Unusual DNA−DNA Cross-Links between a Photolyase Deoxyribozyme, UV1C, and Its Bound Oligonucleotide Substrate
Bibliographic record
Abstract
UV1C is a photolyase deoxyribozyme that repairs thymine dimers in a DNA oligonucleotide substrate. We report that treatment with iodine generates specific DNA-DNA cross-links between UV1C and a bound substrate analogue, LDPs, in which a single phosphate at the photoreactivation site has been replaced with a phosphorothioate. Although iodine has been reported to generate lysine-cysteine cross-links within a protein, the formation of DNA-DNA cross-links is both unexpected and novel. We have used different mapping procedures to identify a number of bases located in loops of the G-quadruplex fold of UV1C as the sites for cross-linking with LDPs. Mutation of one cross-linking adenine, in particular, leads to a major reduction in UVIC's catalytic activity. A map of these contact cross-linking sites enables us to refine an earlier structural-topological model for the folded UV1C.LDPs complex. The surprising facility with which these novel contact cross-links can be generated between a nucleic acid enzyme and its substrate's reaction site opens up a powerful new approach to mapping the active sites of different ribozymes and deoxyribozymes as well as enabling the dissection of key contacts within RNA-protein complexes.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| 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 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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 source (direct Gemma or distilled Codex), 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".