Evidence for Stabilization of DNA/RNA−Protein Complexes Arising from Nucleobase−Amino Acid Stacking and T-Shaped Interactions
Bibliographic record
Abstract
The stacking and T-shaped interactions between the natural DNA or RNA nucleobases (adenine, cytosine, guanine, thymine, uracil) and all aromatic amino acids (histidine, phenylalanine, tyrosine, tryptophan) were investigated using ab initio quantum mechanical calculations. We characterized the potential energy surface of nucleobase-amino acid dimers using the MP2/6-31G*(0.25) method. The stabilization energies in dimers with the strongest interactions were further examined at the CCSD(T)/CBS level of theory. Results at the highest level of theory possible for these systems indicate that both stacking and T-shaped interactions are very close in magnitude to biologically relevant hydrogen bonds. Additionally, T-shaped interactions are as strong, if not stronger, than the corresponding stacking interactions. Our systematic consideration of the interaction energies in 485 possible combinations of monomers shows that a variety of these contacts are essential when considering the role of aromatic amino acids in the binding of proteins to DNA or RNA. This work also illustrates how our calculated binding strengths can be used by biochemists to estimate the magnitude of these noncovalent interactions in a variety of DNA/RNA-protein active sites.
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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".