Single-Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics

DNAzyme is a class of DNA molecules that can perform catalytic functions with high selectivity towards specific metal ions. Due to its potential applications for biosensors and medical therapeutics, DNAzyme has been extensively studied to characterize the relationships between its biochemical properties and functions. Similar to protein enzymes and ribozymes, DNAzymes have been found to undergo conformational changes in a metal-ion-dependent manner for catalysis. Despite the important role the conformation plays in the catalysis process, such structural and dynamic information might not be revealed by conventional approaches. Here, by using the single-molecule fluorescence resonance energy transfer (smFRET) technique, we were able to investigate the detailed conformational dynamics of a uranyl-specific DNAzyme 39E. We observed conformation switches of 39E to a folded state with the addition of Mg2+ and to an extended state with the addition of UO22+. Furthermore, 39E can switch to a more compact configuration with or without divalent metal ions. Our findings reveal that 39E can undergo conformational changes spontaneously between different configurations.

Automated summary

DNAzyme is a class of DNA molecules that can catalyze specific metal ions with high selectivity. Conformational changes in DNAzymes play an important role in catalysis, and these changes can be studied using the smFRET technique. In the case of a uranyl-specific DNAzyme 39E, conformational switches were observed to folded and extended states with the addition of Mg2+ and UO22+ respectively. The findings also showed that 39E can spontaneously undergo conformational changes between different configurations, with or without divalent metal ions.