Hydration Changes Accompanying Helix-to-Coil DNA Transitions
Bibliographic record
Abstract
We applied ultrasonic velocimetric and high-precision densimetric measurements to characterizing the helix-to-coil transition of the GGCATTACGG/CCGTAATGCC decameric DNA duplex. The transition was induced either by temperature or by mixing the two complementary single strands at isothermal conditions. The duplex dissociation causes increases in volume and expansibility while resulting in a decrease in compressibility. Our volumetric data in conjunction with computer-generated structural information are consistent with the picture in which the duplex dissociation is accompanied by an uptake of ∼180 water molecules from the bulk phase into the hydration shell of the DNA. Analysis of our compressibility and expansibility data reveals that the single-stranded conformation is likely to exist as a heterogeneous mixture of nearly isoenergetic subspecies differing in volume and enthalpy. We use our estimate of the change in hydration to evaluate the hydration and configurational contributions to the helix-to-coil transition entropy. The duplex dissociation is accompanied by an increase in configurational entropy, ΔSconf, of ∼23 cal mol(-1) K(-1) per nucleotide, which signifies liberation of manifold frozen degrees of freedom involved in maintaining the conformational stability of the duplex and the related stiffening of the heterocyclic bases and the sugar-phosphate backbone. To the best of our knowledge, this is the first experimental estimate of the change in configurational entropy associated with the helix-to-coil transition of a DNA.
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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".