Kinetics of Proximity-Induced Intramolecular DNA Strand Displacement
Bibliographic record
Abstract
Proximity-induced intramolecular DNA strand displacement (PiDSD) is one of the key mechanisms involved in many DNA-mediated proximity assays and protein-responsive DNA devices. However, the kinetic profile of PiDSD has never been systematically examined before. Herein, we report a systematic study to explore the kinetics of PiDSD by combining the uses of three DNA strand displacement techniques, including a binding-induced DNA strand displacement to generate PiDSD, an intermolecular DNA strand-exchange strategy to measure a set of key kinetic parameters for PiDSD, and a toehold-mediated DNA strand displacement to generate fluorescence signals for the real-time monitoring of PiDSD. By using this approach, we have successfully revealed the kinetic profiles of PiDSD, determined the enhanced local effective concentrations of DNA probes that are involved in PiDSD, and identified a number of key factors that influence the kinetics of PiDSD. Our study on PiDSD establishes knowledge and strategies that can be used to guide the design and operation of various DNA-mediated proximity assays and protein-triggered DNA devices.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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".