AptaDB: Result

Interaction ID: 1111

Aptamer sequence: CAATTGGGCCCGTCCGTATGGTGGGT

Target unique ID: O14786

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_1040	SL2-B	Protein	NRP1_HUMAN	0.5 nM	PBS and 0.005% tween-20 solution mixture was used as the running buffer, and 50 mM NaOH as the regeneration buffer	22359573

Aptamer Sequence:	CAATTGGGCCCGTCCGTATGGTGGGT
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_1040	Description	SL2-B
Aptamer chemistry	DNA	Length	26 nt
GC content	61.5%	Molecular weight	8,034.16 Da
Molarity of 1 μg/μl solution	124.47 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Aptasensor
Sequence	CAATTGGGCCCGTCCGTATGGTGGGT
Applications	Identifying high affinity aptamer sequences for the biological molecules and targeting them as antagonist for cancer cell detection

Type	Detail	Type	Detail
Uniprot ID	O14786	Protein name	Neuropilin-1 (Vascular endothelial cell growth factor 165 receptor) (CD antigen CD304)
Gene name(s)	NRP1 NRP VEGF165R	Organism	Neuropilin-1 (Vascular endothelial cell growth factor 165 receptor) (CD antigen CD304)
Status	reviewed in uniprot database	Length	923
Mass	103,134	Activity regulation	N/A
Involvement in disease	N/A	Catalytic activity	N/A
PDB ID(s)	1KEX;2QQI;2QQM;2QQN;3I97;4DEQ;4RN5;5C7G;5IJR;5IYY;5J1X;5JGI;5JGQ;5JHK;5L73;6FMC;6FMF;6TKK;7JJC;7O1N;
Function	Cell-surface receptor involved in the development of the cardiovascular system, in angiogenesis, in the formation of certain neuronal circuits and in organogenesis outside the nervous system.

	Interaction ID	1111
	Target type	Protein
	Target unique ID	O14786
	Activity	0.5 nM
	Binding Conditions/Buffer	PBS and 0.005% tween-20 solution mixture was used as the running buffer, and 50 mM NaOH as the regeneration buffer
	Assay	Cells were incubated with different SL2-B aptamer concentrations ranging from 0 to 100 nM. The fluorescence intensity originating from the scrambled sequence at each concentration was subtracted from the fluorescence intensity of corresponding SL2-B aptamer. The actual fluorescence intensity was fitted into SigmaPlot software to determine the Kd
	PubMed ID	22359573

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_1039	DNA	GCCCGTCCGTATGGTGGGT	73.08%
Apta_1038	DNA	CCCGTCCGTATGGTGGG	65.38%
Apta_1036	DNA	ATACCAGTCTATTCAATTGGGCCCGTCCGTATGGTGGG	63.16%
Apta_1012	DNA	CACATTAGGGCGGGGTACTCCTATCACGTATGGGGGCCTGT	58.54%
Apta_1199	DNA	CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG	57.14%
Apta_1199	DNA	CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG	57.14%
Apta_1199	DNA	CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG	57.14%
Apta_1199	DNA	CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG	57.14%
Apta_1208	DNA	CCCTGCGGGGCTGCCCGATATGTGTCCAGGTGGTG	57.14%
Apta_677	DNA	CCAAATGCGACGGGGCCTGTTTTAATGGGG	56.67%
Apta_307	DNA	CATTCACCATGGCCCCTTCCTACGTATGTTCTGCGGGTG	56.41%
Apta_648	DNA	GCACACCGATGGCGGTCCTGTTTAGGGGGTGTGC	55.88%
Apta_264	DNA	GGCGTTGTCGGGCGCAGGTGTAGGCCTCGTGGTGGTGGGT	55.00%
Apta_693	DNA	CGAGTTGAGCCGGGCGCGGTACGGGTACTGGTATGTGTGG	55.00%
Apta_965	DNA	CACGGCATGTGTGGCCGGATGCCTATATCGGTCGACTGCA	55.00%
Apta_1203	DNA	CCCTGCGGGGCTACCCGATATGTGTCCGAGTGGTG	54.29%
Apta_649	DNA	GCACACCGATGGCGGTCCTGTTTAGGGGGTGTGCGTG	54.05%
Apta_150	DNA	CCGTAGGTTCGGGGCGGAGTGGTCCGGAAGGTGGCGTGG	53.85%
Apta_483	DNA	ATTGGGAGGGATTGGGTGGG	53.85%
Apta_679	DNA	CAGGTGGCAGATCGGGTGTGGGTGGCCTGG	53.33%

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