Chain Dynamics Limit Electron Transfer from Electrode-Bound, Single-Stranded Oligonucleotides
Bibliographic record
Abstract
A wide range of new devices aimed at in vivo molecular detection and point-of-care diagnostics rely on binding-induced changes in electron-transfer kinetics from an electrode-attached, redox-reporter-modified oligonucleotide as their signaling mechanism. In an effort to better characterize the mechanisms underlying these sensors, we have measured the electron-transfer kinetics associated with surface-attached, single-stranded DNAs modified with a methylene blue redox reporter either at the chain’s distal end or at an internal chain position. We find that although the rate of electron transfer from a reporter placed either terminally or internally is independent of chain length for chains shorter than the length scale of methylene blue (and its linker), for longer chains it follows a power-law dependence on length of exponent approximately −2.2. Such behavior is consistent with a diffusion-controlled mechanism in which the diffusion of the DNA-bound reporter to the surface controls the rate of electron transfer. This said, the observed rates are, at 5–400 s–1, orders of magnitude slower than the intramolecular dynamics of single-stranded oligonucleotides when free in solution. Likewise, the rates of transfer from reporters placed internally are several-fold slower than those seen for the equivalent terminally modified construct. We attribute these effects to electrostatic repulsion between the oligonucleotide and the electrode surface, which is negatively charged at the redox potential of methylene blue. Consistent with this, changing monolayer composition so as to increase the negative charge of the surface reduces the transfer rate still more without significantly altering its power-law chain length dependence. Simple theoretical models and computer simulations performed in support of our experimental studies find similar power-law dependencies, similar electrostatic slowing of the transfer rate, and similar rate differences between terminally an internally modified constructs.
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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".