Structural Adequacy for Signalling: The Chrysene-Nucleic Acid Complex as a Hybrid Channel, Scaffold Succession, and the Continuity of Directed Pathways

Abstract

The enclosure paper establishes a map from a nucleic-acid sequence to the configuration of the membrane enclosing it, setting the stage for how that configuration is read. This paper determines what a reader must be. It shows that a complete signalling architecture requires five elements, that the complex supplies all five entirely from the products of the integrated synthesis, and that together they define the full capacity of any reader.

The framework is naturally hybrid. Seven orders of magnitude separate the persistence of the orientational state from the window in which it is read, allowing a continuous field to carry the state adiabatically as a discrete word and reducing the dynamics to a clean piecewise-deterministic process with the word held fixed. The covalent backbone preserves this timescale separation against lateral diffusion by holding the anchors in strict sequence. The intrinsic ordering established in the enclosure paper is therefore directly load-bearing here as well.

The photon serves directly as the carrier. The chromophore is the vessel skeleton, the bridge is the phosphodiester tether, and the acceptor is the base that tether was formed to carry, making the relay entirely self-contained. Because the two anchor types differ by three backbone atoms, their transfer rates separate by a factor of 45 to 142, reporting the pair type directly as a rate. The arithmetic selects the long-lived triplet state for readout — a sharp structural condition that is directly testable by measurement. This mechanism cleanly resolves the pair type while remaining invariant to the presented face, independently confirming the division established in the enclosure paper.

Discrimination is achieved through the response itself: an in-plane transition dipole absorbs uniformly across presented faces, so the architecture functions directly as a state-discriminating detector. Each window reports the composition of a contiguous subword, and the window length — the optical scale divided by the helical pitch — converges on a single value through two independent routes: the phase filter and the steric width of a unit. Full sequence recovery is enabled by overlapping windows that share their differences: the fibre is exactly, and any local degeneracy remains strictly bounded by the window regardless of strand length.