{
  "abstract": "Reading both physical and chemical properties of a microenvironment from a single fluorophore remains a challenge. Here we demonstrate that two coexisting molecular equilibria within one near-infrared cyanine, CyC4, encode two mechanistically distinct ratiometric reporting channels. A meso-amino group and a pendant carboxylate form a tunable intramolecular hydrogen bond that toggles the dye between closed (700 nm) and open (780 nm) emissive conformers. Time-dependent density functional theory (TD-DFT) calculations show that the hydrogen bond raises the LUMO and blue-shifts the emission, establishing the 700/780 emission ratio as a local reporter of hydrogen bonding and polarity. Independently, the chromophore self-associates under crowding- and cosolvent-rich conditions into an aggregate with a blue-shifted, H-type absorption signature near 530-540 nm and a distinct emission near 610 nm upon 540 nm excitation. The intensity of this aggregate band relative to the monomer emission (Ra) serves as a ratiometric reporter of crowding and self-association. Because the two channels arise from distinct molecular equilibria (intramolecular hydrogen bonding vs. intermolecular self-association) they are largely decoupled: a glycerol titration series confirms that the self-association channel (Ra) can be moved while the hydrogen-bonding channel stays essentially fixed. Applied to protein-PEG biomolecular condensates, the two ratios move oppositely with increasing salt, showing that the interior's chemical (polarity, hydrogen bonding) and physical (packing, self-association) environments co-vary across the salt series; a single CyC4 measurement thereby maps this coupled microenvironment, providing a general strategy for multiparametric, ratiometric sensing of crowded microenvironments.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry, New York University, New York, New York, 10003, United States"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "S. Bais"
    },
    {
      "name": "S. Westrey"
    },
    {
      "name": "C. Samaniego Lopez"
    },
    {
      "name": "M. V. Rivas"
    },
    {
      "name": "C. C. Spagnuolo"
    },
    {
      "affs": [
        0
      ],
      "name": "S. Saurabh"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/dw29gqwp6w31k.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.29.747692",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.29.747692v1.full",
  "id": "dw29gqwp6w31k",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.29.747692v1",
  "language": null,
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "biophysics"
    ],
    [
      "openalex",
      "2505|Luminescence and Fluorescent Materials"
    ]
  ],
  "openalex": "W7204916768",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.29.747692v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-29",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/dw29gqwp6w31k.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:49Z",
      "native_id": "10.64898/2026.08.29.747692",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.29.747692v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:biophysics",
      "subfield": "biophysics"
    }
  ],
  "title": "Multiparametric microenvironment sensing via distinct molecular equilibria in a single cyanine dye",
  "title_text": "Multiparametric microenvironment sensing via distinct molecular equilibria in a single cyanine dye",
  "type": "preprint",
  "updated_at": "2026-10-30T12:17:49Z",
  "url": "https://research.draconitic.com/paper/dw29gqwp6w31k",
  "venue": "bioRxiv",
  "versions": []
}