Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1169
Aptamer sequence: CCGCCCAAATCCCTAAGAGCACAAACACCAAACACAACCACCCCAACCAGACACACTACACACGCA
Target unique ID: Q00973
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_1113 DB99 Protein B4GN1_HUMAN 21.21 nM 1X PBS (pH 7.4) Selections carried out in vivo in six- to eight-week-old female immunodeficient BALB/c mice (CAnN. Cg-Foxn1nu/Crl) 34703655
Structure information of aptamer
Aptamer Sequence: CCGCCCAAATCCCTAAGAGCACAAACACCAAACACAACCACCCCAACCAGACACACTACACACGCA
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_1113 Description DB99
Aptamer chemistry DNA Length 66 nt
GC content 53.0% Molecular weight 19,941.89 Da
Molarity of 1 μg/μl solution 50.15 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence CCGCCCAAATCCCTAAGAGCACAAACACCAAACACAACCACCCCAACCAGACACACTACACACGCA
Applications Precise treatment of NB
Target information
Type Detail Type Detail
Uniprot ID Q00973 Protein name Beta-1,4 N-acetylgalactosaminyltransferase 1 (EC 2.4.1.92) ((N-acetylneuraminyl)-galactosylglucosylceramide) (GM2/GD2 synthase) (GalNAc-T)
Gene name(s) B4GALNT1 GALGT SIAT2 Organism Beta-1,4 N-acetylgalactosaminyltransferase 1 (EC 2.4.1.92) ((N-acetylneuraminyl)-galactosylglucosylceramide) (GM2/GD2 synthase) (GalNAc-T)
Status reviewed in uniprot database Length 533
Mass 58,882 Activity regulation N/A
Involvement in disease Spastic paraplegia 26, autosomal recessive (SPG26) Catalytic activity Reaction=ganglioside GM3 (d18:1(4E)) + UDP-N-acetyl-alpha-D-galactosamine = ganglioside GM2 (d18:1(4E)) + H(+) + UDP
PDB ID(s)
N/A
Function Involved in the biosynthesis of gangliosides GM2, GD2, GT2 and GA2 from GM3, GD3, GT3 and GA3, respectively.
Activity data
Interaction ID 1169
Target type Protein
Target unique ID Q00973
Activity 21.21 nM
Binding Conditions/Buffer

1X PBS (pH 7.4) Selections carried out in vivo in six- to eight-week-old female immunodeficient BALB/c mice (CAnN. Cg-Foxn1nu/Crl)
Assay

Flow cytometry evaluation of the binding affinity of DB99 to GD2+ cells
PubMed ID 34703655
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_316 DNA CCGCCCAAATCCCTAAGAGAAGACTGTAATGACATCAAACCAGACACACTACACACGCA 78.79%
Apta_321 DNA AACCGCCCAAATCCCTAAGAGTCGGACTGCAACCTATGCTATCGTTGATGTCTGTCCAAGCAACACAGACACACTACACACGCACA 65.12%
Apta_662 DNA GGCGCCAAACAGGACCACCATGACAATTACCCATACCACCTCATTATGCCCCATCTCCGC 56.06%
Apta_219 DNA AACCGCCCAAATCCCTAAGAGTCTGCACTTGTCATTTTGTATATGTATTTGGTTTTTGGCTCTCACAGACACACTACACACGCACA 55.81%
Apta_790 DNA GGGAGACAAGAATAAACGCTCAAGAAGTGAAAATGACAGAACACAACATTCGACAGGAGGCTCACAACAGGC 54.17%
Apta_447 RNA ACGCUCAACGAGCCAGGAACAUCGACGUCAGCAAACGCGAGCGCAACCAGUAACACC 53.03%
Apta_689 DNA CCACACAACAGCCTACGTGGATACACCACATACATCCCATAACCCCGTGTCATGTGTCG 53.03%
Apta_1219 DNA GCGCAGAACCGACAGCAAAACGGAAGTCCACCACGACTATTGGTGCCCAATCTACCGTA 53.03%
Apta_458 DNA AGCTCCAGAAGATAAATTACAGGGAGAGTAAACTTTGCAAACACAACAATACCATTCCGGAACGTTCTTAACACAACTAGGATACTATGACCCC 52.13%
Apta_292 RNA CUACGAACUCAUGACACAAGGAUGCAAUCUCAUCCCGCCAGCCCACCGU 51.52%
Apta_665 DNA CGCCAATCTCAAAGCCCGCCACCTGCCCCTCACTGCCCACCTGTGGAATCCATGTCGCTC 51.52%
Apta_728 DNA CGACCCGGCACAAACCCAGAACCATATACACGATCATTAGTCTCCTGGGCCG 51.52%
Apta_1232 DNA GGCCACACAAACAACATGACAACACGTCTCACATAACGCCCACGTGCTGCCGCCTCATCG 51.52%
Apta_83 DNA GGCTTTACACTTTATGCTTCCGTAAAAACACAAACACACGCACATACATAAAATAACAATTTCACACAGGAAACAG 51.32%
Apta_698 DNA AGCAGCACAGAGGTCAGATGCACTCGGACCCCATTCTCCTTCCATCCCTCATCCGTCCACCCTATGCGTGCTACCGTGAA 51.25%
Apta_952 DNA TCACCTCATACGACTCACTATAGCGGACCCCACTCACTGCTCGGACTCTCCCCCTCCCCGCCTGGCTCGAACAAGCTTGC 51.25%
Apta_435 DNA CCTTCGTTGTCTGCCTTCGTAGGACCGCAGACATCGACGCAGGGAAATTCCGCAAGTCCAGCCAAATGCCACCCTTCAGAATTCGCACCA 51.11%
Apta_863 DNA CTCCTCTGACTGTAACCACGCCCAGAAACAGCACCCTTACATCGACTGGACCTTCCGCGGCATAGGTAGTCCAGAAGCC 50.63%
Apta_153 RNA CCACAGUUCAGAGGCACCGCGAACAAAACGCAAGACAGAGUGCCGACAAGAAC 50.00%
Apta_514 DNA ACTCAGCACGCGTGTAGGGAAAACCAACCGCCCACAAGCTGCATGCAACG 50.00%

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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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