Probing Local Folding Allows Robust Metal Sensing Based on a Na<sup>+</sup>‐Specific DNAzyme
Bibliographic record
Abstract
Abstract Fluorescent metal sensors based on DNA often rely on changes in end‐to‐end distance or local environmental near fluorophore labels. Because metal ions can also nonspecifically interact with DNA through various mechanisms, such as charge screening, base binding, and increase or decrease in duplex stability, robust and specific sensing of metal ions has been quite challenging. In this work, a side‐by‐side comparison of two signaling strategies on a Na + ‐specific DNAzyme that contained a Na + ‐binding aptamer was performed. The duplex regions of the DNAzyme was systematically shortened and its effect was studied by using a 2‐aminopurine (2AP)‐labeled substrate strand. Na + binding affected the local environmental of the 2AP label and increased its fluorescence. A synergistic process of Na + binding and forming the duplex on the 5′‐end of the enzyme strand was observed, and this end was close to the aptamer loop. Effective Na + binding was achieved with a five base‐pair stem. The effect on the 3′‐end is more continuous, and the stem needs to form first before Na + can bind. With an optimized substrate binding arm, a FRET‐based sensor has been designed by labeling the two ends of a cis form of the DNAzyme with two fluorophores. In this case, Na + failed to show a distinct difference from that of Li + or K + ; thus indicating that probing changes to the local environment allows more robust sensing of metal ions.
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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".