Sulfur incorporation into nucleic acids accelerates enzymatic activity

Abstract

DNAzymes play a crucial role in biosensors for signal detection, but specific structures are required for diagnostic applications, complicating their design. This study reports a novel approach to the development of DNAzymes by incorporating sulfur atoms into nucleic acids via phosphorothioate (PS) bonds. Unlike traditional DNAzymes that rely on specific structures such as G-quadruplexes, this approach leads to high enzymatic activity without structural constraints. Computational analysis reveals that the change in the electron density of the nucleobases due to PS modification enhances interactions within the DNAzyme-H₂O₂-hemin complex, accelerating the rate-determining step and improving enzymatic activity. Systematic guidelines for the development of non-sequence constrained DNAzymes are provided by investigating the effect of the number of PS modifications, the length of the DNA, and various nucleobase combinations. α-thio-dNTP, a monomer containing PS, exhibits no observable enzymatic activity, but enzymatic activity is recorded for single-stranded DNA (ssDNA) containing PS. However, when the ssDNA is transformed into double-stranded DNA (dsDNA), the bases that react with hemin are blocked by hydrogen bonding, reducing enzymatic activity. An enzymogenic signaling system that differentiates between ssDNA and dsDNA is subsequently developed for sequence-specific colorimetric detection, demonstrating significant promise for overcoming the limitations of conventional DNAzymes in molecular diagnosis.