DNA-duplexes containing abasic sites: correlation between thermostability and acoustic wave properties
Bibliographic record
Abstract
Aldehydic apurinic or apyrimidinic sites that lack a nucleobase moiety are one of the most common forms of toxic lesions in DNA. In the present study, a close structural analog of such a site, the 2-(hydroxymethyl) tetrahydrofuranyl residue, was synthesized in order to act as a model for damaged nucleic acid probes. Prepared oligodeoxyribonucleotides containing one, two or three abasic sites were hybridized to complementary sequences immobilized on a gold surface using the neutravidin-biotin interaction for study by thickness shear mode acoustic wave detector. Measurement of the complex electrical impedance of an AT-cut quartz device with immobilized biotinylated nucleotide allowed the detection of changes of series resonance frequency, Deltafs, and motional resistance, Rm, associated with duplex formation. The changes as detected by the acoustic wave method correlated well with the thermostability of DNA duplexes in solution. With respect to the latter, UV-monitored melting curves indicate that both the number of sites and their localization in the double-stranded structure influence the amount by which a 19 b.p. duplex is destabilized. The presence of 3 abasic sites completely destabilized the DNA duplex.
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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 | 0.001 |
| 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".