pH-controlled DNAzymes: Rational design and their applications in DNA-machinery devices

The availability and reliability of strategies for molecular biosensing over a finely adjustable dynamic range is essential to enhance the understanding and control of vital biological process. To expand the versatility and utility of nucleic acidrelated enzymes, we demonstrated a rational approach to acquiring tunable, pH-dependent deoxyribozymes (DNAzymes) with catalytic activities and response sensitivities that can be tuned through a simple change in solution pH. To do this, we capitalized upon the pH dependence of Hoogsteen interactions and designed i-motif- and triplex-based DNAzymes that can be finely regulated with high precision over a physiologically relevant pH interval. The modified DNAzymes are dependent upon pH for efficient cleavage of substrates, and their catalytic performance can be tuned by regulating the sequence of inserted i-motif/triplex structures. The principle of tunable, pH-dependent DNAzymes provides the opportunity to engineer pH-controlled DNA-machinery devices with unprecedented sensitivity to pH changes. For example, we constructed a DNA-walker device, the stepping rate of which could be adjusted by simply modulating solution pH within an interval of 5.6 to 7.4, as well as a DNA tetrahedron that can be opened at pH 6.4 and kept closed at pH 7.4. The potential of this approach is not limited to serve as pH-dependent devices, but rather may be combined with other elements to expand their practical usefulness.