Thioflavin T Is a More General and Less Interfering Probe for Aptamer Binding Assays Than SYBR Green I
Bibliographic record
Abstract
Label-free fluorescent binding assays employing DNA staining dyes as probes are widely adopted techniques in the aptamer field. While many dyes have been used, thioflavin T (ThT) did not receive much attention for this purpose until recently, since it has long been perceived primarily as a G-quadruplex staining dye. Based on recent studies, ThT appears to serve as a reliable probe for evaluating the binding of non-G-quadruplex aptamers, and we seek to clarify the underlying mechanisms responsible for the exceptional performance of ThT. We investigated three non-G-quadruplex aptamers targeting adenosine, kanamycin, and Tris(hydroxymethyl)aminomethane (Tris). Consistent K d values and fluorescence reductions were observed in the presence of ThT regardless of the aptamer-to-dye ratio. In contrast, SYBR Green I (SGI) exhibited responses with apparent K d values that were far away from the true K d in most cases. Additional assays demonstrated that ThT exhibits a weaker affinity for aptamers and random DNA sequences compared to SGI. In addition, ThT has weaker affinities to double-stranded DNA than to single-stranded DNA, which is opposite to that for SGI. Lastly, testing the T30695 DNA binding with Pb 2+ confirmed that ThT can influence the binding of G-quadruplex aptamers. These findings explain ThT’s reliability for probing non-G-quadruplex aptamers.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.002 | 0.001 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
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".