Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1096
Aptamer sequence: GCTGTGTGACTCCTGCAATGGTAGCGGGTAGGGGAGGGAGGGTGAATGGAGGATGTTCATGGCAGCTGTATCTTGTCTCC
Target unique ID: Q15116
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_1011 C42 aptamer Protein PDCD1_HUMAN 23 nM 5 ml of PBS-T containing 1 μg/ml bovine serum albumin (BSA) and 0.1 μg/ml tRNA 32429721
Structure information of aptamer
Aptamer Sequence: GCTGTGTGACTCCTGCAATGGTAGCGGGTAGGGGAGGGAGGGTGAATGGAGGATGTTCATGGCAGCTGTATCTTGTCTCC
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_1011 Description C42 aptamer
Aptamer chemistry DNA Length 80 nt
GC content 56.3% Molecular weight 25,004.94 Da
Molarity of 1 μg/μl solution 39.99 μM Number of G-quadruplexes 3
G-Score 63 Function Targeted binding
Sequence GCTGTGTGACTCCTGCAATGGTAGCGGGTAGGGGAGGGAGGGTGAATGGAGGATGTTCATGGCAGCTGTATCTTGTCTCC
Applications Inhibited binding of PD1 to PD-L1
Target information
Type Detail Type Detail
Uniprot ID Q15116 Protein name Programmed cell death protein 1 (Protein PD-1) (hPD-1) (CD antigen CD279)
Gene name(s) PDCD1 PD1 Organism Programmed cell death protein 1 (Protein PD-1) (hPD-1) (CD antigen CD279)
Status reviewed in uniprot database Length 288
Mass 31,647 Activity regulation Inhibited by pembrolizumab
Involvement in disease Systemic lupus erythematosus 2 (SLEB2) Catalytic activity N/A
PDB ID(s)
2M2D;3RRQ;4ZQK;5B8C;5GGR;5GGS;5IUS;5JXE;5WT9;6HIG;6J14;6J15;6JBT;6JJP;6K0Y;6R5G;6ROY;6ROZ;6UMT;6UMU;6UMV;6XKR;7BXA;7CGW;7CU5;7E9B;7VUX;
Function Inhibitory receptor on antigen activated T-cells that plays a critical role in induction and maintenance of immune tolerance to self.
Activity data
Interaction ID 1096
Target type Protein
Target unique ID Q15116
Activity 23 nM
Binding Conditions/Buffer

5 ml of PBS-T containing 1 μg/ml bovine serum albumin (BSA) and 0.1 μg/ml tRNA
Assay

The Kd value was calculated using non-linear regression equation for binding of aptamers to protein-loaded beads
PubMed ID 32429721
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1230 DNA GGCGATAGGCAGTGTTGCGGGGTCGGAGAGCGAGGTAATAGCGTGTATGGGTGCTGTGTG 57.50%
Apta_1131 DNA GCCGAGATTGCACTTACTATCTCAAGAAGGGTAGTAAGAGGAGTGGGTGATTATGGGTAAGTTGTATGAGGTAATTGAATAAGCTGGTATGCGC 57.45%
Apta_1133 DNA GCCGAGATTGCACTTACTATCTAAAGAAGAGTAGTAAGAGGCGTGGGTGATTATGGGTAAGTTGTATGAGGTAATTGAATAAGCTGGTATGCGC 56.38%
Apta_1071 DNA TTGAAGTGACTCCGCACTGGGTGGGTGGGAGGGTCGTGCGGCTGGTCATAGCAGGGT 56.25%
Apta_1082 DNA GGCTGGTCCGCTGGGAACAAGGGCGGGAGGGAGGGTGTGGGTGCGACAAGCGGACCAGCC 56.25%
Apta_1137 DNA GCCGAGATTGCACTTACTATCTCAAGAAGAGTAGTAAGAGGAGTGGGTGGTTATGAGTAAGTTGTATGTGGTAATTGAATAAGCTGGTATGCGC 55.32%
Apta_686 DNA GGTCACCAACAACAGGGAGCGCTACGCGAAGGGTCAATGTGACGTCATGCGGATGTGTGG 55.00%
Apta_1136 DNA GCCGAGATTGCACTTACTATCTAAAGAAAGGTAGTAAGAGTGGGTGATTATGGGTAAGTTGTATGAGGTAATTGAATAAGCTGGTATGCGC 54.95%
Apta_1134 DNA GCCGAGATTGCACTTACTATCTGTTGAGGGAAGAAGTGGTGTAATGTGGAATAATTGTTGTAATAGTAATTGATAAGCTGGTATGCGC 54.55%
Apta_455 DNA AGCTCCAGAAGATAAATTACAGGGGCCGGGGTGGCTCAGGCAAGGGGTTGACCTGTCGTAGGGATTGTTTTAACAACTAGGATACTATGACCCC 54.26%
Apta_773 DNA GAATTCAGTCGGACAGCGGTGGTGCTTGTGTATGGGGGTGGTTGGTGGGTTTTATGCTGCTGGATGGACGAATATCGTCTCCC 54.22%
Apta_1135 DNA GCCGAGATTGCACTTACTATCTCATCAATAAAGATTATAGGGTGAAGGTGATAGTAGGTGGTATATAGGGTAATTGAATAAGCTGGTATGCGC 53.76%
Apta_794 DNA ATCCAGAGTGACGCAGCAAGGAGATTCGAGGGGGAAGGTTTGTTATAGGGGTTAATGGACACGGTGGCTTAGT 53.75%
Apta_1034 DNA ATGCGGATCCCGCGCGCGACCGTGTCAGCGGGGACTAGCGGTGTAGCGCGAAGCTTGCGC 53.75%
Apta_454 DNA AGCTCCAGAAGATAAATTACAGGTGAGGGCGGGCGGGTGGTTGTAATATGATCGAATGGTATATGTGTGTTTGCAACTAGGATACTATGACCCCG 53.68%
Apta_771 DNA GAATTCCGTCGGACAGCGGTATGCATGGGAGGTTCTGGAGGGGGTGGGTTGGCGTGCGTTCCAGATGGACGAATATCGTCTCCC 53.57%
Apta_775 DNA GAATTCAGTCGGACAGCGCGGTGTTGGTGGCGGGGGTGGTTGGGGGATTTGGCTGTCCTGAGTGATGGACGAATATCGTCTCCC 53.57%
Apta_584 DNA GTACCAGCTTATTCAATTACACGGACAGAGGGTAGCGGCTCTGCGCATTGAGTTGCTGCGGGCTGAAGCGCGGTACATGGGAGATAGTATGTTCATCAG 53.54%
Apta_151 DNA GCAATGGTACGGTACTTCCGCGGTCCGGGGTGGGTGGGTGGTGGGGGGTGCGGGGGGGCGGCCGCAAAAGTGCACGCTACTTTGCTAA 53.41%
Apta_951 DNA CACCTAATACGACTCACTATAGCGGATCCGAGGGGGTAGCGGGTGGGCCGGTGGATGCGGGGCGCCGGCGCCTGGCTCGAACAAGCTTGC 53.33%

ABOUT

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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