RaptGen-Assisted Generation of an RNA/DNA Hybrid Aptamer Against SARS-CoV-2 Spike Protein

Overview

Journal Biochemistry

Specialty Biochemistry

Date 2024 Mar 8

PMID 38457656

Authors

Tatsuo Adachi

Shigetaka Nakamura

Akiya Michishita

Daiki Kawahara

Mizuki Yamamoto

Michiaki Hamada

Yoshikazu Nakamura

Affiliations

Soon will be listed here.

Abstract

Optimization of aptamers in length and chemistry is crucial for industrial applications. Here, we developed aptamers against the SARS-CoV-2 spike protein and achieved optimization with a deep-learning-based algorithm, RaptGen. We conducted a primer-less SELEX against the receptor binding domain (RBD) of the spike with an RNA/DNA hybrid library, and the resulting sequences were subjected to RaptGen analysis. Based on the sequence profiling by RaptGen, a short truncation aptamer of 26 nucleotides was obtained and further optimized by a chemical modification of relevant nucleotides. The resulting aptamer is bound to RBD not only of SARS-CoV-2 wildtype but also of its variants, SARS-CoV-1, and Middle East respiratory syndrome coronavirus (MERS-CoV). We concluded that the RaptGen-assisted discovery is efficient for developing optimized aptamers.

Citing Articles

A Truncated Multi-Thiol Aptamer-Based SARS-CoV-2 Electrochemical Biosensor: Towards Variant-Specific Point-of-Care Detection with Optimized Fabrication.

Molina Ramirez S, Samiseresht N, Martinez-Roque M, Catania F, Graef K, Rabe M Biosensors (Basel). 2025; 15(1).

PMID: 39852074 PMC: 11763500. DOI: 10.3390/bios15010024.

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