AptaDB: Result

Interaction ID: 280

Aptamer sequence: AGTTGAATGGTGTGGTCACTTCCAGTCCCGCAGGGCACAC

Target unique ID: P09619

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_275	Aptamer ID3	Protein	PGFRB_HUMAN	2.6 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:	AGTTGAATGGTGTGGTCACTTCCAGTCCCGCAGGGCACAC
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_275	Description	Aptamer ID3
Aptamer chemistry	DNA	Length	40 nt
GC content	57.5%	Molecular weight	12,552.84 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	AGTTGAATGGTGTGGTCACTTCCAGTCCCGCAGGGCACAC
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	280
	Target type	Protein
	Target unique ID	P09619
	Activity	2.6 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_60	DNA	GGAATGAGTGCCCTGCAAGCGAGGGCTAGC	57.50%
Apta_597	DNA	TACTGGGCTGGGCTTGGATTAGATCACAGTGGAACATACAGGACACACG	55.10%
Apta_386	DNA	GGAAAAGATGGTATGGGCCCTAGAAAGTCCACCCGGCGCC	55.00%
Apta_971	DNA	TAGTCTAGGAACGGTACGATCGTATTCCAAGGACTTTGCTGGTGGTATCC	54.00%
Apta_846	DNA	GTGCAGACAGCTAGTAGTGGTGACTTTCTGTCCAAATCAAGATAA	53.33%
Apta_273	DNA	ATAAGCTGAGCATCTTAGATCCCCGTCAAGGGCAGCGTAA	52.50%
Apta_274	DNA	GATACTGAGCATCGTACATGATCCCGCAACGGGCAGTATT	52.50%
Apta_471	DNA	CTGTAATTGGCGTATGTAACCCAGGCACCAAACGCCCCAG	52.50%
Apta_543	DNA	GGCACGTGTTGTCTCTCTGTGTCTCGTGCC	52.50%
Apta_912	DNA	TAGTATGGACTTGTCTTCTTGTCAGAGTCTGGCAGCACGT	52.50%
Apta_1259	DNA	GGCGCGGCATGGTGTGGACTCCAGGCGGTAGGGATGTCGT	52.50%
Apta_514	DNA	ACTCAGCACGCGTGTAGGGAAAACCAACCGCCCACAAGCTGCATGCAACG	52.00%
Apta_596	DNA	GGTGGCTGTTGGTCGAGGCTTATTAGTGTAGTCAATGGAGGCAGGCGACG	52.00%
Apta_32	DNA	CGGTAAACTGCGTCCGAAGGGGCTGCAGTGACCCGAATGGGTCCG	51.11%
Apta_642	DNA	ATCCAATACCTCAGAACTCAGTTCGAGTCGTAAAGGGGAATCGCA	51.11%
Apta_749	DNA	GATCGGTGGGTGGGGGGGTTGGAGATCATCCTCAGGGATTACGTC	51.11%
Apta_835	DNA	TATGGCGTGGCAAGCTTGGCCCGCTTCTCAAGCATGGTTATCTAC	51.11%
Apta_486	DNA	GGGAGGGATTGGGTGGGCACAGCTCGCTGATAGGTCCTGGTCTCAC	51.06%
Apta_1125	DNA	TCGGGCGAGTCGTCTGGGGAGGTCAGAACGAAAGGCCCGCATCGTCCTCCC	50.98%
Apta_558	DNA	CCGGTGGGTGGTCAGGTGGGATAGCGTTCCGCGTATGGCCCAGCGCATCACGGGTTCGCACCA	50.79%

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