Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 686
Aptamer sequence: ACCGATCCATCGAGTTTCTGAGAAAGGCCCGGAGAAACCGCGAGA
Target unique ID: 53481794
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_643 B9 Molecule LPS core 15 nM 50 mM Tris-acetate, pH 8.2 22370280
Structure information of aptamer
Aptamer Sequence: ACCGATCCATCGAGTTTCTGAGAAAGGCCCGGAGAAACCGCGAGA
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_643 Description B9
Aptamer chemistry DNA Length 45 nt
GC content 55.6% Molecular weight 13,897.95 Da
Molarity of 1 μg/μl solution 71.95 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence ACCGATCCATCGAGTTTCTGAGAAAGGCCCGGAGAAACCGCGAGA
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 686
Target type Molecule
Target unique ID 53481794
Activity 15 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_181 DNA CCGTGTAAGGTTTCAGTGGCTTATCCGAAGTAACCCGAGA 60.00%
Apta_149 DNA CCGTAGGTTCGGGGTCGGAGTGGTCCGGAAGATGGCGTGG 55.56%
Apta_222 DNA AGCGACTGACGATCTTGAGTAAACCGCTCATCCACGTAGT 55.56%
Apta_142 DNA CGCACATCAGTTTAGCAGCGCCAAAGGCGGAAGCGCA 53.33%
Apta_148 DNA CCGTAGGTTCGGGGTCGGAGTGGTCCGGAAGGTGGCGTGG 53.33%
Apta_262 DNA ACGGACTCGCAAAAGGTGGAACAGGAGTGGGCCCCGCGGC 53.33%
Apta_820 DNA TCCCACGATCTCATTAGTCTGTGGATAAGCGTGGGACGTCTATGA 53.33%
Apta_1035 DNA ATGCGGATCCCGCGCGGGTCTGAGGAGTGCGCGGTGCCAGTGAGTGCGCGAAGCTTGCGC 51.67%
Apta_150 DNA CCGTAGGTTCGGGGCGGAGTGGTCCGGAAGGTGGCGTGG 51.11%
Apta_438 DNA AGCCATGACGATGTCGTTACGTAGATGCAGAGACTCCTAA 51.11%
Apta_440 DNA AAAGACCGTTTTTTAAAACGCTCAATATACACGACATAAA 51.11%
Apta_438 DNA AGCCATGACGATGTCGTTACGTAGATGCAGAGACTCCTAA 51.11%
Apta_444 DNA AGCCATTACGATGTCGTTACGTAGATGCAGAGACTCCTAA 51.11%
Apta_445 DNA AGCCATGACGATGTCGTTACGTAGATGTAGAGACTCCTAA 51.11%
Apta_469 DNA CTGTAATTGGCGTATGTAACCCAGGCACCAAACACCCCAG 51.11%
Apta_498 DNA GAACTCATTGGCTGGAGGCGGCAGTACCGCTTGAGTT 51.11%
Apta_580 DNA ATGCGGGTATATGGTGCGAGAAAACAAGGGGCATACTGGA 51.11%
Apta_675 DNA ACTGTCCGTCGGGTTTAGGGTGGCGTTCGG 51.11%
Apta_715 RNA GGCGCUGCACGCCGAAAGGCCCGUUGAAACGUC 51.11%
Apta_850 DNA CACCAGTGTGTTGAGGTTTGAGCACACTGATAGAGTGTCA 51.11%

ABOUT

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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