Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 143
Aptamer sequence: TTTACTTATTCAATTCCCGTGGGAAGGCTATAGAGGGGCCAGTCTATGAATAAGTTT
Target unique ID: P14151
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_918 Sgc-3b Protein LYAM1_HUMAN N/A PBS with 5 mm MgCl2, 1 mm CaCl2, and 0.1 mg/ml herring sperm DNA 26199357
Structure information of aptamer
Aptamer Sequence: TTTACTTATTCAATTCCCGTGGGAAGGCTATAGAGGGGCCAGTCTATGAATAAGTTT
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_918 Description Sgc-3b
Aptamer chemistry DNA Length 57 nt
GC content 40.4% Molecular weight 17,627.33 Da
Molarity of 1 μg/μl solution 56.73 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence TTTACTTATTCAATTCCCGTGGGAAGGCTATAGAGGGGCCAGTCTATGAATAAGTTT
Applications Targeted binding to selectin L protein
Target information
Type Detail Type Detail
Uniprot ID P14151 Protein name L-selectin (CD62 antigen-like family member L) (Leukocyte adhesion molecule 1) (LAM-1) (Leukocyte surface antigen Leu-8) (Leukocyte-endothelial cell adhesion molecule 1) (LECAM1) (Lymph node homing receptor) (TQ1) (gp90-MEL) (CD antigen CD62L)
Gene name(s) SELL LNHR LYAM1 Organism L-selectin (CD62 antigen-like family member L) (Leukocyte adhesion molecule 1) (LAM-1) (Leukocyte surface antigen Leu-8) (Leukocyte-endothelial cell adhesion molecule 1) (LECAM1) (Lymph node homing receptor) (TQ1) (gp90-MEL) (CD antigen CD62L)
Status reviewed in uniprot database Length 372
Mass 42,187 Activity regulation N/A
Involvement in disease N/A Catalytic activity N/A
PDB ID(s)
2LGF;3CFW;5VC1;
Function Calcium-dependent lectin that mediates cell adhesion by binding to glycoproteins on neighboring cells.
Activity data
Interaction ID 143
Target type Protein
Target unique ID P14151
Activity N/A
Binding Conditions/Buffer

PBS with 5 mm MgCl2, 1 mm CaCl2, and 0.1 mg/ml herring sperm DNA

Assay

Flow cytometry for validating CD62L as a target for aptamer Sgc-3b. (A) Flow cytometry assay of Jurkat E6-1 cells stained with Sgc-3b-FAM and anti-CD62L-PE FAM-labeled random DNA (L45-FAM) and IgG-PE, which do not bind to cells, were used as the negative controls. (B) Flow cytometry results to show the competition of different concentrations of Sgc-3b-FAM with 0.62 g/ml anti-CD62L-PE in binding toward Jurkat E6-1 cells. (C) Flow cytometry results to show the competition of 5 g/ml anti-CD62L-PE with 100 nM Sgc-3b-FAM in binding toward Jurkat E6-1 cells. (D) Flow cytometry assay results showed that the siRNA-mediated depletion of CD62L in Jurkat E6-1 cells led to a reduced binding of aptamer Sgc-3b, but not aptamer Sgc-4e. Binding toward anti-CD62L, Sgc-3b and Sgc-4e were assessed at 72 h after siRNA treatment, where reduced binding toward anti-CD62L indicated the successful, albeit modest, knock-down of CD62L after siRNA treatment

PubMed ID 26199357
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_450 DNA ATACCAGCTTATTCAATTACATGTCCTGAAGGGGAATAATATACAGCTTTGGGTGGGTAGATAGTAAGTGCAATCT 55.26%
Apta_31 DNA ATACCAGTCTATTCAATTGGGCCCGTCCGTATGGTGGGTGTGCTGGCCAGATAGTATGTGCAATCA 54.55%
Apta_1016 DNA ATACCAGCTTATTCAATTTCTTCGCCAGTGCCAGGATCTCAGTTGGCGGTTCATTAGCTGGGTTGGTCGAAGATAGTAAGTGCAATCT 54.55%
Apta_1187 DNA TGTACCGTCTGAGCGATTCGTACTTTATTCGGGAAGGGTATCAGCGGGGTTCAACAAGCCAGTCAGTGTTAAGGAGTGC 54.43%
Apta_1081 DNA CTTACGACTGTGGTCGGGTGGTGGGCCTCTAGAGGGGTGTCGTAAG 54.39%
Apta_451 DNA ATACCAGCTTATTCAATTGAGTAAGAGTGCACTATGTTTTACGAGCCGTTTCCTCGGCAGATAGTAAGTGCAATCT 52.63%
Apta_813 DNA TAGAGATATGACAGCGGGGAAGGTTAAGAGGCGCTAGGAG 52.63%
Apta_987 DNA GTACTGTCAATTGGAAGTGGTGTTACGTTGTGTAGTCAAATCAGTGC 52.63%
Apta_1045 DNA GGTGCTCAGGGAACTGTCTGAGGGATCAGGCTTAAGCCTGTCGAGCAGTT 52.63%
Apta_1235 DNA TGTACCGTCTGAGCGATTCGTACGATCGGGTCGGGGTCTATTTTAGGGCCATTTGGCAGCCAGTCAGTGTTAAGGAGTGC 52.50%
Apta_1015 DNA ATACCAGCTTATTCAATTGACCCGTTTCGTTCCCTCTGGGAAGTTTAGCCCAGTTGCCTGGGCGATACCAAGATAGTAAGTGCAATCT 52.27%
Apta_1104 DNA TACGACTCACTATAGGGATCCCCCCGAGTGAAGAGCAGGACAGCGGGACAGCGTCGAATTCCCTTTAGTGAGGGTT 51.32%
Apta_1110 DNA GTTGACGGATCCCTATTGCAGTGCTTGAGAGAGACCTCGCGTATATTTCGGAAGACCACGTGTAATGCCCCTAACT 51.32%
Apta_495 DNA GGGAATGGATCCACATCTACGTATTACTGCTGGTGACGAGGGCTAGACGACGTACCTTCACTGCAGACTTGACGAAGCTT 51.25%
Apta_1011 DNA GCTGTGTGACTCCTGCAATGGTAGCGGGTAGGGGAGGGAGGGTGAATGGAGGATGTTCATGGCAGCTGTATCTTGTCTCC 51.25%
Apta_792 DNA ATACCAGCTTATTCAATTCCCAAATTGCCACCACTTACAGCATGATAACATACTACATCTTTTCATCAAGATAGTAAGTGCAATCT 51.16%
Apta_805 DNA ATACCAGCTTATTCAATTAGGCGGTGCATTGTGGTTGGTAGTATACATGAGGTTTGGTTGAGACTAGTCGCAAGATATAGATAGTAAGTGCAATCT 51.04%
Apta_625 DNA ATACCAGCTTATTCAATTCAGGGCGGTATGAGGCTCGATCAAGGTCGGAGCGAGAATTTTTTCGCGGAGTCGGCTGGATCAGATAGTAAGTGCAATCT 51.02%
Apta_625 DNA ATACCAGCTTATTCAATTCAGGGCGGTATGAGGCTCGATCAAGGTCGGAGCGAGAATTTTTTCGCGGAGTCGGCTGGATCAGATAGTAAGTGCAATCT 51.02%
Apta_238 DNA CACACATTCCCGTCCTCGATACGTCTAGGCTTAGTGCCACTTGCTTAATC 50.88%