Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 681
Aptamer sequence: TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAACCCCCCG
Target unique ID: 53481794
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_638 B4 Molecule LPS core 21 nM 50 mM Tris-acetate, pH 8.2 22370280
Structure information of aptamer
Aptamer Sequence: TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAACCCCCCG
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_638 Description B4
Aptamer chemistry DNA Length 45 nt
GC content 60.0% Molecular weight 13,840.89 Da
Molarity of 1 μg/μl solution 72.25 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAACCCCCCG
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 681
Target type Molecule
Target unique ID 53481794
Activity 21 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_635 DNA TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAACCCCCCA
97.78%
Apta_636 DNA TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAGCCCCCCA
95.56%
Apta_637 DNA TAGCCGGATCGCGTTGGCCAGATGATATAAAGGGTCAACCCCCCA
95.56%
Apta_965 DNA CACGGCATGTGTGGCCGGATGCCTATATCGGTCGACTGCA 57.78%
Apta_393 DNA AGGAGGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCT 55.56%
Apta_939 DNA TTGCCCACCGTACTGTGCAGGTCGAACTACAGGCACGTCGTG 55.56%
Apta_1126 DNA TCGGGCGAGTCGTCTGCGGGCGGATAGACTACGACACCGCATCGTCCTCCC 54.90%
Apta_392 DNA GGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCT 53.33%
Apta_439 DNA TAACACTCGATTCTCCTAGCCCGCTAGAAATTCCCCTCCC 53.33%
Apta_778 DNA GAAGACGAGCGGCGAGTGTTATTACGCTTGGAAACAACCCC 53.33%
Apta_778 DNA GAAGACGAGCGGCGAGTGTTATTACGCTTGGAAACAACCCC 53.33%
Apta_1125 DNA TCGGGCGAGTCGTCTGGGGAGGTCAGAACGAAAGGCCCGCATCGTCCTCCC 52.94%
Apta_1127 DNA TCGGGCGAGTCGTCTGCGAGGCAACAAGCTCGTAATCCGCATCGTCCTCCC 52.94%
Apta_989 DNA ATGCGGGTACATCTCTCCAACCAGTCAAACTGCTATGATAAGACCTCATTCAACCCCGGTA 52.46%
Apta_981 DNA TATGGAGAGTCAATGAGTACAGTCTCGTCTCAATAACGGAGCCTCGTCCGTGCCCCCG 51.72%
Apta_663 DNA CACGCACAGAAGACACCTACAGGGCCAGATCACAATCGGTTAGTGAACTCGTACGGCGCG 51.67%
Apta_978 DNA GGCGATGAGAACGGGAGCCTGATGATACACACGAGCGATCGCTCATAAAAGCCGTGCCCG 51.67%
Apta_1266 DNA GCATCACACACCGATACTCACCCGCCTGATTAACATTAGCCCACCGCCCACCCCCGCTGC 51.67%
Apta_1279 DNA TTCCAAGACCTGACCGTAATCGTCAAATGTGTTATTGGAGGGGGACTAGCCCCCGGAGGG 51.67%
Apta_164 DNA TATAGACCACAGCCTGAGATTAACCACCAACCCAGGACT 51.11%

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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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