Focus on Function: Single Molecule Enzymology of the VS ribozyme
Bibliographic record
Abstract
Non‐coding RNAs of complex structure are involved in numerous aspects of the replication and processing of genetic information. Within the mitochondria of the bread mold Neurospora, the Varkud satellite (VS) RNA replicates parasitically by cycling between DNA and multimeric RNA forms. The RNA contains the VS ribozyme whose self‐cleavage is thought to be essential for replication. Models of VS ribozyme tertiary structure predict three parallel helical stacks built from two three‐way junctions and a kissing loop interaction. Whether or not such complex RNA architectures are dynamic and how catalytic activity emerges is ill‐understood. Here we exploit single molecule FRET to show that the VS ribozyme exhibits dynamic hierarchical folding. Reversible kissing loop formation involving the upstream substrate is required but only partially rate‐limiting for catalysis. Our results invoke a model whereby the VS ribozyme kinetically selects the distal downstream substrate for cleavage before the proximal upstream substrate, thus facilitating processing of the multimeric RNA replication intermediate. We are currently further testing this model.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".