Structure of a duplex-embedded G-quadruplex system resolved to 7.4 Å resolution by cryo-EM

Structure of a duplex-embedded G-quadruplex system resolved to 7.4 Å resolution by cryo-EM | 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 Research Article Structure of a duplex-embedded G-quadruplex system resolved to 7.4 Å resolution by cryo-EM Robert Monsen, Eugene Chua, Jesse Hopkins, Jonathan Chaires, John Trent This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1902173/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5’ G-tetrad interface with a persistently unstacked 3’ duplex. The surrogate complement poly dT loop preferably stacks onto the 3’ G-tetrad interface resulting in occlusion of both 5’ and 3’ tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. Our results illustrate how the integration of cryo-EM, MD, and SAXS can reveal complementary detailed static and dynamic structural information on DNA G4 systems. Structural Biology quadruplex promoter model cryo EM structure Full Text Additional Declarations There is NO Competing Interest. Supplementary Files DGDMSsupplemental.pdf videos.zip Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions 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. 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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-1902173","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":127392446,"identity":"1f1945ae-db3f-448c-bcac-89919bee3e4a","order_by":0,"name":"Robert Monsen","email":"","orcid":"","institution":"University of Louisville","correspondingAuthor":false,"prefix":"","firstName":"Robert","middleName":"","lastName":"Monsen","suffix":""},{"id":127392447,"identity":"4ff762e5-1bb8-44cb-8d67-4586ad07f044","order_by":1,"name":"Eugene Chua","email":"","orcid":"https://orcid.org/0000-0003-1224-2157","institution":"New York Structural Biology 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Extensive \u003cem\u003ein vivo \u003c/em\u003einvestigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5’ G-tetrad interface with a persistently unstacked 3’ duplex. The surrogate complement poly dT loop preferably stacks onto the 3’ G-tetrad interface resulting in occlusion of both 5’ and 3’ tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. 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