Insight into an oxidative DNA-cleaving DNAzyme: multiple cofactors, the catalytic core map and a highly efficient variant

SUMMARY An oxidative DNA-cleaving DNAzyme (PL) employs a double-cofactor model “X/Cu2+” for catalysis. Inhere, we verified that reduced nicotinamide adenine dinucleotide (NADH), flavin mononucleotide (FMN), cysteine, dithiothreitol, catechol, resorcinol, hydroquinone, phloroglucinol, o-phenylenediamine, 3,3',5,5'-tetramethylbenzidine (TMB) and hydroxylamine acted as cofactor X. According to their structure similarities or fluorescence property, we further confirmed that reduced nicotinamide adenine dinucleotide phosphate (NADPH), 2-mercaptoethanol, dopamine, chlorogenic acid, resveratrol and 5-carboxyfluorescein also played as cofactor X. Superoxide anions might be the commonality behind these cofactors. We subsequently determined the conservative change of individual nucleotides in the catalytic core under four different cofactor X. The nucleotides A4 and C5 are highly conserved, whereas the conservative levels of other nucleotides are dependent on the types of cofactor X. Moreover, we observed that the minor change in the PL’s secondary structure affects electrophoretic mobility. Finally, we characterized a highly efficient variant T3G and converted its double-cofactor NADH/Cu2+ to sole-cofactor NADH.