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Updated: Aug 18, 2026

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes
Published on: November 1, 2012
RNA/DNA hybrid duplexes with identical nearest-neighbor base-pairs have identical stability
N Sugimoto1, M Katoh, S Nakano
1Department of Chemistry, Faculty of Science, Konan University, Kobe, Japan.
Abstract:
Energetic behaviors of eight pairs of RNA/DNA hybrid duplexes with identical nearest neighbors have been investigated by UV melting analysis. In the pairs with identical nearest-neighbor pairs, the melting curve traces at the same strand concentration were very similar. The average difference in stabilization energy of these pairs was 4%, which was about expected within experimental error. These results indicate that the nearest-neighbor model is valid for predicting the stability of RNA/DNA hybrid duplexes as well as RNA/RNA and DNA/DNA duplexes.
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