Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ)

Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ) | 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 Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ) Osman Doluca, Tugay Direk This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4558697/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 29 Oct, 2024 Read the published version in Journal of Computer-Aided Molecular Design → Version 1 posted 9 You are reading this latest preprint version Abstract G-quadruplexes refer to a large group of nucleic acid-based structures. In recent years, they have been attracting attention due to their biological roles in the telomeres and promoter regions. These structures show wide diversity in topology, however, development of methods for structural classification of G-quadruplexes has been evaded for a long time. There has been a limited number of studies aiming to bring forth a secondary structure classification method. The situation was even more complex than imagined, since the discovery of bulged and mismatched G-quadruplexes while most of the available tools fail to distinguish these non-canonical G-quadruplex motifs. Moreover, the interpretation of their analysis output still requires expert knowledge. In this study, we propose a new method for identification of unimolecular G Quadruplexes and classification by secondary structures based on three-dimensional structural data. Briefly, coordinates of guanines are processed to identify tetrads, loops and bulges. Then, we present the secondary structure in the form of a depiction which shows the loop types, bulges and guanines that participate in each tetrad. Finally, the results of our study are compared with DSSR and ElTetrado classification methods, and the advantages of the proposed depiction method for representing secondary structures were discussed. G-quadruplex Secondary structures Loop Bulge G-Tetrad Classification of G-quadruplexes Full Text Additional Declarations No competing interests reported. Supplementary Files Supplementary4.pdf Cite Share Download PDF Status: Published Journal Publication published 29 Oct, 2024 Read the published version in Journal of Computer-Aided Molecular Design → Version 1 posted Editorial decision: Revision requested 06 Jul, 2024 Reviews received at journal 03 Jul, 2024 Reviews received at journal 29 Jun, 2024 Reviewers agreed at journal 20 Jun, 2024 Reviewers agreed at journal 19 Jun, 2024 Reviewers invited by journal 19 Jun, 2024 Editor assigned by journal 19 Jun, 2024 Submission checks completed at journal 11 Jun, 2024 First submitted to journal 10 Jun, 2024 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. 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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-4558697","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":316938612,"identity":"26c00196-65d9-4267-99ae-af4c545e3bab","order_by":0,"name":"Osman Doluca","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA6klEQVRIiWNgGAWjYPACZgY+EPXBAMwzIE4LG5BknAHXkkCkFmYeBiK08POfTvxcwGAtxyaR/PCzTYFNYgN78zYJxh/3cGqRnJG7WXoGQ7oxm0SasXSOQVpiA8+xMgmGhGKcWgxu8G6Q5mE4nNgmkcMA1HI4sUEixwyoBbfLDM6f3fwbqoX5t4XB/8QG+TcEtBzI3QazhU0ayAXawoNfC9Av26x5DIB+4XlmZtljkGzcxpNWbJGQhlsLP//Zzbd5Kqzl+NmTH9/48cdOtp/98MYbH2xwa4E6D4kNiiAiYnIUjIJRMApGAT4AAFEXRa/vuf9aAAAAAElFTkSuQmCC","orcid":"","institution":"İzmir University of Economics","correspondingAuthor":true,"prefix":"","firstName":"Osman","middleName":"","lastName":"Doluca","suffix":""},{"id":316938615,"identity":"39075916-289d-40c9-adb4-7820f96a0281","order_by":1,"name":"Tugay Direk","email":"","orcid":"","institution":"İzmir University of Economics","correspondingAuthor":false,"prefix":"","firstName":"Tugay","middleName":"","lastName":"Direk","suffix":""}],"badges":[],"createdAt":"2024-06-10 14:40:30","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4558697/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4558697/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s10822-024-00573-1","type":"published","date":"2024-10-29T16:20:25+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":68207253,"identity":"db3807b0-0929-44fd-abe7-0d72e3bac2df","added_by":"auto","created_at":"2024-11-04 16:36:12","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":668937,"visible":true,"origin":"","legend":"","description":"","filename":"CIISGQ2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4558697/v1_covered_a36acd7a-9756-420d-910d-5209499c8ec1.pdf"},{"id":59068380,"identity":"bc9859bc-9530-4bad-b5b9-00a9b1165018","added_by":"auto","created_at":"2024-06-26 03:47:04","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":496321,"visible":true,"origin":"","legend":"","description":"","filename":"Supplementary4.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4558697/v1/6f6fedd3aa2c96aae5fbc5a6.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ)\n","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"journal-of-computer-aided-molecular-design","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"jcam","sideBox":"Learn more about [Journal of Computer-Aided Molecular Design](http://link.springer.com/journal/10822)","snPcode":"10822","submissionUrl":"https://submission.nature.com/new-submission/10822/3","title":"Journal of Computer-Aided Molecular Design","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"G-quadruplex, Secondary structures, Loop, Bulge, G-Tetrad, Classification of G-quadruplexes","lastPublishedDoi":"10.21203/rs.3.rs-4558697/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4558697/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"G-quadruplexes refer to a large group of nucleic\nacid-based structures. In recent years, they have been attracting\nattention due to their biological roles in the telomeres and\npromoter regions. These structures show wide diversity in\ntopology, however, development of methods for structural\nclassification of G-quadruplexes has been evaded for a long time.\nThere has been a limited number of studies aiming to bring forth\na secondary structure classification method. The situation was\neven more complex than imagined, since the discovery of bulged\nand mismatched G-quadruplexes while most of the available\ntools fail to distinguish these non-canonical G-quadruplex motifs.\nMoreover, the interpretation of their analysis output still\nrequires expert knowledge. In this study, we propose a new\nmethod for identification of unimolecular G Quadruplexes and\nclassification by secondary structures based on three-dimensional\nstructural data. Briefly, coordinates of guanines are processed to\nidentify tetrads, loops and bulges. 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