A comparison of the folding kinetics of a small, artificially selected DNA aptamer with those of equivalently simple naturally occurring proteins
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Bibliographic record
Abstract
The folding of larger proteins generally differs from the folding of similarly large nucleic acids in the number and stability of the intermediates involved. To date, however, no similar comparison has been made between the folding of smaller proteins, which typically fold without well-populated intermediates, and the folding of small, simple nucleic acids. In response, in this study, we compare the folding of a 38-base DNA aptamer with the folding of a set of equivalently simple proteins. We find that, as is true for the large majority of simple, single domain proteins, the aptamer folds through a concerted, millisecond-scale process lacking well-populated intermediates. Perhaps surprisingly, the observed folding rate falls within error of a previously described relationship between the folding kinetics of single-domain proteins and their native state topology. Likewise, similarly to single-domain proteins, the aptamer exhibits a relatively low urea-derived Tanford β, suggesting that its folding transition state is modestly ordered. In contrast to this, however, and in contrast to the behavior of proteins, ϕ-value analysis suggests that the aptamer's folding transition state is highly ordered, a discrepancy that presumably reflects the markedly more important role that secondary structure formation plays in the folding of nucleic acids. This difference notwithstanding, the similarities that we observe between the two-state folding of single-domain proteins and the two-state folding of this similarly simple DNA presumably reflect properties that are universal in the folding of all sufficiently cooperative heteropolymers irrespective of their chemical details.
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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 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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