{
  "abstract": "Precisely modifying proteins at multiple sites in their native, folded structures offers unique opportunities to answer molecular and cellular-level biological questions. Here, we present a genetic code expansion strategy for site-specific integration of a fluorophore–quencher pair comprising two non-canonical amino acids—acridonylalanine (Acd) and methyltetrazinyl phenylalanine (Tet)—into a protein expressed in E. coli. The Acd and Tet pair requires no post-translational labeling, and quenching can be switched off by bioorthogonal or photochemical reactions of Tet for convenient internal control experiments. Mechanistic studies based on Stern–Volmer quenching, fluorescence lifetime measurements, and “proline ruler” peptides established the distance dependence of quenching. As proof-of-concept, we applied this strategy to study: (1) calmodulin, a calcium-sensing protein, (2) RecA, a DNA damage sensor in bacteria, and (3) LexA, a transcriptional repressor whose activation by RecA governs acquired antibiotic resistance in bacteria. Using these proteins, we demonstrate that dual Acd/Tet labeling provides molecular-level insights into protein dynamics, shows potential for adaptation to high-throughput drug screening, and advances tools for studying protein structure–function relationships.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry, School of Arts and Sciences, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104 USA",
    "Department of Biochemistry & Biophysics, Oregon State University Corvallis OR 97331 USA",
    "Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania 3620 Hamilton Walk Philadelphia PA 19104 USA",
    "Department of Organic Chemistry, Faculty of Science, University of Yaoundé I Yaoundé Cameroon",
    "Department of Medicine, Perelman School of Medicine, University of Pennsylvania 3400 Civic Center Boulevard Philadelphia PA 19104 USA",
    "Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania 421 Curie Boulevard Philadelphia PA 19104 USA"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 11,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Priyanda Giri"
    },
    {
      "affs": [
        0
      ],
      "name": "Yarra Venkatesh",
      "orcid": "0000-0002-4478-1553"
    },
    {
      "affs": [
        1
      ],
      "name": "Moriah H. Mathis",
      "orcid": "0000-0001-5182-0234"
    },
    {
      "affs": [
        2
      ],
      "name": "Christina M. Hurley",
      "orcid": "0000-0002-8821-7233"
    },
    {
      "affs": [
        2
      ],
      "name": "Chloe M. Jones"
    },
    {
      "affs": [
        0,
        3
      ],
      "name": "Olivier Ndogo Eteme"
    },
    {
      "affs": [
        4
      ],
      "name": "Zachary M. Hostetler"
    },
    {
      "affs": [
        1
      ],
      "name": "Richard B. Cooley",
      "orcid": "0000-0003-3928-2757"
    },
    {
      "affs": [
        4,
        5
      ],
      "name": "Rahul M. Kohli",
      "orcid": "0000-0002-7689-5678"
    },
    {
      "affs": [
        1
      ],
      "name": "Ryan A. Mehl"
    },
    {
      "affs": [
        0,
        5
      ],
      "name": "E. James Petersson",
      "orcid": "0000-0003-3854-9210"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1wkc5ykvb3b65.bib",
  "cited_by": 0,
  "doi": "10.1039/d6sc06723a",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13732730/",
  "id": "1wkc5ykvb3b65",
  "issns": [
    "2041-6520",
    "2041-6539"
  ],
  "landing_url": "https://doi.org/10.1039/d6sc06723a",
  "language": "en",
  "licence": "CC-BY-3.0",
  "licence_label": "CC BY 3.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/3.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Chemistry"
    ],
    [
      "openalex",
      "1312|RNA and protein synthesis mechanisms"
    ]
  ],
  "openalex": "W7166577443",
  "pdf_url": null,
  "pmcid": "PMC13732730",
  "pmid": "42985535",
  "published": "2026-11-04",
  "publisher": "Royal Society of Chemistry",
  "ris": "https://research.draconitic.com/paper/1wkc5ykvb3b65.ris",
  "sources": [
    {
      "first_seen": "2026-11-08T12:22:40Z",
      "native_id": "PMC13732730",
      "source": "pmc",
      "url": "https://doi.org/10.1039/d6sc06723a"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|RNA and protein synthesis mechanisms",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Genetic code expansion for site-specific encoding of a switchable, intrinsic fluorophore–quencher pair to monitor protein dynamics",
  "title_text": "Genetic code expansion for site-specific encoding of a switchable, intrinsic fluorophore–quencher pair to monitor protein dynamics",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T12:22:40Z",
  "url": "https://research.draconitic.com/paper/1wkc5ykvb3b65",
  "venue": "Chemical Science",
  "versions": []
}