACCAGAUUUCGAUCUGGAGAGGUGAAGAAUUCGACCACCUAGGCCGGU 45.00%

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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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