Binding of Tetrapentylammonium to a c‐MYC G‐quadruplex Depicted through NMR and Volumetric Assessment
Bibliographic record
Abstract
Abstract We recently have demonstrated that, their structural simplicity notwithstanding, tetraalkylammonium (TAA + ) ions, i.e ., [H(CH 2 ) n ] 4 N + , strongly stabilize the parallel c‐MYC G‐quadruplex while not affecting the thermal stabilities of the antiparallel human telomeric G‐quadruplex or duplex DNA. In the present work, we expand on our discovered paradigm of topology‐selective G‐quadruplex recognition by performing NMR spectroscopic and volumetric characterization of the complex between tetrapentylammonium (TPeA + ) and the c‐MYC G‐quadruplex. The binding of TAA + to the c‐MYC G‐quadruplex is optically silent, which necessitates the use of nonoptical observables, such as density and sound velocity. Our NMR results revealed that TPeA + forms a stable complex with the c‐MYC G‐quadruplex in which the ligand is positioned above the G9‐G13‐G18‐G22 quartet and is surrounded by the 3′‐(T23‐A24‐A25) flanking region. We used our densimetric and ultrasonic velocimetric results to calculate changes in volume, ΔV, and adiabatic compressibility, ΔK S , accompanying the binding of TPeA + to the c‐MYC G‐quadruplex. We rationalized these volumetric properties to determine binding‐induced changes in hydration of the associating molecules and the internal dynamics of the host G‐quadruplex. In general, the structural and physico‐chemical insights emerging from this work lay the foundation for further studies of TAA + ‐based compounds as a possible starting point for designing topology‐sensitive G‐quadruplex‐binding agents.
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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 | 0.000 |
| 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) | 0.001 | 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".