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| Title | Mapping the Structure and Conformational Landscape of the 10-23 DNAzyme. |
|---|---|
| Journal, issue, pages | ACS Chem Biol, Year 2026 |
| Publish date | May 25, 2026 |
 Authors | Evan R Cramer / Holly L Shultz / Michael D Purdy / David R Cooper / Aaron R Robart /  |
| 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 ...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 . 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. |
 External links | ACS Chem Biol / PubMed:42179229 |
| Methods | EM (single particle) |
| Resolution | 4.62 Å |
| Structure data | EMDB-73611, PDB-9yxm: |
| Source |
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 Keywords | DNA / 10-23 DNAzyme / RNA cleavage / T7 RNA Polymerase / Scaffold |
escherichia phage t7 (virus)