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Biochim Biophys Acta Gen Subj. 2019 Jan;1863(1):232-240. doi: 10.1016/j.bbagen.2018.10.006. Epub 2018 Oct 17.

Dimerization of an aptamer generated from Ligand-guided selection (LIGS) yields a high affinity scaffold against B-cells.

Author information

1
Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd, NY 10468, USA.
2
Immunology Program, Memorial Sloan Kettering Cancer Center, 408 E69th street, New York, NY, 10021, USA.
3
Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
4
Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd, NY 10468, USA; Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA; Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA. Electronic address: prabodhika.mallikaratchy@lehman.cuny.edu.

Abstract

Nucleic Acid Aptamers (NAAs) are a class of synthetic DNA or RNA molecules that bind specifically to their target. We recently introduced an aptamer termed R1.2 against membrane Immunoglobulin M (mIgM) expressing B-cell neoplasms using Ligand Guided Selection (LIGS). While LIGS-generated aptamers are highly specific, their lower affinity prevents aptamers from being used for translational applications. Highly specific aptamers with higher affinity can increase targetability, boosting the application of aptamers as diagnostic and therapeutic molecules. Herein, we report that dimerization of R1.2, an aptamer generated from LIGS, leads to high affinity variants without compromising the specificity. Three dimeric aptamer analogues with variable linker lengths were designed to evaluate the effect of linker length in affinity. The optimized dimeric R1.2 against cultured B-cell neoplasms, four donor B-cell samples and mIgM-positive Waldenström's Macroglobulinemia (WM) showed specificity. Furthermore, confocal imaging of dimeric aptamer and anti-IgM antibody in purified B-cells suggests co-localization. Binding assays against IgM knockout Burkitt's Lymphoma cells utilizing CRISPR/Cas9 further validated specificity of dimeric R1.2. Collectively, our findings show that LIGS-generated aptamers can be re-engineered into dimeric aptamers with high specificity and affinity, demonstrating wide-range of applicability of LIGS in developing clinically practical diagnostic and therapeutic aptamers.

KEYWORDS:

Aptamer; B-cell lymphoma; Dimerization; Ligand-guided selection; mIgM

PMID:
30342154
PMCID:
PMC6248343
[Available on 2020-01-01]
DOI:
10.1016/j.bbagen.2018.10.006
[Indexed for MEDLINE]

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