Developing Combined Optical Spectroscopy and Mass Spectrometry Tools to Probe the Conformation of Double-Stranded DNA in the Gas Phase
Bibliographic record
Abstract
Mass spectrometry (MS) has long been a popular analytical technique for the characterization of gas-phase molecules. Beginning in the late 20th century, the coupling of MS with soft ionization techniques such as electrospray ionization (ESI) and the development of various gas-phase methodologies facilitated the structural analysis of intact biomolecules. To that end, this dissertation describes the coupling of MS with optical spectroscopy for the characterization of isolated DNA-binding dyes and non-covalent double-stranded DNA (dsDNA) complexes in the gas phase. MS and optical spectroscopy analysis is performed using a quadrupole ion trap (QIT) that has been modified to perform photodissociation (PD) and laser-induced fluorescence (LIF) on mass-selected ions. First, fluorescence measurements on trapped rhodamine 640 ions are performed to visualize the cloud of trapped ions inside the QIT. Second, the intrinsic photophysical properties of the classic dsDNA intercalator, ethidium bromide, is presented via photodissociation action spectroscopy, dispersed emission spectra, and time-resolved measurements. Finally, latter chapters describe the use of non-covalent DNA-binders that exhibit “turn-on” fluorescence responses in solution and Förster Resonance Energy Transfer (FRET) methodologies to probe the conformation of dsDNA ions in the gas phase. The work described in this dissertation serves to develop methodologies that use MS and optical spectroscopy techniques to investigate the intrinsic intra- and intermolecular interactions present in biomolecules, without competing solvent effects.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".