DNA Adsorption to the Reservoir Walls Causing Irreproducibility in Studies of Protein–DNA Interactions by Methods of Kinetic Capillary Electrophoresis
Bibliographic record
Abstract
Methods of kinetic capillary electrophoresis (KCE) facilitate kinetic studies of protein-DNA interactions and highly efficient selection of DNA aptamers for protein targets. Here, we report a previously unnoticed source of error that affects the precision and accuracy of KCE-based measurements. The error manifests itself in cases that require the use of low concentrations of DNA. In such measurements, the reproducibility of the signal generated by the same fluorescently labeled DNA sample can have a relative standard deviation (RSD) as high as 40%. We have investigated the cause of the irreproducibility and found that it is attributed to DNA adsorption to the surface of the sample vials, in which protein-DNA mixtures are prepared prior to a KCE experiment. The use of commercially available "high DNA recovery" sample vials does not resolve the problem. We have found that the problem can be significantly alleviated by the passivation of the vial surface with blocking agents, such as masking DNA or bovine serum albumin (BSA). The described adsorption of DNA to the surface of sample vials may also be important in other procedures that deal with low DNA concentrations, such as aptamer selection and quantitative PCR.
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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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| 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".