AptaDB: Result

Interaction ID: 279

Aptamer sequence: GATACTGAGCATCGTACATGATCCCGCAACGGGCAGTATT

Target unique ID: P09619

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_274	Aptamer ID2	Protein	PGFRB_HUMAN	2.5 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:	GATACTGAGCATCGTACATGATCCCGCAACGGGCAGTATT
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_274	Description	Aptamer ID2
Aptamer chemistry	DNA	Length	40 nt
GC content	50.0%	Molecular weight	12,544.87 Da
Molarity of 1 μg/μl solution	79.71 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	GATACTGAGCATCGTACATGATCCCGCAACGGGCAGTATT
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	279
	Target type	Protein
	Target unique ID	P09619
	Activity	2.5 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_273	DNA	ATAAGCTGAGCATCTTAGATCCCCGTCAAGGGCAGCGTAA	65.00%
Apta_1162	DNA	AGAGGCTACAGCGATAAGTCGACATTGCTGACCGTACCTAGTAATACGT	55.10%
Apta_1045	DNA	GGTGCTCAGGGAACTGTCTGAGGGATCAGGCTTAAGCCTGTCGAGCAGTT	54.00%
Apta_60	DNA	GGAATGAGTGCCCTGCAAGCGAGGGCTAGC	52.50%
Apta_86	RNA	GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU	52.50%
Apta_162	DNA	CCGTACATACTACGTACGTACGTGAACAGAGGCAGAG	52.50%
Apta_164	DNA	TATAGACCACAGCCTGAGATTAACCACCAACCCAGGACT	52.50%
Apta_222	DNA	AGCGACTGACGATCTTGAGTAAACCGCTCATCCACGTAGT	52.50%
Apta_275	DNA	AGTTGAATGGTGTGGTCACTTCCAGTCCCGCAGGGCACAC	52.50%
Apta_302	DNA	ATCCTGTGAGGAATGCTCATGCATAGCAAGGGCT	52.50%
Apta_363	DNA	ATTGACCGCTGTGTGACGCAACACTCAAT	52.50%
Apta_463	DNA	GTTCTCATGCACACTTATAGCGGGGGGATCCAGTACT	52.50%
Apta_1059	DNA	TCGTGACGCCGTGCAGTTACCGATACGAGCCTCGTTTTG	52.50%
Apta_1061	DNA	TATTTATTGAATGCTGTAATTTCGCCACGCGAAAGTAGG	52.50%
Apta_1204	DNA	GGCACGATGTGGCTACATCGATCGCGGTACTGGTG	52.50%
Apta_1204	DNA	GGCACGATGTGGCTACATCGATCGCGGTACTGGTG	52.50%
Apta_1270	DNA	GTATATCAAGCATCGCGTGTTTACACATGCGAGAGGTGAA	52.50%
Apta_971	DNA	TAGTCTAGGAACGGTACGATCGTATTCCAAGGACTTTGCTGGTGGTATCC	52.00%
Apta_976	DNA	GATGAATATCGCAATGAAATTATATATGTATAATTGGAACGGTGGTATCC	52.00%
Apta_355	DNA	GATGCAGCCACCTACATTGCAGGTTTTATAATACAACTACGCGCCGTTCGCAGGCTAGTT	51.67%

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