AptaDB: Result

Interaction ID: 1120

Aptamer sequence: GCGCGGTACCGCGCTAACGGAGGTTGCGTCCGT

Target unique ID: CRL-2539

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_1067	TEPP	Cell	4T1	110 nM	PBS with 1mM MgCl2, 0.1 mg/mL tRNA, 1mg/mL bovine serum albumin, and 10% FCS	32027209

Aptamer Sequence:	GCGCGGTACCGCGCTAACGGAGGTTGCGTCCGT
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_1067	Description	TEPP
Aptamer chemistry	DNA	Length	33 nt
GC content	69.7%	Molecular weight	10,187.52 Da
Molarity of 1 μg/μl solution	98.16 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted therapy
Sequence	GCGCGGTACCGCGCTAACGGAGGTTGCGTCCGT
Applications	Targeting of EpCAM-positive brain metastases

Type	Detail	Type	Detail
ATCC ID	CRL-2539	Cell name	4T1
Category	Animal cells	Organism	Mus musculus, mouse
Product type	N/A	Cell type	N/A
Morphology	epithelial	Tissue	Breast; Mammary gland
Disease	Mimics human breast cancer; Stage IV	Product format	Frozen
Antigen expression	N/A	Genes expressed	N/A
Cell description	The tumor growth and metastatic spread of 4T1 cells in BALB/c mice very closely mimic human breast cancer. This tumor-derived cell line is an animal model for stage IV human breast cancer. 4T1-induced tumors can be used as a post-operative model as well as a nonsurgical model because the 4T1-induced tumor metastasizes spontaneously in both models with similar kinetics.
Application(s)	3D cell culture

	Interaction ID	1120
	Target type	Cell
	Target unique ID	CRL-2539
	Activity	110 nM
	Binding Conditions/Buffer	PBS with 1mM MgCl2, 0.1 mg/mL tRNA, 1mg/mL bovine serum albumin, and 10% FCS
	Assay	Specificity of bifunctional aptamer-DOX conjugates
	PubMed ID	32027209
	Interaction ID	1121
	Target type	Cell
	Target unique ID	CRM-HTB-26
	Activity	85.6 nM
	Binding Conditions/Buffer	PBS with 1mM MgCl2, 0.1 mg/mL tRNA, 1mg/mL bovine serum albumin, and 10% FCS
	Assay	Specificity of bifunctional aptamer-DOX conjugates
	PubMed ID	32027209

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_1026	DNA	GGGGGGTGTATCGTTGACGAGTTGCGCGTGCGTCTCGTG	58.97%
Apta_329	DNA	GGCGTACGGTAGGCGGGGTCAACTG	57.58%
Apta_722	DNA	CTCTCGGGACGACGGCCCGATCTCAGAGTAGTCGTCCC	55.26%
Apta_1257	DNA	CGACGCACAGTCGCTGGTGCGTACCTGGTTGCCGTTGTGT	55.00%
Apta_1259	DNA	GGCGCGGCATGGTGTGGACTCCAGGCGGTAGGGATGTCGT	55.00%
Apta_359	DNA	GGGAACGCGTTATTGGGTAACTTCCC	54.55%
Apta_362	DNA	GGGAACGCACCGATCGCAGGTTTCCC	54.55%
Apta_420	DNA	AGGGACGGGCTAAGTAACTGTGGAGGGT	54.55%
Apta_675	DNA	ACTGTCCGTCGGGTTTAGGGTGGCGTTCGG	54.55%
Apta_335	DNA	ACCGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTG	54.00%
Apta_255	DNA	TAGCGATACTGCGTGGGTTGGGGCGGGTAGGGCCAGCAGTCTCGT	53.33%
Apta_819	DNA	GCGCCCTCTCACGTGGCACTCAGAGTGCCGGAAGTTCTGCGTTAT	53.33%
Apta_585	DNA	GATCGAGGGCAGCGATAGCTGGGCTAATAAGGTTAGCCCCATCGGTC	53.19%
Apta_697	DNA	CTCTCGGGACGACGGACGCTAATCTTACAAGGGCGTAGTGTATGTCGTCCC	52.94%
Apta_370	RNA	GGGAGGACGCGUCGCCGUAAUGGAUGUUUUGCUCCCUG	52.63%
Apta_35	DNA	TGGGTGGCCTCCCGTTTATTCGAGATTTGGTTGAATTTGT	52.50%
Apta_263	DNA	AGAGGGGAGGGTCGGGTATCGGCGTGTTCGGGGGATCTGC	52.50%
Apta_264	DNA	GGCGTTGTCGGGCGCAGGTGTAGGCCTCGTGGTGGTGGGT	52.50%
Apta_437	DNA	TCACAGTCCCGGTGCCGCACTAAAACCCATTGTTGTGCGA	52.50%
Apta_579	DNA	ACTGAGGGCACGGACAGGAGGGGGAGAGATGGCGTGAGGT	52.50%

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