Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 344
Aptamer sequence: CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTGT
Target unique ID: P16234
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_339 36t Protein PGFRA_HUMAN 0.094 nM 10.1 mM Na2HPO4, 1.8 mM K2HPO4, 137 mM NaCl and 2.7 mM KCl, 1 mM MgCl2 (pH 7.4) 8916928
Structure information of aptamer
Aptamer Sequence: CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTGT
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_339 Description 36t
Aptamer chemistry DNA Length 40 nt
GC content 55.0% Molecular weight 12,505.83 Da
Molarity of 1 μg/μl solution 79.96 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTGT
Applications Inhibitory effect on PDGF dependent [3H]thymidine incorporation in PAE cells expressing the PDGF receptors
Target information
Type Detail Type Detail
Uniprot ID P16234 Protein name Platelet-derived growth factor receptor alpha (PDGF-R-alpha) (PDGFR-alpha) (EC 2.7.10.1) (Alpha platelet-derived growth factor receptor) (Alpha-type platelet-derived growth factor receptor) (CD140 antigen-like family member A) (CD140a antigen) (Platelet-derived growth factor alpha receptor) (Platelet-derived growth factor receptor 2) (PDGFR-2) (CD antigen CD140a)
Gene name(s) PDGFRA PDGFR2 RHEPDGFRA Organism Platelet-derived growth factor receptor alpha (PDGF-R-alpha) (PDGFR-alpha) (EC 2.7.10.1) (Alpha platelet-derived growth factor receptor) (Alpha-type platelet-derived growth factor receptor) (CD140 antigen-like family member A) (CD140a antigen) (Platelet-derived growth factor alpha receptor) (Platelet-derived growth factor receptor 2) (PDGFR-2) (CD antigen CD140a)
Status reviewed in uniprot database Length 1089
Mass 122,670 Activity regulation Present in an inactive conformation in the absence of bound ligand. Binding of PDGFA and/or PDGFB leads to dimerization and activation by autophosphorylation on tyrosine residues
Involvement in disease A chromosomal aberration involving PDGFRA is found in some cases of hypereosinophilic syndrome Catalytic activity Reaction=ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein]
PDB ID(s)
1GQ5;5GRN;5K5X;6A32;6JOI;6JOJ;6JOK;6JOL;7LBF;
Function Tyrosine-protein kinase that acts as a cell-surface receptor for PDGFA, PDGFB and PDGFC and plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemotaxis.
Activity data

No relevant experimental diagram

 Interaction ID 344
Target type Protein
Target unique ID P16234
Activity 0.094 nM
Binding Conditions/Buffer

10.1 mM Na2HPO4, 1.8 mM K2HPO4, 137 mM NaCl and 2.7 mM KCl, 1 mM MgCl2 (pH 7.4)
Assay

N/A
PubMed ID 8916928
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_158 DNA CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTG
97.50%
Apta_873 DNA CCACCGAGCCTACCACATGTGACATCCCAGGACATAGCTG 60.00%
Apta_406 DNA AAAGCCCACTGCATAGAGGCCGCTCAACATGCGAGCCGGT 57.50%
Apta_821 DNA CACAGTCACTCAGACGGCCGCTATTGTTGCCAGATTGCCTTTGGC 55.56%
Apta_847 DNA CACTAGGATCTAGGGAAAAATCTCGTAAATACTATACTCCTGAGC 55.56%
Apta_1162 DNA AGAGGCTACAGCGATAAGTCGACATTGCTGACCGTACCTAGTAATACGT 55.10%
Apta_573 DNA CGTACAGTGGGCTATATTGCTGACGTAAGAGCTGCTTTCAATGCATTGGCATAGATGTCA 55.00%
Apta_850 DNA CACCAGTGTGTTGAGGTTTGAGCACACTGATAGAGTGTCA 55.00%
Apta_985 DNA CCAGGAGGACCCTATTCTCGTGTATCGACGAGATCCAGTG 55.00%
Apta_1257 DNA CGACGCACAGTCGCTGGTGCGTACCTGGTTGCCGTTGTGT 55.00%
Apta_1260 DNA GAAAGGGACGTTCCAAGTTCGTATAAGCAGTCCTGTGCGT 55.00%
Apta_1012 DNA CACATTAGGGCGGGGTACTCCTATCACGTATGGGGGCCTGT 53.66%
Apta_1152 DNA GACAAGGATAAATCCTTCAATGAAGTGGGTCACTCATCTGTGA 53.49%
Apta_640 DNA CAATGGACCTATTCGAGTACTGAATAGAACAGTCGGCGCTCTGGG 53.33%
Apta_1033 DNA CACAGGTTCCAGGTAATACCTAAGGGTATGCTCTCGCCTATTATATGGAGCAC 52.83%
Apta_689 DNA CCACACAACAGCCTACGTGGATACACCACATACATCCCATAACCCCGTGTCATGTGTCG 52.54%
Apta_162 DNA CCGTACATACTACGTACGTACGTGAACAGAGGCAGAG 52.50%
Apta_164 DNA TATAGACCACAGCCTGAGATTAACCACCAACCCAGGACT 52.50%
Apta_215 DNA AGGAAGGCTTTAGGTCCGAGATCTCGGAAT 52.50%
Apta_222 DNA AGCGACTGACGATCTTGAGTAAACCGCTCATCCACGTAGT 52.50%

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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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