New fluorescent nucleobases derived from 5-alkynylpyrimidines
Bibliographic record
Abstract
Fluorescent reporter groups are widely used in many areas of macromolecular science. In nucleic acid chemistry, fluorescently labeled oligonucleotides find use in the study of nucleic acid conformations, as reporters of the state of hybridization and as probes of nucleic acid-protein interactions, as well as, probes and primers for the detection and quantification of desired sequences. Often, the fluorophore is a separate and independent entity covalently attached to an otherwise unmodified oligonucleotide. Another class of fluorophore is the nucleobase analog - a chemically modified nucleobase that is unable to base pair properly. Recently, we have become interested in pyrrolocytosine ( pC ) as an intrinsically fluorescent, pairing-competent nucleobase. It has previously been shown that incorporation of pyrrolocytidine into oligonucleotides gives a fluorescent molecule that responds to the state of hybridization. We have refined the syntheses of pyrrolocytosine derivatives and the related modified uracil derivatives, furanouracil ( fU ), from cytosine and uracil respectively via three sequential steps: iodination of the nucleobase; Pd-catalyzed cross-coupling with a terminal alkyne; and metal-catalyzed cyclization. The fluorescence properties of the 5-alkynyl nucleobases and the bicyclic pC and fU analogs have been characterized and depend on: 1) the nature of the substituent on the alkyne, 2) whether the nucleobase is 5-alkynyl or cyclized, and 3) the presence of a substituent on the N 1 -position of the nucleobase. The chemistry and properties of peptide nucleic acid oligomers incorporating these types of base modifications and their possible use in point-mutation detection is presented.
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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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".