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Updated: Oct 19, 2026

CD Spectroscopy to Study DNA-Protein Interactions
Published on: February 10, 2022
ARCaDia-selected short DNA core positions a latent warhead for protein-gated covalent capture
Chaohui Li1, Naoyuki Miyashita1,2, Masayasu Kuwahara3
1Department of Engineering Science, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu Tokyo 182-8585 Japan jyang75@wisc.edu taki@pc.uec.ac.jp +81-42-443-5980.
Abstract:
A single-round affinity/reactivity co-selection of aptamer (ARCaDia), combined with Fast String-Based Clustering (FSBC) analysis of the selection output, identified a compact 10-nucleotide DNA-warhead core motif for streptavidin-selective covalent capture, showing that protein-gated covalent chemistry can arise from a short sequence-dependent placement of a latent warhead in a biotin-sensitive reaction microenvironment. This demonstrates that functional warhead-positioning information is already present after a single selection round.
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