Assembly and solution phase properties of Ag+–mediated adenine-thymine DNA duplexes
Bibliographic record
Abstract
Silver cations (Ag+) exhibit site-specific coordination with the natural nucleobases, which can be exploited within DNA nanostructures. Understanding the thermodynamics of formation and organization of DNA complexes formed by these interactions is essential for rationally designing Ag+-mediated DNA nanostructures. In this study, we use temperature controlled circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC), Förster resonance energy transfer (FRET), and cryogenic-transmission electron microscopy (cryo-TEM) to investigate the formation stoichiometry and resulting morphology of Ag+-mediated duplexes of dA and dT homobase strands. CD shows that duplex formation occurs at room temperature and is sensitive to solution phase conditions. ITC reveals that 0.5 [Ag+]/[base] is required to form thermodynamically stable dA–Ag+–dT structures with one Ag+ per base pair. FRET experiments show that dA–Ag+–dT duplexes maintain anti-parallel strand orientation, even with excess Ag+, and cryo-TEM shows that dA–Ag+–dT duplexes adopt morphologies similar to WCF duplexes. Despite these similarities, dA–Ag+–dT duplexes exhibit significantly greater thermal stability compared to their WCF counterparts. These findings provide new insights into dA–Ag+–dT duplex formation and structure that are essential for the development of programmable Ag+–DNA nanostructures.
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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".