AptaDB: Result

Interaction ID: 281

Aptamer sequence: CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTG

Target unique ID: P01127

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_158	36t	Protein	PDGFB_HUMAN	0.093 nM	PBSM (10.1 mM Na2HPO4, 1.8 mM K2HPO4, 137 mM NaCl and 2.7 mM KCl, 1 mM MgCl2 (pH 7.4))	8916928

Aptamer Sequence:	CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTG
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_158	Description	36t
Aptamer chemistry	DNA	Length	39 nt
GC content	56.4%	Molecular weight	12,201.64 Da
Molarity of 1 μg/μl solution	81.96 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTG
Applications	Inhibitory effect on PDGF dependent [3H]thymidine incorporation in PAE cells expressing the PDGF receptors

Type	Detail	Type	Detail
Uniprot ID	P01127	Protein name	Platelet-derived growth factor subunit B (PDGF subunit B) (PDGF-2) (Platelet-derived growth factor B chain) (Platelet-derived growth factor beta polypeptide) (Proto-oncogene c-Sis) (Becaplermin)
Gene name(s)	PDGFB PDGF2 SIS	Organism	Platelet-derived growth factor subunit B (PDGF subunit B) (PDGF-2) (Platelet-derived growth factor B chain) (Platelet-derived growth factor beta polypeptide) (Proto-oncogene c-Sis) (Becaplermin)
Status	reviewed in uniprot database	Length	241
Mass	27,283	Activity regulation	N/A
Involvement in disease	Basal ganglia calcification, idiopathic, 5 (IBGC5)	Catalytic activity	N/A
PDB ID(s)	1PDG;3MJG;4HQU;4HQX;4QCI;6T9E;
Function	Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis.

	Interaction ID	162
	Target type	Protein
	Target unique ID	P04085
	Activity	0.094 nM
	Binding Conditions/Buffer	PBSM (10.1 mM Na2HPO4, 1.8 mM K2HPO4, 137 mM NaCl and 2.7 mM KCl, 1 mM MgCl2 (pH 7.4))
	Assay	Binding of minimal DNA ligands to PDGF
	PubMed ID	8916928
	Interaction ID	281
	Target type	Protein
	Target unique ID	P01127
	Activity	0.093 nM
	Binding Conditions/Buffer	PBSM (10.1 mM Na2HPO4, 1.8 mM K2HPO4, 137 mM NaCl and 2.7 mM KCl, 1 mM MgCl2 (pH 7.4))
	Assay	Binding of minimal DNA ligands to PDGF
	PubMed ID	8916928

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_339	DNA	CACAGGCTACGGCACGTAGAGCATCACCATGATCCTGTGT	97.50%
Apta_873	DNA	CCACCGAGCCTACCACATGTGACATCCCAGGACATAGCTG	62.50%
Apta_406	DNA	AAAGCCCACTGCATAGAGGCCGCTCAACATGCGAGCCGGT	57.50%
Apta_985	DNA	CCAGGAGGACCCTATTCTCGTGTATCGACGAGATCCAGTG	57.50%
Apta_1012	DNA	CACATTAGGGCGGGGTACTCCTATCACGTATGGGGGCCTGT	56.10%
Apta_640	DNA	CAATGGACCTATTCGAGTACTGAATAGAACAGTCGGCGCTCTGGG	55.56%
Apta_821	DNA	CACAGTCACTCAGACGGCCGCTATTGTTGCCAGATTGCCTTTGGC	55.56%
Apta_847	DNA	CACTAGGATCTAGGGAAAAATCTCGTAAATACTATACTCCTGAGC	55.56%
Apta_507	DNA	GGCGGGGCTACGAAGTAGTGATTTTTTCCGATGGCCCGTG	55.00%
Apta_959	DNA	GGACCGCTAGGTTCGTGGCTGAGATCACGCGATATCAGTA	55.00%
Apta_162	DNA	CCGTACATACTACGTACGTACGTGAACAGAGGCAGAG	53.85%
Apta_1152	DNA	GACAAGGATAAATCCTTCAATGAAGTGGGTCACTCATCTGTGA	53.49%
Apta_573	DNA	CGTACAGTGGGCTATATTGCTGACGTAAGAGCTGCTTTCAATGCATTGGCATAGATGTCA	53.33%
Apta_735	DNA	AGGCCCCCAGGCTCGGTGGATGCAAACACATGACTATGGGCCCGT	53.33%
Apta_1162	DNA	AGAGGCTACAGCGATAAGTCGACATTGCTGACCGTACCTAGTAATACGT	53.06%
Apta_1033	DNA	CACAGGTTCCAGGTAATACCTAAGGGTATGCTCTCGCCTATTATATGGAGCAC	52.83%
Apta_284	DNA	CACTCCGTCACTTTAGTGGATCTTTATAAAACCGATGCTG	52.50%
Apta_385	DNA	ACAGATACGGAACTACAGAGGTCAATTACGGTGGCCACGC	52.50%
Apta_850	DNA	CACCAGTGTGTTGAGGTTTGAGCACACTGATAGAGTGTCA	52.50%
Apta_852	DNA	CATCTGTGTGAAGACTATATGGCGCTCACATATTTCTTTC	52.50%

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