Influence of C5‐Substituents on Repair of <i>O</i> <sup>4</sup> ‐Methyl Adducts of Pyrimidines by <i>O</i> <sup>6</sup> ‐Alkylguanine DNA Alkyltransferases
Bibliographic record
Abstract
Abstract The DNA repair protein O 6 ‐alkylguanine‐DNA alkyltransferase (AGT), found in numerous organisms, can remove methyl groups from the O 6 ‐ and O 4 ‐atoms of 2′‐deoxyguanosine and thymidine in DNA. AGT variants demonstrate different repair efficiencies towards these lesions. To understand the influence of C5 nucleobase substituents on O 4 ‐methyl removal by AGTs, DNA duplexes containing 5‐chloro‐, 5‐bromo‐ 5‐iodo‐ and 5‐trifluoromethyl‐ O 4 ‐methyl‐2′‐deoxyuridine were studied. UV thermal denaturation revealed a stability reduction of 11 °C for the O 4 ‐methyl halogen series and 5‐trifluoromethyl analog relative to their controls. For the 5‐chloro analog efficient repair was observed by human and E.coli AGTs. For the larger halogens (5‐bromo and 5‐iodo) and 5‐trifluoromethyl analog, human AGT showed moderate repair of the O 4 ‐methyl adduct. E.coli OGT and Ada‐C readily repaired most adducts with reduced efficiency for the larger groups, except C5‐iodo. These results suggest electronic contributions and favourable interactions of the C5‐halogens within the AGT active site contribute to efficient dealkylation.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 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".