Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 850
Aptamer sequence: GAATTCAGTCGGACAGCGACGGTGGGAGCCCCAAATAATTCTTGCGATTATTAGTGTAAGCGGATGGACGAATATCGTCTCCC
Target unique ID: HTB-15
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_767 GBM128 Cell human glioblastoma cell line U118-MG 20 nM 25 μM glucose 4 μM yeast tRNA 15 μM BSA 5 mM MgCl2 in PBS (pH = 7.4) 1 hour incubation with cells 23056171
Structure information of aptamer
Aptamer Sequence: GAATTCAGTCGGACAGCGACGGTGGGAGCCCCAAATAATTCTTGCGATTATTAGTGTAAGCGGATGGACGAATATCGTCTCCC
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_767 Description GBM128
Aptamer chemistry DNA Length 83 nt
GC content 49.4% Molecular weight 25,689.46 Da
Molarity of 1 μg/μl solution 38.93 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence GAATTCAGTCGGACAGCGACGGTGGGAGCCCCAAATAATTCTTGCGATTATTAGTGTAAGCGGATGGACGAATATCGTCTCCC
Applications Early detection, Targeted therapy, and guided surgery of glioblastoma leading to effective treatment of glioblastoma
Target information
Type Detail Type Detail
ATCC ID HTB-15 Cell name human glioblastoma cell line U118-MG
Category Human cells Organism Homo sapiens, human
Product type N/A Cell type N/A
Morphology mixed Tissue Brain
Disease Glioblastoma; Grade IV Product format Frozen
Antigen expression Blood Type A, Rh+; HLA Aw24, A28, B12, Bw47 Genes expressed N/A
Cell description U-118 MG is a cell line exhibiting mixed morphology that was isolated in 1966 from malignant gliomas from a 50-year-old, male with Grade IV glioblastoma.
Application(s) 3D cell culture; Neuroscience
Activity data
Interaction ID 850
Target type Cell
Target unique ID HTB-15
Activity 20 nM
Binding Conditions/Buffer

25 μM glucose 4 μM yeast tRNA 15 μM BSA 5 mM MgCl2 in PBS (pH = 7.4) 1 hour incubation with cells
Assay

The binding affinity of aptamers GBM128 with U118 MG and SVGp12 cells
PubMed ID 23056171
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_775 DNA GAATTCAGTCGGACAGCGCGGTGTTGGTGGCGGGGGTGGTTGGGGGATTTGGCTGTCCTGAGTGATGGACGAATATCGTCTCCC 70.24%
Apta_1182 DNA GAATTCAGTCGGACAGCGTCAGTCGTCCCTTTATGCTTGGTGCTCACCGTCTGAATTTCTTCAGATGGACGAATATCGTCTCCC 69.05%
Apta_772 DNA GAATTCAGTCGGACAGCGCGGTGTTGGTGGTGGGGTGGTTTGGGAATCTGTTCGGCTGGAGATGGACGAATATCGTCTCCC 68.67%
Apta_773 DNA GAATTCAGTCGGACAGCGGTGGTGCTTGTGTATGGGGGTGGTTGGTGGGTTTTATGCTGCTGGATGGACGAATATCGTCTCCC 68.67%
Apta_1179 DNA GAATTCAGTCGGACAGCGAAGTAGTTTTCCTTCTAACCTAAGAACCCGCGGCAGTTTAATGTAGATGGACGAATACGTCTCCC 67.47%
Apta_1180 DNA GAATTCAGTCGGACAGCGCAATTGTGGTTCTTACCCTATCCCTTGTGTTTGGCGTTCGTTGCGATGGACGAATATCGTCTCCC 67.47%
Apta_1181 DNA GAATTCAGTCGGACAGCGTAGTAAGAATCTGTTTCTGGTCCTAGTCTTGCTTGTGTTTCCTGATGGACGAATATCGTCTCCC 67.47%
Apta_769 DNA GAATTCAGTCGGACAGCGAGTTGTTGTTAGGGTGTTGGGTTGGGGTTTTAGGGTCCCTGTCGTCGATGGACGAATATCGTCTCCC 67.06%
Apta_768 DNA GAATTCAGTCGGACAGCGGCACTTGCGACACGTTTGTCGGGTAAATGCGTGTATTTTCTTTTCGATGGACGAATATCGTCTCCC 66.67%
Apta_774 DNA GAATTCAGTCGGACAGCGAGGAAAATTTCGTTATTTTCGTTTCCGGGAACTCGGGCATTTAGAGATGGACGAATATCGTCTCCC 66.67%
Apta_1183 DNA GAATTCAGTCGGACAGCGGCGTGAGTCTTTTGCGGTGGCTCGGGTTCGAATATCTACGACCTTGATGGACGAATATCGTCTCCC 66.67%
Apta_770 DNA GAATTCAGTCGGACAGCGGCATTTACATTCCATGGGAAATTTCTCAAGCGGTATTTCATTTCGATGGACGAATATCGTCTCCC 66.27%
Apta_1184 DNA GAATTCAGTCGGACAGCGTAATCCCTTGTGTTTGACGTTCGAAGATTATTTCTATCTTTTAGGATGGACGAATATCGTCTCCC 66.27%
Apta_771 DNA GAATTCCGTCGGACAGCGGTATGCATGGGAGGTTCTGGAGGGGGTGGGTTGGCGTGCGTTCCAGATGGACGAATATCGTCTCCC 64.29%
Apta_351 DNA TTCTCGGTTGGTCTCTGGCGGAGCGATCATCTCAGAGCATTCTTAGCGTTTTGTTCTTGTGTATGATTCGCTTTTCCC 54.22%
Apta_78 DNA ATCTCGACTAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACAATACTCGT 53.01%
Apta_611 DNA GCTGCGAGGTGGGTGGGTGGGAGCAATTGGTCCTTGCTTAGCTTCTACGGTGGGCTATCT 53.01%
Apta_999 DNA ATAGGAGTCGACCGACCAGAGGACCCCGCTATCTAATTTATAGGCAATAAGTGCGTCTACATCTAGACTC 53.01%
Apta_704 DNA GTACGAATTCACGAGGTTGCCAGCGGGGCCAGCCACTTCTGTCAGTGAATTCCTGCTCGTATATCTACTCGCCCGCCTGCGAGCATGGAGTCGGATCCTCTA 51.96%
Apta_128 DNA GGTATTGAGGGTCGCATCCCGTAGTGTGTTCTTATTCGTGTCTGTGTGTGTTCTGTCGGATGGCTCTAACTCTCCTCT 51.81%

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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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