AptaDB: Result

Interaction ID: 278

Aptamer sequence: ATAAGCTGAGCATCTTAGATCCCCGTCAAGGGCAGCGTAA

Target unique ID: P09619

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_273	Aptamer ID1	Protein	PGFRB_HUMAN	2.7 nM	0.1 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 2.7 mM KCl, and 1 mM MgCl2 (PBSM), pH 7.4	20705898

Aptamer Sequence:	ATAAGCTGAGCATCTTAGATCCCCGTCAAGGGCAGCGTAA
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

Type	Detail	Type	Detail
Aptamer ID	Apta_273	Description	Aptamer ID1
Aptamer chemistry	DNA	Length	40 nt
GC content	50.0%	Molecular weight	12,553.88 Da
Molarity of 1 μg/μl solution	79.66 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	ATAAGCTGAGCATCTTAGATCCCCGTCAAGGGCAGCGTAA
Applications	Binding to PDGF-BB protein

Type	Detail	Type	Detail
Uniprot ID	P09619	Protein name	Platelet-derived growth factor receptor beta (PDGF-R-beta) (PDGFR-beta) (EC 2.7.10.1) (Beta platelet-derived growth factor receptor) (Beta-type platelet-derived growth factor receptor) (CD140 antigen-like family member B) (Platelet-derived growth factor receptor 1) (PDGFR-1) (CD antigen CD140b)
Gene name(s)	PDGFRB PDGFR PDGFR1	Organism	Platelet-derived growth factor receptor beta (PDGF-R-beta) (PDGFR-beta) (EC 2.7.10.1) (Beta platelet-derived growth factor receptor) (Beta-type platelet-derived growth factor receptor) (CD140 antigen-like family member B) (Platelet-derived growth factor receptor 1) (PDGFR-1) (CD antigen CD140b)
Status	reviewed in uniprot database	Length	1106
Mass	123,968	Activity regulation	Present in an inactive conformation in the absence of bound ligand
Involvement in disease	A chromosomal aberration involving PDGFRB is found in a form of chronic myelomonocytic leukemia (CMML)	Catalytic activity	Reaction=ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein]
PDB ID(s)	1GQ5;1H9O;1SHA;2IUI;2L6W;2PLD;2PLE;3MJG;
Function	Tyrosine-protein kinase that acts as cell-surface receptor for homodimeric PDGFB and PDGFD and for heterodimers formed by PDGFA and PDGFB, and plays an essential role in the regulation of embryonic development, cell proliferation, survival, differentiation, chemotaxis and migration.

	Interaction ID	278
	Target type	Protein
	Target unique ID	P09619
	Activity	2.7 nM
	Binding Conditions/Buffer	0.1 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 2.7 mM KCl, and 1 mM MgCl2 (PBSM), pH 7.4
	Assay	The three most highly enriched sequences from QSAS R3∕R2 were tested for their affinity
	PubMed ID	20705898

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_274	DNA	GATACTGAGCATCGTACATGATCCCGCAACGGGCAGTATT	65.00%
Apta_1025	DNA	GAAGAGTAGATGAAACGTTTTTTCGCCCGATAAAAGGGACGTGCGTCAGACA	55.77%
Apta_642	DNA	ATCCAATACCTCAGAACTCAGTTCGAGTCGTAAAGGGGAATCGCA	55.56%
Apta_1087	DNA	CTTACGACTCAGGCATTTTGCCGGGTAACGAAGTTACTGTCGTAAG	54.35%
Apta_597	DNA	TACTGGGCTGGGCTTGGATTAGATCACAGTGGAACATACAGGACACACG	53.06%
Apta_222	DNA	AGCGACTGACGATCTTGAGTAAACCGCTCATCCACGTAGT	52.50%
Apta_260	DNA	GACGTTAAGCTAGCAGGTGTTAGGTCCCGTGGTGATGAAT	52.50%
Apta_275	DNA	AGTTGAATGGTGTGGTCACTTCCAGTCCCGCAGGGCACAC	52.50%
Apta_406	DNA	AAAGCCCACTGCATAGAGGCCGCTCAACATGCGAGCCGGT	52.50%
Apta_441	DNA	TGAATCTCGCGCTCGTTGGTACCCTTAAAATAAAGGCATA	52.50%
Apta_462	DNA	GGTATAGACCCCTGAGTCCTACCGAGGGCACGGCA	52.50%
Apta_513	DNA	TAGGGAAAACCAACCGCCCAGAACTGCAGCATAAC	52.50%
Apta_340	DNA	TACTCAGGGCACTGCAAGCAATTGTGGTCCCAATGGGCTGAGTA	52.27%
Apta_1081	DNA	CTTACGACTGTGGTCGGGTGGTGGGCCTCTAGAGGGGTGTCGTAAG	52.17%
Apta_835	DNA	TATGGCGTGGCAAGCTTGGCCCGCTTCTCAAGCATGGTTATCTAC	51.11%
Apta_510	DNA	TGTAATTTGTCTGCAGCGGTTCTTGATCGCTGACACCATATTATGAAGA	51.02%
Apta_287	DNA	CAGCACCGACCTTGTGCTTTGGGAGTGCTGGTCCAAGGGCGTTAATGGACA	50.98%
Apta_979	DNA	ATGAGTAGTGCGGAGGGATGTGAATACTGACGCGGTCATAGTCGCTGTTGTACCATTGA	50.85%
Apta_60	DNA	GGAATGAGTGCCCTGCAAGCGAGGGCTAGC	50.00%
Apta_142	DNA	CGCACATCAGTTTAGCAGCGCCAAAGGCGGAAGCGCA	50.00%

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