Molecular Basis of RNA-Mediated Gene Regulation on the Adenine Riboswitch by Single-Molecule Approaches
Bibliographic record
Abstract
The adenine-specific pbuE riboswitch undergoes metal ion-dependent folding that involves a long-range tertiary loop-loop interaction between two stem loops. Fluorescence resonance energy transfer (FRET) and single-molecule FRET studies demonstrate the ability of the loops to interact in the absence of the ligand. Although the riboswitch can fold in the absence of adenine, ligand binding stabilizes this folded conformation by increasing the folding and decreasing the unfolding rates of the riboswitch. The presence of the ligand also decreases the magnesium ion concentration required to promote the loop-loop interaction. Single-molecule FRET studies demonstrate that individual aptamer molecules exhibit great heterogeneity in the rates of folding and unfolding, which is reduced in the presence of adenine. Moreover, single-molecule FRET proposes that riboswitch folding proceeds through a complex landscape that involves a discrete intermediate.
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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) | 0.000 | 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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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 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".