The L1 cell adhesion molecule (L1CAM) plays important roles in the development and plasticity of the nervous system as well as in tumor formation, progression, and metastasis. New ligands are necessary tools for biomedical research and the detection of L1CAM. Here, DNA aptamer yly12 against L1CAM was optimized to have much stronger binding affinity (10–24 fold) at room temperature and 37 °C via sequence mutation and extension. This interaction study revealed that the optimized aptamers (yly20 and yly21) adopted a hairpin structure containing two loops and two stems. The key nucleotides for aptamer binding mainly located in loop I and its adjacent area. Stem I mainly played the role of stabilizing the binding structure. The yly-series aptamers were demonstrated to bind the Ig6 domain of L1CAM. This study reveals a detailed molecular mechanism for the interaction between yly-series aptamers and L1CAM and provides guidance for drug development and detection probe design against L1CAM.
Cell-SELEX is a powerful tool to generate aptamers that
specifically
bind the native molecules on living cells. Here, we report an aptamer
ZAJ4a generated by cell-SELEX. The molecular target of ZAJ4a was pulled
down by the enriched cell-SELEX pool and identified to be the receptor-type
tyrosine-protein phosphatase F (PTPRF) through a stable isotope labeling
using amino acids in cell culture (SILAC)-based quantitative proteomic
method. ZAJ4a showed high binding affinity with nanomolar range to
cancer cells expressing PTPRF. Meanwhile, PTPRF was proven to highly
express on several cancer cell lines using ZAJ4a as a molecular probe
and to highly express in many kinds of cancer samples using gene expression
profiling interactive analysis (GEPIA2) from the TCGA and GTEx databases.
These results indicate that the aptamer generated by cell-SELEX showed
good specificity at the molecular level. This cell-SELEX and target
identification strategies show great potential for identifying biomarkers
on the cell surface.
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