Improving aptamer performance with nucleic acid mimics: de novo and post-SELEX approaches. Issue 5 (May 2022)

• Record Type: Journal Article
• Authors: Oliveira, Ricardo; Pinho, Eva; Sousa, Ana Luísa; DeStefano, Jeffrey J.; Azevedo, Nuno Filipe; Almeida, Carina
• Is Part Of: Trends in biotechnology. Volume 40:Issue 5(2022)
• Page Start: 549
• Page End: 563
• Publication Date: 2022-05
• Subjects: aptamers -- de novo systematic evolution of ligands by exponential enrichment (SELEX) -- post-SELEX modifications -- nucleic acid mimics -- engineered polymerases -- xeno nucleic acids; Biotechnology -- Periodicals; Biochemical engineering -- Periodicals; Genetic engineering -- Periodicals; Industrial microbiology -- Periodicals; 660.605
• DOI: 10.1016/j.tibtech.2021.09.011
• Languages: English
• ISSNs: 0167-7799

Abstract

Abstract : Aptamers are structural single-stranded oligonucleotides generated in vitro to bind to a specific target molecule. Aptamers' versatility can be enhanced with nucleic acid mimics (NAMs) during or after a selection process, also known as systematic evolution of ligands by exponential enrichment (SELEX). We address advantages and limitations of the technologies used to generate NAM aptamers, especially the applicability of existing engineered polymerases to replicate NAMs and methodologies to improve aptamers after SELEX. We also discuss the limitations of existing methods for sequencing NAM sequences and bioinformatic tools to predict NAM aptamer structures. As a conclusion, we suggest that NAM aptamers might successfully compete with molecular tools based on proteins such as antibodies for future application. Highlights: Nucleic acid mimics (NAMs) add new conformational motifs and chemical groups that improve the binding affinity and stability of aptamers, boosting their applicability in vivo . De novo systematic evolution of ligands by exponential enrichment (SELEX) is limited by access to unnatural nucleotides and enzymes that can use unnatural nucleotides as substrates. Engineered polymerases can perform de novo selection of NAM aptamers, but the protocol still is complex and time consuming. The post-SELEX approach lacks the complexity of de novo SELEX because NAM aptamers are chemically synthetized. However, inserting unnatural nucleotides often disturbs aptamer binding interactions, and the effects of such modifications are difficult to establish. Computational tools to predict tertiary structure and docking elucidate aptamer–target interactions and allow tailored modifications that reduce the experimental time of the conventional trial-and-error approach.