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• W3209157902 endingPage "563" @default.
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• W3209157902 abstract "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. 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. 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. strength of the aptamer interaction with its unique target, usually characterized by the solution equilibrium dissociation constant (Kd, M−1). the multidimensional property space spanned by all possible molecules and chemical compounds. In terms of aptamers, the limits of biologically relevant chemical space are defined by the specific binding interactions between target molecules and the 3D molecular recognition patterns on aptamers. SELEX methodology applied to the discovery of new aptamers for a specific target molecule. The application of modified nucleotides in de novo SELEX involves their insertion at the beginning of the selection process through the synthesis of an initial pool with NAMs. oligonucleotide-containing chemical modifications on the heterocyclic base or sugar-phosphate backbone that confer different structural, chemical, and biological characteristics to native nucleic acids. It includes unnatural nucleotides with a typical structure: a nucleobase, a five-carbon sugar (ribose or deoxyribose), and a phosphate moiety; or nucleic acid analogues with atypical structures, such as peptide nucleic acids. process for the selection of aptamers that involves repetitive steps of partitioning with no amplification steps between them. approach used to replace specific residues by modified nucleotides in aptamers previously obtained by SELEX processes. Ideally, this approach requires rational planning to improve some characteristics, such as stability, without affecting the binding affinity of the original aptamer. combinatorial selection technique in molecular biology for developing single-stranded oligonucleotides, called ‘aptamers,’ that specifically bind to a target molecule. It can be summarized in four steps: (i) a random library of nucleic acid molecules is synthesized and (ii) challenged to bind to a target under an established set of conditions; (iii) the molecules capable of binding with the target are separated from the unbound sequences; and (iv) those molecules are amplified by PCR to generate an enriched population of binding sequences. This process is repeated for several rounds until potential aptamers for the target are selected. At the end, it is anticipated that the diversity present in the initial pool (~1013 to 1015 different sequences) and the stringency of the selection/amplification rounds, provide ligands with high affinity. Recovering a high-affinity aptamer using SELEX is a complex and time-consuming procedure that can take weeks to months. aptamer property of selective binding to the chosen target to the detriment of the noncognate target. aptamer ability to establish a stable complex in different chemical (e.g., temperature, pH, and ionic strength) and biological conditions (e.g., nuclease degradation). oligonucleotides containing unnatural nucleotides with chemical modifications on the sugar moiety that confer different structural, chemical, and biological characteristics to the nucleic acids." @default.
• W3209157902 created "2021-11-08" @default.
• W3209157902 creator A5008742438 @default.
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• W3209157902 creator A5040223728 @default.
• W3209157902 creator A5049438791 @default.
• W3209157902 date "2022-05-01" @default.
• W3209157902 modified "2023-10-12" @default.
• W3209157902 title "Improving aptamer performance with nucleic acid mimics: de novo and post-SELEX approaches" @default.
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