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| Format: | Recurso digital |
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Zenodo
2026
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| Online Access: | https://doi.org/10.5281/zenodo.20371340 |
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- <div class="qMYqUG_convSearchResultHighlightRoot"> <div class=""> <div class="text-base my-auto mx-auto pb-10 [--thread-content-margin:var(--thread-content-margin-xs,calc(var(--spacing)*4))] @w-sm/main:[--thread-content-margin:var(--thread-content-margin-sm,calc(var(--spacing)*6))] @w-lg/main:[--thread-content-margin:var(--thread-content-margin-lg,calc(var(--spacing)*16))] px-(--thread-content-margin)"> <div class="[--thread-content-max-width:40rem] @w-lg/main:[--thread-content-max-width:48rem] mx-auto max-w-(--thread-content-max-width) flex-1 group/turn-messages focus-visible:outline-hidden relative flex w-full min-w-0 flex-col agent-turn"> <div class="flex max-w-full flex-col gap-4 grow"> <div class="min-h-8 text-message relative flex w-full flex-col items-end gap-2 text-start break-words whitespace-normal outline-none keyboard-focused:focus-ring [.text-message+&]:mt-1"> <div class="flex w-full flex-col gap-1 empty:hidden"> <div class="streaming-animation markdown prose dark:prose-invert wrap-break-word w-full light markdown-new-styling"> <p>This paper extends the <strong>Scretching framework</strong> into <strong>fluorescence resonance energy transfer (FRET)</strong>, fluorescence lifetime imaging microscopy (FLIM), and oscillator-strength-corrected biomolecular distance recovery. FRET is one of the most important spectroscopic methods for measuring nanoscale distances in DNA, RNA, proteins, aptamers, folding systems, ligand-binding systems, and conformational-transition assays. Classical Förster theory relates donor–acceptor energy-transfer efficiency to distance, but the standard formula assumes that donor and acceptor optical properties remain effectively fixed or are already captured in the Förster radius. The Scretching–FRET extension adds an explicit oscillator-strength correction to account for chromophore environment, folding state, binding state, solvent exposure, quenching, and electronic-structure perturbation.</p> <p>The proposed <strong>Scretching–FRET efficiency correction</strong> is:</p> <p><strong>E_SF = E_FRET [(f_D f_A) / (f°_D f°_A)]¹ᐟ²</strong></p> <p>where <strong>E_FRET</strong> is the classical Förster efficiency, <strong>f_D</strong> is the actual donor oscillator strength, <strong>f_A</strong> is the actual acceptor oscillator strength, <strong>f°_D</strong> is the donor reference oscillator strength, and <strong>f°_A</strong> is the acceptor reference oscillator strength. The square-root correction preserves the classical FRET structure while allowing donor and acceptor electronic transition strengths to vary under real biomolecular conditions.</p> <p>The physical interpretation is that FRET efficiency is not controlled only by donor–acceptor distance. It is also affected by the electromagnetic strength of the donor and acceptor transitions. If folding, binding, hydration, base stacking, aromatic burial, protein conformational change, or chromophore shielding reduces oscillator strength, the effective transfer efficiency can be lower than predicted by the classical Förster expression. If the environment increases chromophore exposure or transition strength, the oscillator-strength-adjusted efficiency can increase relative to the reference state.</p> <p>This paper also connects the Scretching–FRET correction to FLIM. Because FLIM measures spatially resolved excited-state lifetimes, it provides an independent experimental route for testing whether oscillator-strength changes alter the apparent FRET efficiency and distance recovery. In the Scretching framework, donor lifetime, acceptor response, oscillator strength, and Förster efficiency become linked electromagnetic observables rather than isolated fitting parameters.</p> <p>The corrected Scretching–FRET distance relationship may be written by inserting <strong>E_SF</strong> into the Förster distance equation:</p> <p><strong>r_SF = R₀ [(1 / E_SF) − 1]¹ᐟ⁶</strong></p> <p>where <strong>r_SF</strong> is the oscillator-strength-adjusted donor–acceptor distance and <strong>R₀</strong> is the reference Förster radius. This provides a method for correcting apparent biomolecular distances when chromophore electronic structure changes during folding, binding, hybridization, denaturation, or conformational rearrangement.</p> <p>Illustrative validation is presented across seven biomolecular FRET systems, including DNA duplexes, protein β-hairpins, RNA hairpins, aptamers, ligand-binding complexes, folded proteins, and a protein molten-globule state. These examples show how the Scretching–FRET correction can recover distance estimates that differ from the classical Förster formula when donor or acceptor oscillator strengths are perturbed by molecular environment.</p> <p>The main contribution of this paper is the proposal that FRET and FLIM can be incorporated into the broader <strong>Maxwell–Scretching / SQC electromagnetic closure architecture</strong>. Classical FRET remains intact, but the Scretching layer adds a physically interpretable correction based on measurable or computable oscillator strengths. This allows fluorescence transfer efficiency, lifetime imaging, chromophore exposure, folding state, and biomolecular distance to be analyzed within one unified optical-closure model.</p> <p>In summary, this paper establishes the <strong>Scretching–FRET correction</strong> as a proposed framework for oscillator-strength-adjusted FRET and FLIM analysis. It provides a bridge between classical Förster theory, fluorescence lifetime measurements, biomolecular folding, chromophore electronic structure, and Scretching electromagnetic closure. Independent validation requires paired datasets containing classical FRET efficiency, FLIM lifetime maps, donor and acceptor oscillator strengths, known structural distances, and controlled folding or binding perturbations.</p> </div> </div> </div> </div> </div> </div> </div> </div> <div class="pointer-events-none -mt-px h-px translate-y-[calc(var(--scroll-root-safe-area-inset-bottom)-14*var(--spacing))]"> </div> <div class="pointer-events-none translate-y-(--scroll-root-safe-area-inset-bottom) R6Vx5W_threadScrollVars min-h-(--gutter-remaining-height,0px) group-data-stream-active/scroll-root:h-[calc(var(--thread-response-height)-16*var(--spacing))]"> </div>