Download MendeleyMapping the Structure and Conformational Landscape of the 10-23 DNAzyme.
Cramer, E.R., Shultz, H.L., Purdy, M.D., Cooper, D.R., Robart, A.R.(2026) ACS Chem Biol
- PubMed: 42179229 Search on PubMed
- DOI: https://doi.org/10.1021/acschembio.6c00184
- Primary Citation Related Structures:
9YXM - PubMed Abstract:
Deoxyribozymes (DNAzymes) are programmable DNA catalysts with therapeutic and diagnostic potential. The RNA-cleaving 10-23 DNAzyme was the first DNAzyme shown to function using common bioavailable metal ion cofactors, establishing the potential for DNA-based RNA knockdown in vivo . Despite extensive biochemical characterization, structural knowledge on the 10-23 DNAzyme is limited, hindering efforts to rationally improve its activity for physiological applications. To address this need, we developed a T7 RNA polymerase-based protein scaffold that enables cryo-EM visualization of the 10-23 DNAzyme. Using this approach, we obtained a 4.5 Å reconstruction of the DNAzyme-substrate complex and used dimethyl sulfate (DMS) labeling to further examine DNAzyme dynamics. Our structural work supports a model in which the palindromic core folds into a pseudoknot stabilized by guanine stacking, creating a rigid element that organizes subsequent folding of the catalytic core and active site. DMS probing further indicates that magnesium binding collapses a flexible A9-A15 loop onto the pseudoknot, compacting the catalytic core. Together, these findings provide insight into 10-23 DNAzyme dynamics through a proposed metal-dependent hinged activation mechanism. The protein scaffolding approach may also serve as a broadly applicable framework for further structural investigations of DNAzymes.
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia 26506, United States.
Organizational Affiliation:
