De novo Design of Near Infrared Fluorescent Proteins

De novo Design of Near Infrared Fluorescent Proteins | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article De novo Design of Near Infrared Fluorescent Proteins David Baker, Chunfu Xu, Yulai Liu, Bernardo Arús, Kanuj Mishra, and 19 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4652998/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Fluorescent proteins have revolutionized the field of molecular imaging, enabling the visualization of diverse biological processes. Biological imaging in the near-infrared (NIR, 800-1000 nm) and shortwave infrared (SWIR, 1000-2000 nm) ranges confers a number of photophysical advantages, but remains a challenge in practice due to the dearth of suitable fluorescent proteins for these optical windows. To address this limitation, we sought to develop a general approach integrating computational protein design with organic synthesis for creating long-wavelength fluorescent proteins from scratch. We used this approach to design a new class of proteins that specifically bind to synthetic merocyanine dyes, forming Schiff base covalent linkages, which when protonated activate fluorescence with large redshifts in both excitation and emission wavelengths. Our de novo designed far-red fluorescent protein MC7BP34 exhibited a brightness greater than that of existing protein probes in a similar wavelength range. The de novo designed NIR fluorescent protein MC9BP81 with excitation at 892 nm and emission extending into the SWIR range demonstrated higher contrast and imaging sensitivity in vivo than the previously developed iRFP720 (excitation 672 nm) owing to the reduced tissue autofluorescence at longer wavelengths. Our results are a substantial step towards genetically encodable probes in the SWIR region, and our approach lays the groundwork for the development of NIR biosensors for specific biological applications. Biological sciences/Biochemistry/Proteins Biological sciences/Chemical biology/Protein design Biological sciences/Biophysics/Biological fluorescence Biological sciences/Biotechnology/Molecular engineering/Protein design Full Text Additional Declarations There is NO Competing Interest. Supplementary Files Supplementarymovie1.mp4 Supplementary movie 1 Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4652998","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":333102538,"identity":"a8c34c9e-9fae-4c3e-a62b-453e3bd73046","order_by":0,"name":"David 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