DNA end sequestration by DNA‐dependent protein kinase and end joining of sterically constrained substrates in whole‐cell extracts
Bibliographic record
Abstract
Extracts of Xenopus eggs and of cultured human and hamster cells have the capacity to join nonhomologous DNA ends, and all do so with similar specificity. To examine the formation of repair complexes on DNA under conditions of end joining, end-labeled fragments were incubated with the various extracts and then subjected to DNase-I footprinting. Human and Xenopus extracts produced footprints virtually identical to that of purified DNA-dependent protein kinase holoenzyme (Ku plus DNA-PKcs), with protection of the terminal 28 bp. Extracts of hamster cells were more variable, but usually produced a 16-bp footprint, similar to that of Ku alone. In all cases a 28-bp holoenzyme-like footprint was associated with wortmannin-sensitive end joining, minimal 3'-5' exonucleolytic resection, and a predominance of accurate end-joining products. To determine whether the short segments of DNA occupied by Ku and DNA-PK were sufficient to support end joining, Y-shaped substrates were constructed in which only one arm was available for end joining. A Y substrate with a 31-bp arm bearing a partially cohesive 3' overhang was accurately joined by a Xenopus egg extract, whereas a substrate with a 21-bp arm was not. Surprisingly, a human cell extract did not join the Y substrates at all. The results suggest that differences in wortmannin sensitivity and in the distribution of in vitro end-joining products may be attributable to the variations in the levels of DNA-PKcs in the extracts. In addition, end joining in human extracts appears to involve interactions with significantly longer segments of DNA than the approximately 28 bp occupied by DNA-PK.
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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) | 0.001 | 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 | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".