Bibliographic record
Abstract
The role of counterion condensation as a dominant force governing the stability of DNA duplexes and triplexes is well established. In contrast, the effect of counterion condensation on the stability of G-quadrupex conformations is poorly understood. Unlike other ordered nucleic acid structures, G-quadruplexes exhibit a specific binding of counterions (typically, Na+ or K+) which are buried inside the central cavity and coordinated to the O6 carbonyls of the guanines forming the G-quartets. While it has been known that the G-quadruplex-to-coil transition temperature, TM, increases with an increase in the concentration of the stabilizing ion, the contributions of the specific (coordination in the central cavity) and nonspecific (condensation) ion binding have not been resolved. In the first part of the work performed in this dissertation, we used G-quadruplexes formed by four different sequences derived from the human telomeric region, c-MYC, and VEGF genes to separate the two ionic contributions. We studied the change in TM of preformed G-quadruplexes following the addition of nonstabilizing ions Li+, Cs+, and TMA+ (tetramethylammonium). Our data suggest that the stabilizing action of cations on the G-quadruplex conformation is, primarily, due to the central ions which act as specifically bound ligands. Nonspecifically bound (condensed) counterions may slightly stabilize the G-quadruplex conformation or exert no influence on its stability (human telomeric G-quadruplexes) or may strongly destabilize it (c-MYC and VEGF). After investigating the salt effect in G-quadruplexes, the latter part of the thesis project was devoted to understanding the folding/unfolding transitions of i-motif, a distinct tetraplex structure formed by c-rich complementary sequences of G-quadruplexes.We described the pH-induced folding/unfolding transitions of i-motifs formed by c-MYC sequence by a linkage thermodynamics-based formalism in terms of three pKa’s of cytosines, namely, an apparent pKa in the unfolded conformation, pKau, and two apparent pKa’s in the folded state, pKaf1 and pKaf2.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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".