A Stereochemical Glimpse of the Active Site of the 8−17 Deoxyribozyme from Iodine-Mediated Cross-Links Formed with the Substrate’s Scissile Site
Bibliographic record
Abstract
A powerful approach for defining the active site of a complexly folded ribozyme or deoxyribozyme (DNAzyme) is to map the contact cross-links formed between the substrate's reaction site and component residues of the enzyme. Here, we use a novel iodine- and phosphorothioate-mediated method for generating contact cross-links to define key residues of the 8-17 DNAzyme most proximal to the scissile phosphodiester of its bound substrate. Substitution of a phosphorothioate for the scissile phosphodiester renders that site chiral. The cross-linking maps we obtain using chirally resolved substrates give us, for the first time, a stereochemical glimpse of the 8-17's active site. Thus, we identifiy the asymmetric positioning of the DNAzyme's C13 residue, which is catalytically indispensable. We also identify, for the first time, the previously unheralded C3 residue. On the basis of the latter's proximal location to the cleavage site and the impact of its mutation on the DNAzyme's catalytic rate, we hypothesize it may play an acid-base role in the catalysis of the 8-17 DNAzyme. Overall, the approach described in this paper should find wide application in the study of the tertiary folding of RNAs and DNAs, as well as of complexes formed by RNA and DNA with proteins and other ligands.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".