Binding-Induced Formation of DNA Three-Way Junctions and Its Application to Protein Detection and DNA Strand Displacement
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Bibliographic record
Abstract
DNA three-way junctions (DNA TWJs) are important building blocks to construct DNA architectures and dynamic assemblies. We describe here a binding-induced DNA TWJ strategy that is able to convert protein bindings to the formation of DNA TWJ. The binding-induced DNA TWJ makes use of two DNA motifs each conjugated to an affinity ligand. The binding of two affinity ligands to the target molecule triggers assembly of the DNA motifs and initiates the subsequent DNA strand displacement, resulting in a binding-induced TWJ. Real-time fluorescence monitoring of the binding-induced TWJ enables detection of the specific protein targets. A detection limit of 2.8 ng/mL was achieved for prostate-specific antigen. The binding-induced TWJ approach compares favorably with the toehold-mediated DNA strand-displacement, the associative (combinative) toehold-mediated DNA strand-displacement, and the binding-induced DNA strand-displacement. Importantly, the binding-induced TWJ broadens the scope of dynamic DNA assemblies and provides a new strategy to design protein-responsive DNA devices and assemblies.
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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 | 0.000 |
| 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 it