DNA Dynamic Regulation Theory Based on Potassium Channel “Origami Windmill” Model

DNA Origami Windmill Tetramer Model | 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Cite Share Download PDF Systematic Review DNA Origami Windmill Tetramer Model Zuodong Sun This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8200131/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 Although the classic DNA double helix model proposed by Watson and Crick explains the static storage mechanism of genetic information, it fails to reasonably account for the physical driving force behind high-speed and high-fidelity DNA replication. Furthermore, the core features of Rosalind Franklin's X-ray diffraction Pattern 51—"alternating black and white stripes with a slight tilt"—have not been fully interpreted within the static framework. Based on the standard B-type DNA double helix as the basic unit, this hypothesis proposes an original DNA Origami Windmill Tetramer Model by drawing on MacKinnon's research on the tetrameric structure of potassium ion channels and the mechanical principles of the potassium ion channel origami windmill model. Four DNA double helices assemble into an inverted conical tetrameric functional unit at a non-90° oblique angle corresponding to the diffraction characteristics of Franklin's Pattern 51, forming an inverted conical ion channel at the center. Its dynamic drive relies on the electrostatic repulsion of intracellular cations such as K⁺ and Na⁺, without the need for ATP hydrolysis for energy supply. The core of the model follows the logic of whole-chain non-denaturing replication, realizing genetic transmission through pairing and recombination between double-helix units, thereby avoiding the mismatch risk caused by single-strand exposure⁷. This reasonably explains the replication phenomenon in minimalist systems such as archaea and φ29 bacteriophages that do not require helicases, and clarifies that the classic enzyme system is only an auxiliary regulatory factor in the complex chromatin environment. Combining the core laws of molecular theory and 2ⁿ exponential logic, this study corrects the definition deviation between traditional DNA structural units and genetic functional units, confirming that the tetramer composed of 4 double helices is the optimal functional unit for complete DNA inheritance. Meanwhile, it is the first to reveal the direct correlation between the diffraction characteristics of Franklin's Pattern 51 and the folded stacking shape of the model's blades, breaking through the limitations of static cognition. This hypothesis provides a new and testable theoretical framework for dynamic DNA replication, whose predictions can be verified through five layers of decisive experiments. It is highly compatible with the classic double helix model and offers a testable theoretical perspective and experimental basis for research in related fields. DNA Origami Windmill Tetramer Inverted Conical Ion Channel Ion Repulsion-Driven Whole-Chain Non-Denaturing Replication ATP-Independent Franklin's Pattern 51 Dynamic DNA Regulation Molecular Theory G-Quadruplex Biophysics Higher-Order DNA Structure Genetic Functional Unit Full Text Additional Declarations The authors declare no competing interests. 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. 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-8200131","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Systematic Review","associatedPublications":[],"authors":[{"id":550864255,"identity":"8a3b66b5-356f-468e-b055-f2efc4c381bc","order_by":0,"name":"Zuodong Sun","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA60lEQVRIiWNgGAWjYPACZhA+wMBgUMPD2EC8FrYEoJZjMswkaOExADFs2AlpkZ+Re/gzT4W1nDn/mm8PfhSw8fA2MD98dAOPFoMbeQnGPGfSjS1nvN1u2GMgwyPZwGZsnINPi0SOQTJv2+HEDTfObpPgMWDjMWzgYZPGp0V+Ro7BYYiWM88k/xgw89gfIKCF4UaOYTNYy/keNmkeoBZGQrYYnHljzDgH6BeDG2zmxjIGx3gYmwn4Rb49x/jDG2CIGZw//Ozhmz819oztzQ8f43UYHEgksEEYzEQpBwH+A2xEqx0Fo2AUjIKRBQCzzEhI3wxFaAAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0002-5956-4826","institution":"Ya’ou Brain Science Institute of Heilongjiang Province","correspondingAuthor":true,"prefix":"","firstName":"Zuodong","middleName":"","lastName":"Sun","suffix":""}],"badges":[],"createdAt":"2025-11-25 07:26:09","currentVersionCode":2,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-8200131/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-8200131/v2","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":101753067,"identity":"1a866a2c-7171-43d7-8d5a-ae1e5a97ac1b","added_by":"auto","created_at":"2026-02-03 10:39:08","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":319154,"visible":true,"origin":"","legend":"","description":"","filename":"DNAOrigamiWindmillTetramerModel.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8200131/v2_covered_11162c3d-21f7-4161-9a31-b52f494d8303.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eDNA Origami Windmill Tetramer Model\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"Ya'ou Brain Science Institute of Heilongjiang province","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"DNA Origami Windmill Tetramer, Inverted Conical Ion Channel, Ion Repulsion-Driven, Whole-Chain Non-Denaturing Replication, ATP-Independent, Franklin's Pattern 51, Dynamic DNA Regulation, Molecular Theory, G-Quadruplex, Biophysics, Higher-Order DNA Structure, Genetic Functional Unit","lastPublishedDoi":"10.21203/rs.3.rs-8200131/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8200131/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eAlthough the classic DNA double helix model proposed by Watson and Crick explains the static storage mechanism of genetic information, it fails to reasonably account for the physical driving force behind high-speed and high-fidelity DNA replication. Furthermore, the core features of Rosalind Franklin's X-ray diffraction Pattern 51\u0026mdash;\"alternating black and white stripes with a slight tilt\"\u0026mdash;have not been fully interpreted within the static framework. Based on the standard B-type DNA double helix as the basic unit, this hypothesis proposes an original DNA Origami Windmill Tetramer Model by drawing on MacKinnon's research on the tetrameric structure of potassium ion channels and the mechanical principles of the potassium ion channel origami windmill model. Four DNA double helices assemble into an inverted conical tetrameric functional unit at a non-90\u0026deg; oblique angle corresponding to the diffraction characteristics of Franklin's Pattern 51, forming an inverted conical ion channel at the center. Its dynamic drive relies on the electrostatic repulsion of intracellular cations such as K⁺ and Na⁺, without the need for ATP hydrolysis for energy supply.\u003c/p\u003e \u003cp\u003eThe core of the model follows the logic of whole-chain non-denaturing replication, realizing genetic transmission through pairing and recombination between double-helix units, thereby avoiding the mismatch risk caused by single-strand exposure⁷. This reasonably explains the replication phenomenon in minimalist systems such as archaea and φ29 bacteriophages that do not require helicases, and clarifies that the classic enzyme system is only an auxiliary regulatory factor in the complex chromatin environment. Combining the core laws of molecular theory and 2ⁿ exponential logic, this study corrects the definition deviation between traditional DNA structural units and genetic functional units, confirming that the tetramer composed of 4 double helices is the optimal functional unit for complete DNA inheritance. Meanwhile, it is the first to reveal the direct correlation between the diffraction characteristics of Franklin's Pattern 51 and the folded stacking shape of the model's blades, breaking through the limitations of static cognition. This hypothesis provides a new and testable theoretical framework for dynamic DNA replication, whose predictions can be verified through five layers of decisive experiments. It is highly compatible with the classic double helix model and offers a testable theoretical perspective and experimental basis for research in related fields.\u003c/p\u003e","manuscriptTitle":"DNA Origami Windmill Tetramer Model","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2026-01-30 22:24:51","doi":"10.21203/rs.3.rs-8200131/v2","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2025-11-26 02:36:53","doi":"10.21203/rs.3.rs-8200131/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"edd2a62d-4d5a-4952-b165-78f94334997f","owner":[],"postedDate":"January 30th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-11-26T02:36:53+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-30 22:24:51","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-8200131","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8200131","identity":"rs-8200131","version":["v2"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}