Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 777
Aptamer sequence: GTACGAATTCACGAGGTTGCCAGCGGGGCCAGCCACTTCTGTCAGTGAATTCCTGCTCGTATATCTACTCGCCCGCCTGCGAGCATGGAGTCGGATCCTCTA
Target unique ID: 643987
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_704 S1-11 Molecule 6'-Sialyllactose 4.9 μM 50 mM Tris-HCl (pH 7.6), 250 mM NaCl, 5 mM MgCl2 14980623
Structure information of aptamer
Aptamer Sequence: GTACGAATTCACGAGGTTGCCAGCGGGGCCAGCCACTTCTGTCAGTGAATTCCTGCTCGTATATCTACTCGCCCGCCTGCGAGCATGGAGTCGGATCCTCTA
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_704 Description S1-11
Aptamer chemistry DNA Length 102 nt
GC content 56.9% Molecular weight 31,346.99 Da
Molarity of 1 μg/μl solution 31.90 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence GTACGAATTCACGAGGTTGCCAGCGGGGCCAGCCACTTCTGTCAGTGAATTCCTGCTCGTATATCTACTCGCCCGCCTGCGAGCATGGAGTCGGATCCTCTA
Applications Binding to sialyllactose
Target information
Type Detail Type Detail
PubChem ID 643987 Molecular name 6-Sialyllactose
Molecular formula C23H39NO19 Molecular weight 633.6
IUPAC name (2R,4S,5R,6R)-5-acetamido-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-2-[[(2R,3R,4S,5R,6S)-3,4,5-trihydroxy-6-[(2R,3R,4R,5R)-1,2,4,5-tetrahydroxy-6-oxohexan-3-yl]oxyoxan-2-yl]methoxy]oxane-2-carboxylic acid InChIKey VMWYCXKMRSTDSP-GIGDJUIZSA-N
LogP -8.381 Topological polar surface area 342.92
Hydrogen bond acceptor 18 Hydrogen bond donor 13

Synonym(s):
6'-Sialyllactose; 35890-39-2; 6'-a-Sialyllactose; 6'-Monosialyllactose; 6'-alpha-Sialyllactose; LU9DTA2WHJ; UNII-LU9DTA2WHJ; (2>6')-Sialyllactose; (2>6')-a-Sialyllactose; (2R,4S,5R,6R)-5-acetamido-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-2-[[(2R,3R,4S,5R,6S)-3,4,5-trihydroxy-6-[(2R,3R,4R,5R)-1,2,4,5-tetrahydroxy-6-oxohexan-3-yl]oxyoxan-2-yl]methoxy]oxane-2-carboxylic acid; N-acetylneuramin-lactose; D-Glucose,O-(N-acetyl-a-neuraminosyl)-(26)-O-b-D-galactopyranosyl-(14)-; (2->6')-Sialyllactose; 6'-N-Gycolyneuraminyllactose; (2>6')-alpha-Sialyllactose; SCHEMBL22259190; DTXSID40349248; ZINC85552768; AS-78716; D-Glucose, O-(N-acetyl-a-neuraminosyl)-(2~6)-O-b-D-galactopyranosyl-(1~4)- (9CI); D-Glucose, O-(N-acetyl-alpha-neuraminosyl)-(2->6)-o-beta-D-galactopyranosyl-(1->4)-; D-Glucose,O-(N-acetyl-a-neuraminosyl)-(2?6)-O-b-D-galactopyranosyl-(1?4)-; O-(N-acetyl-alpha-neuraminosyl)-(2-3)-O-beta-D-galactopyranosyl-(1-4)-D-Glucose; O-(N-acetyl-alpha-neuraminosyl)-(2-3)-O-beta-delta-galactopyranosyl-(1-4)-delta-Glucose; (2R,4S,5R,6R)-5-Acetamido-4-hydroxy-2-(((2R,3R,4S,5R,6S)-3,4,5-trihydroxy-6-(((2R,3R,4R,5R)-1,2,4,5-tetrahydroxy-6-oxohexan-3-yl)oxy)tetrahydro-2H-pyran-2-yl)methoxy)-6-((1R,2R)-1,2,3-trihydroxypropyl)tetrahydro-2H-pyran-2-carboxylic acid; (2R,4S,5R,6R)-5-ACETAMIDO-4-HYDROXY-2-{[(2R,3R,4S,5R,6S)-3,4,5-TRIHYDROXY-6-{[(2R,3R,4R,5R)-1,2,4,5-TETRAHYDROXY-6-OXOHEXAN-3-YL]OXY}OXAN-2-YL]METHOXY}-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]OXANE-2-CARBOXYLIC ACID; D-glucose, O-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-2-nonulopyranonosyl-(2->6)-O-beta-D-galactopyranosyl-(1->4)-

Activity data

No relevant experimental diagram

 Interaction ID 777
Target type Molecule
Target unique ID 643987
Activity 4.9 μM
Binding Conditions/Buffer

50 mM Tris-HCl (pH 7.6), 250 mM NaCl, 5 mM MgCl2
Assay

N/A
PubMed ID 14980623
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1183 DNA GAATTCAGTCGGACAGCGGCGTGAGTCTTTTGCGGTGGCTCGGGTTCGAATATCTACGACCTTGATGGACGAATATCGTCTCCC 56.86%
Apta_768 DNA GAATTCAGTCGGACAGCGGCACTTGCGACACGTTTGTCGGGTAAATGCGTGTATTTTCTTTTCGATGGACGAATATCGTCTCCC 54.90%
Apta_920 DNA ATCCAGAGTGACGCAGCACGGCACTCACTCTTTGTTAAGTGGTCTGCTTCTTAACCTTCATCGACACGGTGGCTTA 53.92%
Apta_932 DNA ATACGACTCACTATTAGGGATGTCCACCATATAGATCGATTTAAGTCCCTCGTTATTAATGCTAGACTACTGACTACAA 53.92%
Apta_933 DNA GACGCTTACTCAGGTGTGACTCGGGGTGTAGCTCGTTATGATTCGGACAAGACTTACCTTGCGCCTCTGGGATCGAAGGACGCAGATGAAGTCTC 53.92%
Apta_128 DNA GGTATTGAGGGTCGCATCCCGTAGTGTGTTCTTATTCGTGTCTGTGTGTGTTCTGTCGGATGGCTCTAACTCTCCTCT 52.94%
Apta_281 DNA CCGTAATACGACTCACTATAGGGGAGCTCGGTACCGAATTCATGTTGGTAGTTGGCTTGTGTTCGTGTGTTAAGCTTTCAGAGAGGATCCTT 52.94%
Apta_824 DNA ATACGGGAGCCAACACCATCCCTCTTAGGATACAAAGCCAAACTGAGCCCGTGCAGAGCAGGTGTGACGGAT 52.94%
Apta_860 DNA CACGGATCCTGACAAGGATGTGTGCGTTGTCGAGACCTGCGACCGGAACACTACACTGTGTGGGATGGATTTCTTTACAGTTGTGTGCAGCTCCGTCCGACTCTTCCTAGCTATGGTTCGATCAAGA 52.76%
Apta_401 DNA ATCCAGAGTGACGCAGCAGATAAGTAGGTATCCGTTTGAAAAACTTTTCTGACCGTCCGACTATGGACACGGTGGCTTAGT 51.96%
Apta_403 DNA GTCTTGACTAGTTACGCCCCCAAGAACCCGCTTGCCGTGGTGACGTTGATCATGTCGTTTGGTCATTCAGTTGGCGCCTC 51.96%
Apta_404 DNA GTCTTGACTAGTTACGCCCACAAGAACCTGCTTGCCATGGTGACGCCGATCATGCTTTTTGGTCATTCAGTTGGCGCCTC 51.96%
Apta_583 DNA GTACCAGCTTATTCAATTGCGAGCAGGGTCAATGGAATTAATGATCAATTGACAGACGCAAGTCTCCTGCGGTCCTGTGTTGAGATAGTATGTTCATCAG 51.96%
Apta_767 DNA GAATTCAGTCGGACAGCGACGGTGGGAGCCCCAAATAATTCTTGCGATTATTAGTGTAAGCGGATGGACGAATATCGTCTCCC 51.96%
Apta_770 DNA GAATTCAGTCGGACAGCGGCATTTACATTCCATGGGAAATTTCTCAAGCGGTATTTCATTTCGATGGACGAATATCGTCTCCC 51.96%
Apta_772 DNA GAATTCAGTCGGACAGCGCGGTGTTGGTGGTGGGGTGGTTTGGGAATCTGTTCGGCTGGAGATGGACGAATATCGTCTCCC 51.96%
Apta_773 DNA GAATTCAGTCGGACAGCGGTGGTGCTTGTGTATGGGGGTGGTTGGTGGGTTTTATGCTGCTGGATGGACGAATATCGTCTCCC 51.96%
Apta_878 DNA TCGCACATTCCGCTTCTACCGGGGGGGTCGAGCTGAGTGGATGCGAATCTGTGGGTGGGCTTCGCACACACGGACTTAC 51.96%
Apta_908 DNA ATACGGGAGCCAACACCAATTCCGCCAAAGTCTGCTAATAAACGGACGCCGGGGAGAGCAGGTGTGACGGAT 51.96%
Apta_934 DNA GACGCTTACTCAGGTGTGACTCGTGAACCCACCTCAGGGCATCTTACATTTCTTCTAAGTTGTTACCATGTTTCGAAGGACGCAGATGAAGTCTC 51.96%

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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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