The effect of different divalent cations on the kinetics and fidelity of <em>Bacillus stearothermophilus</em> DNA polymerase
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Bibliographic record
Abstract
Although Mg<sup>2+</sup> is the metal ion that functions as the cofactor for DNA polymerases (DNA pols) <em>in vivo</em>, Mn<sup>2+</sup> can also serve in this capacity but it reduces base discrimination. Metal ions aside from Mg<sup>2+</sup> or Mn<sup>2+</sup> can act as cofactors for some DNA pols but not for others. Here we report on the ability of several divalent metal ions to substitute for Mg<sup>2+</sup> or Mn<sup>2+</sup> with BST DNA polymerase (BST pol), an A family DNA pol. We selected the metal ions based on whether they had previously been shown to be effective with other DNA pols. We found that Co<sup>2+</sup> and Cd<sup>2+</sup> were the only cations tested that could replace Mg<sup>2+</sup> or Mn<sup>2+</sup>. When Co<sup>2+</sup> was substituted for Mg<sup>2+</sup>, the incorporation efficiency for correct dNTPs increased 6-fold but for incorrect dNTPs there was a decrease which depended on the incoming dNTP. With Mn<sup>2+</sup>, base selectivity was impaired compared to Co<sup>2+</sup> and Cd<sup>2+</sup>. In addition, Co<sup>2+</sup> and Mn<sup>2+</sup> helped BST pol to catalyze primer-extension past a mismatch. Finally both Co<sup>2+</sup> and Mn<sup>2+</sup> enhanced ground-state binding of both correct and incorrect dNTPs to BST pol: Dideoxy terminated primer-template complexes.
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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 | 0.000 | 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 it