Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1032
Aptamer sequence: TCCAGCACTCCACGCATAACCCCGTCCTCGGAAAGAGCGCGGGCCTGGGACGGCTACTGCCCGGATTTATGTGTTATGCGTGCGACGGTGAA
Target unique ID: P16422
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_949 | XMU3 | Protein | EPCAM_HUMAN | 9.3 nM | PBS containing 0.55 mM MgCl2 and 0.2 mg/mL yeast tRNA, pH = 7.4 | 33206450 |
Structure information of aptamer
| Aptamer Sequence: | TCCAGCACTCCACGCATAACCCCGTCCTCGGAAAGAGCGCGGGCCTGGGACGGCTACTGCCCGGATTTATGTGTTATGCGTGCGACGGTGAA |
| 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
Aptamer information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Aptamer ID | Apta_949 | Description | XMU3 |
| Aptamer chemistry | DNA | Length | 92 nt |
| GC content | 60.9% | Molecular weight | 28,366.10 Da |
| Molarity of 1 μg/μl solution | 35.25 μM | Number of G-quadruplexes | 2 |
| G-Score | 17 | Function | Targeted binding |
| Sequence | TCCAGCACTCCACGCATAACCCCGTCCTCGGAAAGAGCGCGGGCCTGGGACGGCTACTGCCCGGATTTATGTGTTATGCGTGCGACGGTGAA | ||
| Applications | XMU3-bcd aptamer can directly regulate the cell adhesion via the “structure-binding affinity-protein function” pathway, rather than following the Central Dogma | ||
Target information
| 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. |
Activity data
 |
Interaction ID | 1032 |
| Target type | Protein | |
| Target unique ID | P16422 | |
| Activity | 9.3 nM | |
| Binding Conditions/Buffer | PBS containing 0.55 mM MgCl2 and 0.2 mg/mL yeast tRNA, pH = 7.4 |
|
| Assay | A) Schematic illustration of the formation of aptamer-ZNCTS-EpCAM complex. B) The binding affinity curves of XMU3-bcd aptamer with EpCAM by flow cytometry in the presence and absence of Z-NCTS |
|
| PubMed ID | 33206450 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_99 | DNA | AGCAGCACAGAGGTCAGATGTCGGGCGGTTCGGGACCTTGCTGCGACATATGCGTATTATCCTATGCGTGCTACCGTGAA | |
| Apta_99 | DNA | AGCAGCACAGAGGTCAGATGTCGGGCGGTTCGGGACCTTGCTGCGACATATGCGTATTATCCTATGCGTGCTACCGTGAA | |
| Apta_103 | DNA | AGCAGCACAGAGGTCAGATGCATCGCATTATTCGCGGCCGGCCAACGAGAGTATGTTTCTCCTATGCGTGCTACCGTGAA | |
| Apta_103 | DNA | AGCAGCACAGAGGTCAGATGCATCGCATTATTCGCGGCCGGCCAACGAGAGTATGTTTCTCCTATGCGTGCTACCGTGAA | |
| Apta_101 | DNA | AGCAGCACAGAGGTCAGATGTGTTAGGCTGGGACACGTATTACACTTACCGTAAATATTTCCTATGCGTGCTACCGTGAA | |
| Apta_107 | DNA | AGCAGCACAGAGGTCAGATGTTCATTTCAGTTGACCGATAGCATTGAGCAATGATCTATTCCTATGCGTGCTACCGTGAA | |
| Apta_110 | DNA | AGCAGCACAGAGGTCAGATGGTTAGGAAGGTGAATAGGTACGACTGCAGGTCTATCGCAGCCTATGCGTGCTACCGTGAA | |
| Apta_101 | DNA | AGCAGCACAGAGGTCAGATGTGTTAGGCTGGGACACGTATTACACTTACCGTAAATATTTCCTATGCGTGCTACCGTGAA | |
| Apta_107 | DNA | AGCAGCACAGAGGTCAGATGTTCATTTCAGTTGACCGATAGCATTGAGCAATGATCTATTCCTATGCGTGCTACCGTGAA | |
| Apta_110 | DNA | AGCAGCACAGAGGTCAGATGGTTAGGAAGGTGAATAGGTACGACTGCAGGTCTATCGCAGCCTATGCGTGCTACCGTGAA | |
| Apta_104 | DNA | AGCAGCACAGAGGTCAGATGCAAACCACAGCCTGAGTGGTTAGCGTATGTCATTTACGGACCTATGCGTGCTACCGTGAA | |
| Apta_105 | DNA | AGCAGCACAGAGGTCAGATGATGCTCTAGGCGAAAGACTTGGCGTAGAACGACGGGAGGCCCTATGCGTGCTACCGTGAA | |
| Apta_109 | DNA | AGCAGCACAGAGGTCAGATGTGCGACCACCTGGATAGACGAGGGTAGTAAGGAGTGTGTTCCTATGCGTGCTACCGTGA | |
| Apta_104 | DNA | AGCAGCACAGAGGTCAGATGCAAACCACAGCCTGAGTGGTTAGCGTATGTCATTTACGGACCTATGCGTGCTACCGTGAA | |
| Apta_105 | DNA | AGCAGCACAGAGGTCAGATGATGCTCTAGGCGAAAGACTTGGCGTAGAACGACGGGAGGCCCTATGCGTGCTACCGTGAA | |
| Apta_109 | DNA | AGCAGCACAGAGGTCAGATGTGCGACCACCTGGATAGACGAGGGTAGTAAGGAGTGTGTTCCTATGCGTGCTACCGTGA | |
| Apta_173 | DNA | AGCAGCACAGAGGTCAGATGGCAGGTTTCGACGTACAATGCTATGGAGGCTTTATGATCGCCTATGCGTGCTACCGTGAA | |
| Apta_232 | DNA | AGCAGCACAGAGGTCAGATGCTATGAGCAGATCCGATAGAAAGTTAATGCCCTAGAACATCCTATGCGTGCTACCGTGAA | |
| Apta_1105 | DNA | TACGACTCACTATAGGGATCCAATGGCACAGCGCCTGGAACGTACTCTGTACCTGGAATTCCCTTTAGTGAGGGTT | |
| Apta_61 | DNA | AGCAGCACAGAGGTCAGATGGCAGGTAAGCAGGCGGCTCACAAAACCATTCGCATGCGGCCCTATGCGTGCTACCGTGAA |
DEV TOOL
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