Two independently selected capping ribozymes share similar substrate requirements
Bibliographic record
Abstract
We report the isolation and characterization of a second capping ribozyme, called 6.17. This ribozyme has substrate requirements that are very similar to a previously isolated capping ribozyme called Iso6. Both ribozymes promote capping and cap exchange reactions with a broad range of nucleotide substrates. The ribozymes mediate a reaction where the terminal phosphate of the nucleotide substrate attacks the alpha-phosphate found at the ribozyme's 5' terminus. This reaction involves the release of pyrophosphate during capping or a nucleotide during cap exchange. The second-order rate constants for 6.17 and Iso6 depend strongly on the length of the phosphate group found on the nucleotide substrate. Nucleoside diphosphates or triphosphates are efficiently utilized, while monophosphates are used approximately 20-fold less efficiently by both ribozymes. These ribozymes also have rates that increase as pH is decreased. Despite these similarities, the ribozymes are not identical and 6.17 performs optimally when incubated with divalent magnesium ions, while Iso6 displays a preference for calcium ions. Further, the ribozymes have globally different secondary structures; 6.17 has a complicated pseudoknot structure consisting of five helical elements, while Iso6 likely consists of four helical elements. We hypothesize that capping proceeds via an invariant phosphate dependent mechanism that imposes a nearly identical "catalytic fingerprint" on these two distinct ribozymes.
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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 | 0.000 |
| 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 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".