Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 683
Aptamer sequence: CAATGGACCTATTCGAGTACTGAATAGAACAGTCGGCGCTCTGGG
Target unique ID: 53481794
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_640 B6 Molecule LPS core 298 nM 50 mM Tris-acetate, pH 8.2 22370280
Structure information of aptamer
Aptamer Sequence: CAATGGACCTATTCGAGTACTGAATAGAACAGTCGGCGCTCTGGG
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_640 Description B6
Aptamer chemistry DNA Length 45 nt
GC content 51.1% Molecular weight 13,909.95 Da
Molarity of 1 μg/μl solution 71.89 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence CAATGGACCTATTCGAGTACTGAATAGAACAGTCGGCGCTCTGGG
Applications Detection of endotoxin
Target information
Type Detail Type Detail
PubChem ID 53481794 Molecular name LPS core
Molecular formula C175H317N5O101P6 Molecular weight 4293
IUPAC name (2R,4R,5S,6R)-2-[(2R,4R,5S,6R)-5-[(3S,4R,5R,6R)-4-[(3S,4S,5R,6R)-4-[(3R,4S,5R,6R)-4-[(2R,3R,4S,5R,6R)-3-[(3R,4S,5S,6R)-3-[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-3,5-dihydroxy-6-[[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]oxan-2-yl]oxy-6-[(1S)-2-[(3S,4R,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3,4-dihydroxy-5-phosphonooxyoxan-2-yl]oxy-1-hydroxyethyl]-3,5-dihydroxyoxan-2-yl]oxy-5-[[2-aminoethoxy(hydroxy)phosphoryl]oxy-hydroxyphosphoryl]oxy-6-[(1S)-1,2-dihydroxyethyl]-3-hydroxyoxan-2-yl]oxy-2-carboxy-6-[(1S)-1,2-dihydroxyethyl]-2-[[(2R,3S,4R,5R,6R)-5-[[(3R)-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2R,3S,4R,5R,6R)-3-hydroxy-5-[[(3R)-3-hydroxytetradecanoyl]amino]-4-[(3R)-3-hydroxytetradecanoyl]oxy-6-phosphonooxyoxan-2-yl]methoxy]-3-phosphonooxy-4-[(3R)-3-tetradecanoyloxytetradecanoyl]oxyoxan-2-yl]methoxy]oxan-4-yl]oxy-4-[(2R,4R,5R,6R)-4-[2-aminoethoxy(hydroxy)phosphoryl]oxy-2-carboxy-6-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxan-2-yl]oxy-6-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxane-2-carboxylic acid InChIKey AAXCQFOXUJMCCW-PETQGJDISA-N
LogP -5.141 Topological polar surface area 1673.8
Hydrogen bond acceptor 91 Hydrogen bond donor 53

Synonym(s):
LPS core; Endotoxin LPS core; Ra-LPS; Lipopolysaccharide Ra component; Endotoxin Lipopolysaccharide core; Lipopolysaccharide core endotoxin; CHEBI:89983

Activity data

No relevant experimental diagram

 Interaction ID 683
Target type Molecule
Target unique ID 53481794
Activity 298 nM
Binding Conditions/Buffer

50 mM Tris-acetate, pH 8.2
Assay

N/A
PubMed ID 22370280
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1091 DNA CCATGGTAGGTATTGCTTGGTAGGGATAGTGGGCTTGATG 57.78%
Apta_1260 DNA GAAAGGGACGTTCCAAGTTCGTATAAGCAGTCCTGTGCGT 57.78%
Apta_158 DNA CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTG 55.56%
Apta_286 DNA TACTCCGTCACTTTAGTGGATATAACAACCTCCCTATGGG 55.56%
Apta_1092 DNA CCCATGGTAGGTATTGCTTGGTAGGGATAGTGGGCTTGATG 55.56%
Apta_943 DNA GAAGGTGGAGCGGTTAGGATACTAGCGAATGAAGACACGTTAGCTGATCT 54.00%
Apta_1068 DNA CGGGACAAGACAACGAACGAACAGGAAGAGAACCGGAATGCAGACGTCAGGG 53.85%
Apta_1276 DNA TCAATGGGATGTTAGTATGCAAAGATATTCTGTTCAGTGTGTGCCCAGGCCCCCAGGG 53.45%
Apta_162 DNA CCGTACATACTACGTACGTACGTGAACAGAGGCAGAG 53.33%
Apta_163 DNA GCGCATGACCATTGATGTCTGCACCATCAGAGGCAGAG 53.33%
Apta_267 DNA GAGTGCGTAATGGTACGATTTGGGAAGTGGCTTGGGGTGG 53.33%
Apta_306 DNA CAAGGTAACCAGTACAAGGTGCTAAACGTAATGGCTTCG 53.33%
Apta_339 DNA CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTGT 53.33%
Apta_580 DNA ATGCGGGTATATGGTGCGAGAAAACAAGGGGCATACTGGA 53.33%
Apta_675 DNA ACTGTCCGTCGGGTTTAGGGTGGCGTTCGG 53.33%
Apta_1268 DNA CACACACGCAGCAAGGTCGTCGATACAAAACGTATCGACCCGTCACAGACTGCCCCGGGT 53.33%
Apta_652 DNA CCTGCACCTCGTCCAGCATGCACACCGATGGCGGTCCTGGCAGGGGGTGTGCGTG 52.73%
Apta_994 DNA GCAATGGTACGGTACTTCCGGACAGTGCTGAAAACTGTGACCCCCCAAAAGTGCACGCTACTTTGCTAA 52.17%
Apta_882 DNA AATAGTCTGGTTCGGTGCTTGGTGCGATGTGTTAGTCAGACTCTTGTGTG 52.00%
Apta_974 DNA CATGGTGTCAATACTATACCTTTTGCCGATGGTAACAGTTGGTGGTATCC 52.00%

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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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