9YXM

10-23 DNAzyme in complex with T7 RNA Polymerase

Summary for 9YXM

• Entry DOI: 10.2210/pdb9yxm/pdb
• EMDB information: 73611
• Descriptor: RNA polymerase, DNA (44-MER), DNA/RNA (5'-D(P*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*AP*GP*AP*AP*T)-R(P*A)-D(P*TP*TP*T)-3') (3 entities in total)
• Functional Keywords: 10-23 dnazyme, rna cleavage, t7 rna polymerase, scaffold, dna
• Biological source: Escherichia phage T7; More
• Total number of polymer chains: 3
• Total formula weight: 124075.77

Authors

Cramer, E.R.,Shultz, H.L.,Robart, A.R.,Purdy, M.D.,Cooper, D.R. (deposition date: 2025-10-27, release date: 2026-06-10)

Primary citation

Cramer, E.R.,Shultz, H.L.,Purdy, M.D.,Cooper, D.R.,Robart, A.R.
Mapping the Structure and Conformational Landscape of the 10-23 DNAzyme.
Acs Chem.Biol., 2026

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 . 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.

PubMed: 42179229
DOI: 10.1021/acschembio.6c00184

Experimental method

ELECTRON MICROSCOPY (4.62 Å)