Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 343
Aptamer sequence: GGGCGCGTTCTTCGTGGTTACTTTTAGTCCCG
Target unique ID: P16234
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_338 20t Protein PGFRA_HUMAN 0.147 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: GGGCGCGTTCTTCGTGGTTACTTTTAGTCCCG
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_338 Description 20t
Aptamer chemistry DNA Length 32 nt
GC content 56.3% Molecular weight 10,060.22 Da
Molarity of 1 μg/μl solution 99.40 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence GGGCGCGTTCTTCGTGGTTACTTTTAGTCCCG
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 343
Target type Protein
Target unique ID P16234
Activity 0.147 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_359 DNA GGGAACGCGTTATTGGGTAACTTCCC 62.50%
Apta_146 DNA GGTGCGGTTCGTGCGGTTGTAGTACTCGTGGCCG 61.76%
Apta_1215 DNA GTCGAATCAGCACCTCTGCATAGGTTACGTTTATACTGCG 57.50%
Apta_229 DNA GGGGCACGTTTATCCGTCCCTCCTAGTGGCGTGCCCC 56.76%
Apta_145 DNA GGTGCGGTTCGTGCGGTTGTAGTACTCGTGGCCGATAGA 56.41%
Apta_602 DNA GGGCGAGAACAGTGTCCCAGTCGCTAGTTTTCTCTGCCC 56.41%
Apta_147 DNA TGCGGTTGTAGTACTCGTGGCCG 56.25%
Apta_1236 DNA GGACTGTTGTGGTATTATTTTTGGTTGTGC 56.25%
Apta_691 DNA CGACGCGCGTTGGTGGTGGATGGTGTGTTACACGTGTTGT 55.00%
Apta_1255 DNA GGCGCATGATCATTCGGTGGGTAAGGTGGTGGTAACGTTG 55.00%
Apta_564 DNA GGGGACTGTTGTGGTATTATTTTTGGTTGTGCAGT 54.29%
Apta_1026 DNA GGGGGGTGTATCGTTGACGAGTTGCGCGTGCGTCTCGTG 53.85%
Apta_846 DNA GTGCAGACAGCTAGTAGTGGTGACTTTCTGTCCAAATCAAGATAA 53.33%
Apta_73 DNA GGGGAGTAGGTTGGTGTGGTTGGGGCTCCCC 53.12%
Apta_216 DNA TGGTTGGTTTTTGGTTTTTTTTTTTGGTTT 53.12%
Apta_360 DNA GGGAACGCATACGCCGCAGTATTTCCC 53.12%
Apta_361 DNA GGGAACGCCCGTATTGCTCGGTTCCC 53.12%
Apta_539 DNA CGTGTTGTCTCTCTGTGTCTCG 53.12%
Apta_543 DNA GGCACGTGTTGTCTCTCTGTGTCTCGTGCC 53.12%
Apta_631 DNA GGGATCGAAACGTAGCGCCTTCGATCCC 53.12%

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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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