Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1234
Aptamer sequence: GACGCCACTGACTACCCCAGTATCTCTTCAACGCGTATTGAAGTCAGTCGGTCGTCA
Target unique ID: HTB-14
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_1172 W5 Cell Cells expressing integrin a5b1 4.9 nM 4.5 g/L glucose, 5 mM MgCl₂ in Dulbecco’s PBS pH=7.4 31179688
Structure information of aptamer
Aptamer Sequence: GACGCCACTGACTACCCCAGTATCTCTTCAACGCGTATTGAAGTCAGTCGGTCGTCA
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_1172 Description W5
Aptamer chemistry DNA Length 57 nt
GC content 52.6% Molecular weight 17,424.17 Da
Molarity of 1 μg/μl solution 57.39 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence GACGCCACTGACTACCCCAGTATCTCTTCAACGCGTATTGAAGTCAGTCGGTCGTCA
Applications Detect glioma stem cells
Target information
Type Detail Type Detail
ATCC ID HTB-14 Cell name Cells expressing integrin a5b1
Category Human cells Organism Homo sapiens, human
Product type N/A Cell type N/A
Morphology epithelial Tissue Brain
Disease Likely Glioblastoma Product format Frozen
Antigen expression N/A Genes expressed N/A
Cell description U-87 MG is a cell line with epithelial morphology that was isolated from malignant gliomas from a male patient, likely with Glioblastoma. Use these cells in your neuroscience and immuno-oncology research.
Application(s) 3D cell culture; Neuroscience; Immuno-oncology
Activity data
Interaction ID 1234
Target type Cell
Target unique ID HTB-14
Activity 4.9 nM
Binding Conditions/Buffer

4.5 g/L glucose, 5 mM MgCl₂ in Dulbecco’s PBS pH=7.4
Assay

Dissociation constant of the aptamer W5 to glioma stem cells
PubMed ID 31179688
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1173 DNA TTGACTTGCCACTGACTACCCCAGTATCTCTTCAACGCTATGGTGCATGTACTACGTATTGAAGTCAGTCGGTCGTCATC 71.25%
Apta_721 DNA CTCTCGGGACGACCGCGGTAGTCTTAACCTAAAGCGGTGTCAGGTCGTCCC 57.89%
Apta_663 DNA CACGCACAGAAGACACCTACAGGGCCAGATCACAATCGGTTAGTGAACTCGTACGGCGCG 56.67%
Apta_883 DNA CGTACCGGCCAGTGATTACGACGAGACGAGCTTATGCGTATTGATGCCTAACTATCTACA 56.67%
Apta_1099 DNA ATCCATTGCCACTGACTACCAGCCGGGTGGGTGGGGGGGTTTGCTGGTATCGCATTGTGCGAAGTCAGTCGGTCGTTAGT 56.25%
Apta_1152 DNA GACAAGGATAAATCCTTCAATGAAGTGGGTCACTCATCTGTGA 56.14%
Apta_664 DNA CACGCAACAACACAACATGCCCAGCGCCTGGAACATATCCTATGAGTTAGTCCGCCCACA 55.00%
Apta_217 DNA CGCCTGATTAGCGATACTCAGGCGTTGGGTGGGTGGGTGGG 54.39%
Apta_395 DNA AATCCACGTATCGACTAGCTCAAACCAGCCTGATAGAGCCATTCGCTTTA 54.39%
Apta_586 DNA GGGAGACAAGGAAAATCCTTCAATGAAGTGGGTCGACA 54.39%
Apta_642 DNA ATCCAATACCTCAGAACTCAGTTCGAGTCGTAAAGGGGAATCGCA 54.39%
Apta_697 DNA CTCTCGGGACGACGGACGCTAATCTTACAAGGGCGTAGTGTATGTCGTCCC 54.39%
Apta_819 DNA GCGCCCTCTCACGTGGCACTCAGAGTGCCGGAAGTTCTGCGTTAT 54.39%
Apta_834 DNA CGCAATACCAAAGTGGCGAGAGCGCTGTCTTGAGTGAGTGGTTGG 54.39%
Apta_1087 DNA CTTACGACTCAGGCATTTTGCCGGGTAACGAAGTTACTGTCGTAAG 54.39%
Apta_529 DNA ATCCGTCACACCTGCTCTACACTCCGCACGATCTTTTTTAGAACGCGTACCCGTTGGTGTTGGCTCCCGTAT 54.17%
Apta_530 DNA ATCCGTCACACCTGCTCTGTGTACGCCCGTATTTACGTTCCTAGCAATTGCTATGTGGTGTTGGCTCCCGTAT 53.42%
Apta_888 DNA GGCGACCCCCGGGCTACCAGACAATGTACGCAGCAAGAGTGACGGTCGTACCTCGGAGTC 53.33%
Apta_931 DNA ATACGACTCACTATTAGGGACCACATAAACATGCATCGCTCAATAACGGGATATTGTTGTGCTAGACTACTGACTACAA 53.16%
Apta_999 DNA ATAGGAGTCGACCGACCAGAGGACCCCGCTATCTAATTTATAGGCAATAAGTGCGTCTACATCTAGACTC 52.86%

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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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