Synthesis of <i>Ortho</i>‐Functionalized Tetrachlorinated Azobenzene Phosphoramidites for Incorporation Into siRNAzos for Photocontrolled Gene Silencing
Bibliographic record
Abstract
Abstract This paper contains the detailed synthesis and characterization protocols of ortho‐functionalized tetrachlorinated azobenzene‐containing small interfering RNAs (siRNAs), which have photoswitchable properties effectively controlled with visible light. To design this tetrachlorinated azobenzene scaffold, a late‐stage chlorination with N‐chlorosuccinimide and palladium is used. Next, a single hydroxyl group from the tetrachlorinated azobenzene is protected with a 4,4′‐dimethoxytrityl (DMT) group, followed by phosphitylation with 2‐cyanoethyl‐N,N‐diisopropylchlorophosphoramidite. These phosphoramidite monomers are compatible with automated solid‐phase oligonucleotide synthesis to generate tetrachlorinated azobenzene‐containing oligonucleotides. This paper also contains the detailed biophysical characterization, biological testing, and photo‐switching protocols of ortho‐functionalized chlorinated azobenzene‐containing siRNAs (Cl‐siRNAzos), which have photoswitchable properties that can be controlled with visible light. First, the Cl‐siRNAzos are characterized by annealing the sense and antisense strands together and then measuring the circular dichroism (CD) profile, and the melting temperatures (Tm) of the duplexes. Secondly, the biological testing of the Cl‐siRNAzos in cell culture is done to determine their gene silencing efficacy. Finally, their gene‐silencing activities are measured after exposure to red light in order to inactivate the Cl‐siRNAzo, and then either violet light or infrared thermal relaxation is deployed, which re‐activates the Cl‐siRNAzo. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 4,4′‐bis(hydroxyethyl) ortho‐functionalized tetrachlorinated azobenzene phosphoramidite (5) Basic Protocol 2: Synthesis, purification, and characterization of siRNAs containing ortho‐functionalized tetrachlorinated azobenzene Basic Protocol 3: Gene‐silencing evaluation of ortho‐functionalized tetrachlorinated azobenzene using firefly luciferase
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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".