B−Z Conformational Transition of DNA Monitored by Vibrational Circular Dichroism. Ab Initio Interpretation of the Experiment
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Bibliographic record
Abstract
The B−Z conformational transition was induced by Mn 2+ ions in a synthetic oligonucleotide (dG-dC) 20 and monitored by the vibrational circular dichroism (VCD). For the first time, the spectra were analyzed on the basis of quantum-mechanical computations. Force field and intensity tensors computed ab initio for smaller DNA fragments were transferred to a d(GCGCGCGC) 2 octamer model including explicit water molecules. The method allowed us to assign and explain most of the frequency and intensity features observed in the absorption and VCD spectra of the B- and Z-forms. Particularly, the computations reproduced the VCD sign flip caused by the transition due to the C O stretching and allowed us to assign most spectral bands in the nitrogen bases vibrational region. Also, known isotopic effects (deuteration and a 18 O substitution) were reproduced correctly. For the sugar−phosphate modes, the assignment of the VCD bands was hindered by a weak experimental signal. The approach based on quantum-mechanical computations was found superior to previous models based on coupled oscillator theory. Water molecules hydrogen-bonded to the DNA skeleton had to be included for reliable interpretation of the VCD and IR spectral patterns, namely, for the sugar−phosphate vibrations.
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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 it