Effect of protein binding on charge transfer in DNA: A simple model based on the superexchange mechanism
Bibliographic record
Abstract
The effect of protein binding on the electronic coupling between distant redox centers in DNA is investigated in DNAprotein complex systems using the superexchange formalism. The systems (bridges) studied are described by a tight-binding electronic Hamiltonian in which site orbitals interact with one another through an exponentially decaying function of distance. Based on the "continuous-medium approximation," previously developed for large homogeneous three-dimensional systems (J.-M. Lopez-Castillo et al. J. Phys. Chem. 99, 6864 (1995)), the intervening bridge is defined by a unique dimensionless parameter Γ /E that controls the distance dependence of the electronic coupling. Here, E is the energy separation between the orbitals of the bridging medium and the redox sites (tunneling energy), and Γ is the electronic bandwidth of the bridge taken as a continuous medium. It was found that, for a given value of (Γ/E)DNA far from the DNA's resonance conditions and for (Γ/E)protein values near the protein's resonance conditions, the electronic coupling is independent of the donoracceptor distance when the acceptor lies within the "recognition region" of DNA. Moreover, when the redox centers are located on both sides of this region, the electronic coupling is many orders of magnitude larger than it should be, far from the protein's resonance conditions.Key words: DNA, DNAprotein complexes, long-range electron and hole transfers, electronic coupling, superexchange mechanism, energetic control, continuous-medium approximation.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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 source (direct Gemma or distilled Codex), 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".