Structural optimization of an aptamer generated from Ligand-Guided Selection (LIGS) resulted in high affinity variant toward mIgM expressed on Burkitt's lymphoma cell lines

• Published in: Biochimica et biophysica acta 2017-07, Vol.1861 (7), p.1825-1832
• Main Authors: Zümrüt, Hasan E., Batool, Sana, Van, Nabeela, George, Shanell, Bhandari, Sanam, Mallikaratchy, Prabodhika
• Format: Article
• Language: English
• Subjects: antibodies; Antibodies, Anti-Idiotypic - metabolism; Antibody Affinity; antigens; Aptamer; Aptamers, Peptide - chemistry; B-Cell Receptor; B-lymphocytes; Burkitt Lymphoma - immunology; Cell Line, Tumor; Humans; immunoglobulin M; Immunoglobulin M - metabolism; Ligands; LIGS; lymphoma; medicine; neoplasm cells; nucleic acids; oligonucleotides; screening; SELEX; SELEX Aptamer Technique; systematic evolution of ligands by exponential enrichment; temperature; truncation
• ISSN: 0304-4165; 0006-3002; 1872-8006; 1878-2434
• DOI: 10.1016/j.bbagen.2017.03.020

Aptamers are synthetic, short nucleic acid molecules capable of specific target recognition. Aptamers are selected using a screening method termed Systematic Evolution of Ligands by Exponential enrichment (SELEX). We recently have introduced a variant of SELEX called “Ligand-Guided-Selection” (LIGS) that allows the identification of specific aptamers against known cell-surface proteins. Utilizing LIGS, we introduced three specific aptamers against membrane-bound IgM (mIgM), which is the hallmark of B cells. Out of the three aptamers selected against mIgM, an aptamer termed R1, in particular, was found to be interesting due to its ability to recognize mIgM on target cells and then block anti-IgM antibodies binding their antigen. We systematically truncated parent aptamer R1 to design shorter variants with enhanced affinity. Importantly, herein we show that the specificity of the most optimized variant of R1 aptamer is similar to that of anti-IgM antibody, indicating that the specificity of the ligand utilized in selective elution of the aptamer determines the specificity of the LIGS-generated aptamer. Furthermore, we report that truncated variants of R1 are able to recognize mIgM-positive human B lymphoma BJAB cells at physiological temperature, demonstrating that LIGS-generated aptamers could be re-optimized into higher affinity variants. Collectively, these findings show the significance of LIGS in generating highly specific aptamers with potential applications in biomedicine. •An aptamer selected from Ligand-Guided-Selection (LIGS) can be truncated into shorter variants to improve affinity.•The specificity of the ligand utilized in selective elution determines the specificity of LIGS-generated aptamers.•A truncated variant of LIGS-generated aptamer recognizes cells expressing mIgM at physiological temperature.