Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 687
Aptamer sequence: TCAATCTAACCATGCATGCAGTTTAGGCAGGATTCGTTATCGCAA
Target unique ID: 53481794
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_644 B10 Molecule LPS core 2.34 μM 50 mM Tris-acetate, pH 8.2 22370280
Structure information of aptamer
Aptamer Sequence: TCAATCTAACCATGCATGCAGTTTAGGCAGGATTCGTTATCGCAA
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_644 Description B10
Aptamer chemistry DNA Length 45 nt
GC content 42.2% Molecular weight 13,818.91 Da
Molarity of 1 μg/μl solution 72.36 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence TCAATCTAACCATGCATGCAGTTTAGGCAGGATTCGTTATCGCAA
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 687
Target type Molecule
Target unique ID 53481794
Activity 2.34 μM
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_1066 DNA CCTACGTTGGAGTGGGGTTTGCGCAGGCCGTTCTTTCCAA 57.78%
Apta_779 DNA TACGGGCTGGATCCACTGTTACGGCGTGTATCCGCTATCAA 55.56%
Apta_283 DNA ACTCCGTCATCTTTAGTGGCCCCAATGTCGTTATCACCGA 53.33%
Apta_306 DNA CAAGGTAACCAGTACAAGGTGCTAAACGTAATGGCTTCG 53.33%
Apta_437 DNA TCACAGTCCCGGTGCCGCACTAAAACCCATTGTTGTGCGA 53.33%
Apta_444 DNA AGCCATTACGATGTCGTTACGTAGATGCAGAGACTCCTAA 53.33%
Apta_666 DNA TCGACCTCGCGCGAGGAGGGTGGAGGGTCGTAGAGCGCGTA 53.33%
Apta_1155 DNA TAGTTTTATTTGTTCATTTTGTGTATTGTTTTGA 53.33%
Apta_1191 DNA TAATACTACCAACTTCTTTGCCTGGCGTAAGTAACAGTCA 53.33%
Apta_1214 DNA GTCCATTATTCTGGTAGCGTTGAACAACATTCAACACGCC 53.33%
Apta_1270 DNA GTATATCAAGCATCGCGTGTTTACACATGCGAGAGGTGAA 53.33%
Apta_591 DNA CTCTCGGGACGACGGCTGGCACGTTTGGTTCAAGAATGTGGGTGTCGTCCC 52.94%
Apta_1280 DNA TCATATCCTTCTTGGTATCATTGCGTCATTTAGTCATTCATGTTATTCCCGAGGG 52.73%
Apta_569 DNA TGCGCATGTGAAAGGTTGCCTAACTGGACAGGGTTTAGGAGCGACTAGACACAG 51.85%
Apta_614 DNA AATCGCATTACCTTATACCAGCTTATTCAATTACGTCTGCACATACCAGCTTATTCAATT 51.67%
Apta_1006 DNA ATAGGAGTCGACCGACCAGAACTTGTCTTAGGAGGTTTACGGTGGGAATAGTGCGTCTACATCTAGACTC 51.43%
Apta_49 DNA CTTCCATGTTGAGGCGTTTATACCAGTTATCATCGGACTA 51.11%
Apta_165 DNA TGGACGAACTGCCCTCAGCTACTTTCATGTTGCTGACGCA 51.11%
Apta_220 DNA ATCAACTCACCGTAGGTCTAGTGAGAACTTCAAGTCTACT 51.11%
Apta_259 DNA GCAAGTATGAGCGCAGGAGTTAGGTCCCGTGGCGATGGGT 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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