Conformational, Molecular, Spectral and Binding Properties of Zn(II)-Coordinated Glycol Nucleic Acid Monophosphate: A DFT, Docking and Molecular Dynamics Assessment

Conformational, Molecular, Spectral and Binding Properties of Zn(II)-Coordinated Glycol Nucleic Acid Monophosphate: A DFT, Docking and Molecular Dynamics Assessment | 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 Conformational, Molecular, Spectral and Binding Properties of Zn(II)-Coordinated Glycol Nucleic Acid Monophosphate: A DFT, Docking and Molecular Dynamics Assessment Mwikwm Basumatary, Phulung Basumatary, Satyajit Barman, Gunajyoti Das This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8926499/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 27 Apr, 2026 Read the published version in Structural Chemistry → Version 1 posted 10 You are reading this latest preprint version Abstract Glycol Nucleic Acid (GNA), the simplest xeno nucleic acid (XNA) featuring a propylene glycol unit, has attracted considerable attention due to its emerging therapeutic and biotechnological applications. The conformational, molecular, and spectral properties of the GNA nucleotide conformers containing cytosine, thymine, and uracil in both free and Zn(II)-coordinated forms were investigated for the first time using B3LYP/6-311 + + G(d,p). Further, binding characteristics of the metal coordinated entities with KRAS protein were investigated through docking and molecular dynamics simulations. The results suggest that incorporation of Zn(II) into the nucleobases induces significant deviations in the system’s electronic landscape including dipole moments, HOMO-LUMO gaps, chemical hardness, and electrophilicity. Docking and MD simulations highlight significant interactions of metal-GNA ligand with KRAS residues (ASP30, VAL29, GLU31), including characteristic hydrogen bonding patterns across the simulated replicas. Overall, the results presented herein are expected to provide valuable insights into the research field of engineered genetic materials. GNA Conformers DFT Docking MD Simulations Full Text Additional Declarations No competing interests reported. Supplementary Files SUPPORTINGINFORMATIONS.docx Cite Share Download PDF Status: Published Journal Publication published 27 Apr, 2026 Read the published version in Structural Chemistry → Version 1 posted Editorial decision: Revision requested 21 Mar, 2026 Reviews received at journal 15 Mar, 2026 Reviews received at journal 13 Mar, 2026 Reviewers agreed at journal 08 Mar, 2026 Reviewers agreed at journal 06 Mar, 2026 Reviewers agreed at journal 06 Mar, 2026 Reviewers invited by journal 05 Mar, 2026 Editor assigned by journal 03 Mar, 2026 Submission checks completed at journal 02 Mar, 2026 First submitted to journal 20 Feb, 2026 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. 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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-8926499","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":602529623,"identity":"e7a267ef-ad34-419a-b847-225b716985ae","order_by":0,"name":"Mwikwm Basumatary","email":"","orcid":"","institution":"Central Institute of Technology","correspondingAuthor":false,"prefix":"","firstName":"Mwikwm","middleName":"","lastName":"Basumatary","suffix":""},{"id":602529624,"identity":"8b5fbded-2e66-4861-8f8b-cbe8f4306028","order_by":1,"name":"Phulung Basumatary","email":"","orcid":"","institution":"Central Institute of 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