AptaDB: Result

Interaction ID: 348

Aptamer sequence: GCGACUGGUUACCCGGUCG

Target unique ID: P16422

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_342	EpDT3	Protein	EPCAM_HUMAN	12 nM	DPBS with 5 mM MgCl2, 0.1 mg/ml tRNA, 0.1 mg/ml salmon sperm DNA and 5% FCS. The final concentration of MgCl2 was 2.5 mM	21281402

Aptamer Sequence:	GCGACUGGUUACCCGGUCG
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_342	Description	EpDT3
Aptamer chemistry	RNA	Length	19 nt
GC content	68.4%	Molecular weight	6,308.58 Da
Molarity of 1 μg/μl solution	158.51 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	GCGACUGGUUACCCGGUCG
Applications	Binding to EpCAM

Type	Detail	Type	Detail
Uniprot ID	P16422	Protein name	Epithelial cell adhesion molecule (Ep-CAM) (Adenocarcinoma-associated antigen) (Cell surface glycoprotein Trop-1) (Epithelial cell surface antigen) (Epithelial glycoprotein) (EGP) (Epithelial glycoprotein 314) (EGP314) (hEGP314) (KS 1/4 antigen) (KSA) (Major gastrointestinal tumor-associated protein GA733-2) (Tumor-associated calcium signal transducer 1) (CD antigen CD326)
Gene name(s)	EPCAM GA733-2 M1S2 M4S1 MIC18 TACSTD1 TROP1	Organism	Epithelial cell adhesion molecule (Ep-CAM) (Adenocarcinoma-associated antigen) (Cell surface glycoprotein Trop-1) (Epithelial cell surface antigen) (Epithelial glycoprotein) (EGP) (Epithelial glycoprotein 314) (EGP314) (hEGP314) (KS 1/4 antigen) (KSA) (Major gastrointestinal tumor-associated protein GA733-2) (Tumor-associated calcium signal transducer 1) (CD antigen CD326)
Status	reviewed in uniprot database	Length	314
Mass	34,932	Activity regulation	N/A
Involvement in disease	Diarrhea 5, with tufting enteropathy, congenital (DIAR5)	Catalytic activity	N/A
PDB ID(s)	4MZV;6I07;
Function	May act as a physical homophilic interaction molecule between intestinal epithelial cells (IECs) and intraepithelial lymphocytes (IELs) at the mucosal epithelium for providing immunological barrier as a first line of defense against mucosal infection.

	Interaction ID	348
	Target type	Protein
	Target unique ID	P16422
	Activity	12 nM
	Binding Conditions/Buffer	DPBS with 5 mM MgCl2, 0.1 mg/ml tRNA, 0.1 mg/ml salmon sperm DNA and 5% FCS. The final concentration of MgCl2 was 2.5 mM
	Assay	Determination of equilibrium dissociation constants (K’d) for the interaction between serially truncated clones of epithelial cell adhesion molecule (EpCAM) aptamers and Kato III human gastric cancer cells
	PubMed ID	21281402

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_319	RNA	ACCCUGAUGGUAGACGCCGGGGUG	54.17%
Apta_1292	RNA	GGCACGUGUAUUACCCUAGUGGUCGACGUGCC	50.00%
Apta_85	RNA	UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA	48.57%
Apta_712	RNA	GGCGGUGCUCGCCGAAAGGCUCCUGGAUACGUC	48.48%
Apta_716	RNA	GGCGCUUCAUGCCGAAAGGCCCGUUGUAACGUC	48.48%
Apta_326	DNA	GCAACAGGGTATCCAAAGGATCAAA	48.00%
Apta_147	DNA	TGCGGTTGTAGTACTCGTGGCCG	47.83%
Apta_1	RNA	ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA	45.95%
Apta_95	RNA	CCGCGACAGUCGUAAGUUUUGACUGACUGAACGUU	45.71%
Apta_711	RNA	GGCGAUACCAGCCGAAAGGCCCUUGGCAGCGUC	45.45%
Apta_560	RNA	GGAAGAGAUGGCGACUAAAACGACUUGUCGC	45.16%
Apta_141	DNA	GTTGACGGGCGATTGGTCTT	45.00%
Apta_243	RNA	GCUUGAAGCUAGCAGUAAGACUAGCGCUACGGAUGGGUGUGCG	44.19%
Apta_23	DNA	TGTGGGGGTGGACGGGCCGAGTACG	44.00%
Apta_27	DNA	AGGGGGAGGGGTGGGGCCGGGCAGA	44.00%
Apta_29	DNA	AGAGGGGGGGGACGGCCCGGGTAGA	44.00%
Apta_231	RNA	GGGAGGACGAUGCGGGUGUGGGGCG	44.00%
Apta_329	DNA	GGCGTACGGTAGGCGGGGTCAACTG	44.00%
Apta_1086	DNA	GCAGTTGATCCTTTGGATACCCTGG	44.00%
Apta_1194	DNA	GGGAGAGGTGGGAGCGGGGCCAGGG	44.00%

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