A 5′-BODIPY End-label for Monitoring DNA Duplex-Quadruplex Exchange
Bibliographic record
Abstract
Abstract Fluorescent probes that can distinguish different DNA topologies through changes in optical readout are sought after for DNA-based diagnostics. In this work, the 4,4-difluoro-4-bora-3a, 4a-diaza-s-indacene (BODIPY) chromophore attached to cyanophenyl substituents (BODIPY-CN) has been tethered to the 5′-end of the 15-mer thrombin binding aptamer (TBA) that contains the guanine (G) nucleobase. TBA folds into a unimolecular antiparallel G-quadruplex (GQ) upon binding thrombin and certain metal ions. The 5′-BODIPY-CN-TBA sample possesses a Stokes shift of ~40 nm with wavelengths of excitation/emission at 550/590 nm and exhibits a 2-fold increase in emission intensity compared to the free BODIPY-CN in aqueous buffer that possesses a brightness (εΦfl) of ~16,956 M−1. cm−1. However, when 5′-BODIPY-CN-TBA is base-paired to a complementary strand in the B-form duplex, the emission of the BODIPY-CN end-label increases 7-fold, 14-fold compared to the free-dye. This signal-on response enables the BODIPY-CN end-label to serve as a quencher-free fluorescent probe for monitoring duplex-GQ exchange. The visible end-label minimally perturbs GQ stability and thrombin binding affinity, and the modified TBA can act as a combinatorial logic circuit having INHIBIT logic functions. These attributes make BODIPY-CN a highly useful end-label for creating nanomolecular devices derived from G-rich oligonucleotides.
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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".