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Updated: Jan 17, 2026

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

RaptScore: a large language model-based algorithm for versatile aptamer evaluation.

Akira Kimura-Yamazaki¹, Tatsuo Adachi², Shigetaka Nakamura²

¹Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku Okubo 3-4-1, 169-0072 Tokyo, Japan.

Nucleic Acids Research

|January 14, 2026

Summary

This summary is machine-generated.

Researchers developed RaptScore, a new metric using large language models to evaluate RNA aptamer binding activity. This tool identifies shorter, effective aptamers and improves discovery efficiency, reducing experimental work.

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Area of Science:

Biotechnology
Computational Biology
Drug Discovery

Background:

RNA aptamers are valuable tools in life sciences, particularly for drug discovery.
Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is a common method for aptamer generation but has limitations.
Existing evaluation metrics for aptamers are restricted to sequences found in SELEX and cannot assess varying lengths.

Purpose of the Study:

To develop a novel binding activity evaluation metric for RNA aptamers that overcomes SELEX limitations.
To enable assessment of arbitrary sequences, including those not identified by SELEX, and accommodate sequence length variations.
To enhance aptamer design optimization and discovery efficiency.

Main Methods:

Development of RaptScore, a new metric leveraging large language models for RNA aptamer binding activity evaluation.
Integration of RaptScore with in silico maturation for aptamer sequence optimization.
Combination of RaptScore with RaptGen, a variational autoencoder-based aptamer discovery tool.

Main Results:

RaptScore demonstrated a strong correlation with actual binding activity.
Identification of shorter RNA aptamers with maintained or enhanced binding properties.
Achieved a 10-nucleotide sequence truncation while preserving binding efficiency through RaptScore and in silico maturation.
Improved aptamer discovery efficiency when RaptScore was combined with RaptGen.

Conclusions:

RaptScore is a powerful tool for evaluating and optimizing RNA aptamer sequences.
The metric facilitates the discovery of high-activity aptamers, including shorter variants.
RaptScore significantly reduces experimental effort in aptamer research and development.