Ligase-mediated synthesis of CuII-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases

• Published in: Chemical science (Cambridge) Vol. 15; no. 7; pp. 2365 - 2370
• Main Authors: Takezawa, Yusuke, Zhang, Hanci, Mori, Keita, Hu, Lingyun, Shionoya, Mitsuhiko
• Format: Journal Article
• Language: English
• Published: Cambridge Royal Society of Chemistry 14.02.2024; The Royal Society of Chemistry
• Subjects: Chemical synthesis; Chemistry; Deoxyribonucleic acid; DNA; Hydrogen bonding
• ISSN: 2041-6520; 2041-6539
• DOI: 10.1039/d3sc05042d

A CuII-responsive allosteric DNAzyme has been developed by introducing bifacial 5-carboxyuracil (caU) nucleobases, which form both hydrogen-bonded caU–A and metal-mediated caU–CuII–caU base pairs. The base sequence was logically designed based on a known RNA-cleaving DNAzyme so that the caU-modified DNAzyme (caU-DNAzyme) can form a catalytically inactive structure containing three caU–A base pairs and an active form with three caU–CuII–caU pairs. The caU-DNAzyme was synthesized by joining short caU-containing fragments with a standard DNA ligase. The activity of caU-DNAzyme was suppressed without CuII, but enhanced 21-fold with the addition of CuII. Furthermore, the DNAzyme activity was turned on and off during the reaction by the addition and removal of CuII ions. Both ligase-mediated synthesis and CuII-dependent allosteric regulation were achieved by the bifacial base pairing properties of caU. This study provides a new strategy for designing stimuli-responsive DNA molecular systems.