Sweeping Capillary Electrophoresis: A Non-Stopped-Flow Method for Measuring Bimolecular Rate Constant of Complex Formation between Protein and DNA
Bibliographic record
Abstract
We introduce sweeping capillary electrophoresis (SweepCE), a non-stopped-flow method for directly measuring the bimolecular rate constant of complex formation, and demonstrate its use for studying protein-DNA interaction. The capillary is prefilled with a solution of DNA, and electrophoresis is then carried out from a solution of the protein in a continuous mode. Because the electrophoretic mobility of the protein is greater than that of DNA, the protein continuously mixes with DNA and forms the protein-DNA complex. The complex migrates with a velocity higher than that of DNA and causes sweeping of DNA, which gave the name to the method. The bimolecular rate constant, kon, of complex formation can be determined from the time profile of DNA concentration using a simple mathematical model of the sweeping process. In this proof-of-principle work, we used SweepCE to directly measure kon = (3.4 +/- 0.6) x 106 M-1 s-1 for the interaction between single-stranded DNA-binding protein and a 15-mer DNA oligonucleotide. Along with nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM), SweepCE establishes a universal and comprehensive platform for studying kinetic and equilibrium parameters of complex formation between biopolymers.
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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".