AptaDB: Result

Interaction ID: 231

Aptamer sequence: ACGCGCCTATGGTGCATCGCATGCCGACC

Target unique ID: P05532

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_227	Kit-129	Protein	KIT_MOUSE	12.21 nM	Buffer composed of Dulbecco's phosphate-buffered saline with calcium and magnesium and 5 mM MgCl2, 0.45% glucose and 100 mg/ml tRNA	23967247

Aptamer Sequence:	ACGCGCCTATGGTGCATCGCATGCCGACC
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_227	Description	Kit-129
Aptamer chemistry	DNA	Length	29 nt
GC content	65.5%	Molecular weight	9,079.62 Da
Molarity of 1 μg/μl solution	110.14 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted therapy
Sequence	ACGCGCCTATGGTGCATCGCATGCCGACC
Applications	Recognizes c-kit endogenously expressed by a mast cell line or hematopoietic progenitor cells, and specifically blocks binding of the c-kit ligand stem cell factor (SCF)

Type	Detail	Type	Detail
Uniprot ID	P05532	Protein name	Mast/stem cell growth factor receptor Kit (SCFR) (EC 2.7.10.1) (Proto-oncogene c-Kit) (Tyrosine-protein kinase Kit) (CD antigen CD117)
Gene name(s)	Kit Sl	Organism	Mast/stem cell growth factor receptor Kit (SCFR) (EC 2.7.10.1) (Proto-oncogene c-Kit) (Tyrosine-protein kinase Kit) (CD antigen CD117)
Status	reviewed in uniprot database	Length	979
Mass	109,343	Activity regulation	Present in an inactive conformation in the absence of bound ligand
Involvement in disease	Defects in Kit are the cause of the white-spotting phenotype (W)	Catalytic activity	Reaction=ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein]
PDB ID(s)	2O26;
Function	Tyrosine-protein kinase that acts as cell-surface receptor for the cytokine KITLG/SCF and plays an essential role in the regulation of cell survival and proliferation, hematopoiesis, stem cell maintenance, gametogenesis, mast cell development, migration and function, and in melanogenesis.

	Interaction ID	231
	Target type	Protein
	Target unique ID	P05532
	Activity	12.21 nM
	Binding Conditions/Buffer	Buffer composed of Dulbecco's phosphate-buffered saline with calcium and magnesium and 5 mM MgCl2, 0.45% glucose and 100 mg/ml tRNA
	Assay	Kit-129 has high specificity for BJAB c-kit cells. Shown are mean fluorescence values of Alexa-647-labeled Kit-129 aptamer tested in serial dilutions from 0 to 100 nM by flow cytometry
	PubMed ID	23967247

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_504	DNA	TTGCTCCTTATAGAGCCGTCCGAGC	58.62%
Apta_166	DNA	ATCGCGCTCTCCTGCTTAAGCAGCTATCAAATAGCCCACT	57.50%
Apta_960	DNA	CCCGAGGCACGAGGGGGAACGTATCGTCATGTGCCGGCCA	57.50%
Apta_163	DNA	GCGCATGACCATTGATGTCTGCACCATCAGAGGCAGAG	52.63%
Apta_506	DNA	AAGCGCGCGAGACTACGTTTGTAGGGATACCGATGTCG	52.63%
Apta_877	DNA	GTGCGAAGCGCCTCCACTGTACATCCACTCCTTCTGCC	52.63%
Apta_7	DNA	CCAGTCTCCCGTTTACCGCGCCTACACATGTCTGAATGCC	52.50%
Apta_222	DNA	AGCGACTGACGATCTTGAGTAAACCGCTCATCCACGTAGT	52.50%
Apta_262	DNA	ACGGACTCGCAAAAGGTGGAACAGGAGTGGGCCCCGCGGC	52.50%
Apta_284	DNA	CACTCCGTCACTTTAGTGGATCTTTATAAAACCGATGCTG	52.50%
Apta_406	DNA	AAAGCCCACTGCATAGAGGCCGCTCAACATGCGAGCCGGT	52.50%
Apta_873	DNA	CCACCGAGCCTACCACATGTGACATCCCAGGACATAGCTG	52.50%
Apta_875	DNA	GCCGCGACCATACAACGCAAACAACACGCCTGTACGCTTG	52.50%
Apta_914	DNA	CGCTCCGTTTACTCGGTCTGCTATTGGCTTGCCTTTGTTT	52.50%
Apta_1216	DNA	AGCGTCCTCTGCATAGTGATTTACGCTATGTGTACAGTGC	52.50%
Apta_125	DNA	TGGTGGATGGCGCAGTCGGCGACAA	51.72%
Apta_147	DNA	TGCGGTTGTAGTACTCGTGGCCG	51.72%
Apta_323	DNA	GGCTATAGCACATGGGTAAAACGAC	51.72%
Apta_323	DNA	GGCTATAGCACATGGGTAAAACGAC	51.72%
Apta_323	DNA	GGCTATAGCACATGGGTAAAACGAC	51.72%

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