Residual benzamide contamination in synthetic oligonucleotides observed using UV resonance Raman spectroscopy
Bibliographic record
Abstract
Abstract Spectroscopic methods based on Raman scattering have for many years employed synthetic oligonucleotides in a broad range of applications, either as probes or as model analytes for biophysical investigations. Benzamide is commonly used as a protecting group in the phosphoramidite synthesis of oligonucleotides and, while standard desalting used after synthesis yields sufficiently pure reagents for most assay reactions or other routine uses of the oligomer, it does not completely remove benzamide. We show that the 1609 cm −1 band of residual benzamide contamination can interfere with certain nucleic acid bands, particularly when using excitation wavelengths near 244 nm where the benzamide band is strongly enhanced. For example, the 1609 cm −1 band of benzamide could obscure (or be mistaken as) a weak vibration attributed to an NH 2 scissoring. The extent of benzamide contamination in desalted preparations varies considerably among different commercial sources, and hence caution is advised when making direct comparisons of ultraviolet Raman data of oligonucleotides from different sources. Copyright © 2010 John Wiley & Sons, Ltd.
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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 | 0.001 | 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 | 0.001 |
| 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".