Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 345
Aptamer sequence: TACTCAGGGCACTGCAAGCAATTGTGGTCCCAATGGGCTGAGTA
Target unique ID: P16234
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_340 41t Protein PGFRA_HUMAN 0.138 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: TACTCAGGGCACTGCAAGCAATTGTGGTCCCAATGGGCTGAGTA
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_340 Description 41t
Aptamer chemistry DNA Length 44 nt
GC content 52.3% Molecular weight 13,836.68 Da
Molarity of 1 μg/μl solution 72.27 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence TACTCAGGGCACTGCAAGCAATTGTGGTCCCAATGGGCTGAGTA
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 345
Target type Protein
Target unique ID P16234
Activity 0.138 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_591 DNA CTCTCGGGACGACGGCTGGCACGTTTGGTTCAAGAATGTGGGTGTCGTCCC 56.86%
Apta_579 DNA ACTGAGGGCACGGACAGGAGGGGGAGAGATGGCGTGAGGT 56.82%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 56.82%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 56.82%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 56.82%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 56.82%
Apta_1208 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAGGTGGTG 56.82%
Apta_652 DNA CCTGCACCTCGTCCAGCATGCACACCGATGGCGGTCCTGGCAGGGGGTGTGCGTG 56.36%
Apta_573 DNA CGTACAGTGGGCTATATTGCTGACGTAAGAGCTGCTTTCAATGCATTGGCATAGATGTCA 55.00%
Apta_992 DNA TCACTGACAGTAGGCCCATACGCACATTCAACAATCGGTAGTCCATACAACCGCGCCCCGTG 54.84%
Apta_260 DNA GACGTTAAGCTAGCAGGTGTTAGGTCCCGTGGTGATGAAT 54.55%
Apta_621 DNA AAGCTTGCTTTATAGCCTGCAGCGATTCTTGATCGGAAAAGGCTGAGAGCTACGC 54.55%
Apta_910 DNA TCACGTGCATGATAGACGGCGAAGCCGTCGAGTTGCTGTGTGCCGATGCACGTGA 54.55%
Apta_651 DNA CCTGCACCTCGTCCAGCATGCACACCGATGGCGGTCCTGTTTAGGGGGTGTGCGTG 53.57%
Apta_405 DNA TCTAGCCCACTGCATAGAGGTAGCCACGTATGTGGGTGTTACCCATTCGTAGCTACCGGTG 52.46%
Apta_165 DNA TGGACGAACTGCCCTCAGCTACTTTCATGTTGCTGACGCA 52.27%
Apta_221 DNA GTCCTAGCAGACACTCGGCCATCACGCCCATTGGTTTGCA 52.27%
Apta_258 DNA CACTGCGGGGGTCTATACGTGAGGAAGAAGTGGGCAGGTC 52.27%
Apta_259 DNA GCAAGTATGAGCGCAGGAGTTAGGTCCCGTGGCGATGGGT 52.27%
Apta_261 DNA TAAACCCCAAAACAGTGCAACTAGGTGTAGGTCCCGTGGT 52.27%

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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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