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Photophysics tunability through alteration of framework aperture (metal-organic framework (MOF) = variable; guest = constant) was probed for the first time in comparison with previously explored concepts (MOF = constant; guest = variable). In particular, analysis of the confinement effect on a photophysical response of integrated 5-(3-chlorobenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one (Cl-BI) chromophore allowed us to establish a photophysics-aperture relationship. To shed light on the observed correlation, the framework confined environment was replicated using a molecular cage, Pd6(TPT)4 (TPT = 2,4,6-tri(pyridin-4-yl)-1,3,5-triazine), thus allowing for utilization of crystallography, spectroscopy, and theoretical simulations to reveal the effect a confined space has on the chromophore's molecular conformation (including disruption of strong hydrogen bonding and novel conformer formation) and any associated changes on a photophysical response. Furthermore, the chosen Cl-oHBI@Pd6(TPT)4 (Cl-oHBI = 5-(5-chloro-2-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one, chromophore) system was applied as a tool for targeted cargo delivery of a chromophore to the confined space of DNA, which resulted in promotion of chromophore-DNA interactions through a well-established intercalation mechanism. Moreover, the developed principles were applied toward utilizing a HBI-based chromophore as a fluorescent probe on the example of macrophage cells. For the first time, suppression of non-radiative decay pathways of a chromophore was tested by anchoring the chromophore to a framework metal node, portending a potential avenue to develop an alternative to natural biomarkers. Overall, these studies are among the first attempts to demonstrate the unrevealed potential of a confined scaffold environment for tailoring a material's photophysical response.

BACKGROUND Single-molecule detection (SMD) technologies are well suited for clinical diagnostic applications by offering the prospect of minimizing precious patient sample requirements while maximizing clinical information content. Not yet available, however, is a universal SMD-based platform technology that permits multiplexed detection of both nucleic acid and protein targets and that is suitable for automation and integration into the clinical laboratory work flow. METHODS We have used a sensitive, specific, quantitative, and cost-effective homogeneous SMD method that has high single-well multiplexing potential and uses alternating-laser excitation (ALEX) fluorescence-aided molecule sorting extended to 4 colors (4c-ALEX). Recognition molecules are tagged with different-color fluorescence dyes, and coincident confocal detection of ≥2 colors constitutes a positive target-detection event. The virtual exclusion of the majority of sources of background noise eliminates washing steps. Sorting molecules with multidimensional probe stoichiometries (S) and single-molecule fluorescence resonance energy transfer efficiencies (E) allows differentiation of numerous targets simultaneously. RESULTS We show detection, differentiation, and quantification—in a single well—of (a) 25 different fluorescently labeled DNAs; (b) 8 bacterial genetic markers, including 3 antibiotic drug–resistance determinants found in 11 septicemia-causing Staphylococcus and Enterococcus strains; and (c) 6 tumor markers present in blood. CONCLUSIONS The results demonstrate assay utility for clinical molecular diagnostic applications by means of multiplexed detection of nucleic acids and proteins and suggest potential uses for early diagnosis of cancer and infectious and other diseases, as well as for personalized medicine. Future integration of additional technology components to minimize preanalytical sample manipulation while maximizing throughput should allow development of a user-friendly (“sample in, answer out”) point-of-care platform for next-generation medical diagnostic tests that offer considerable savings in costs and patient sample.