Symmetry Breaking and Chiral Amplification in Prebiotic Ligation Reactions

Symmetry Breaking and Chiral Amplification in Prebiotic Ligation Reactions | 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 Symmetry Breaking and Chiral Amplification in Prebiotic Ligation Reactions Min Deng, Jinhan Yu, Donna G. Blackmond This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3694563/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 A general rationalization of the single chirality of biological molecules, a signature of life, remains a challenging goal. 1 Research has commonly focused on initial symmetry breaking and subsequent enantioenrichment of monomeric building blocks – sugars and amino acids – that comprise the genetic polymers RNA, DNA, and peptides. If these building blocks are only partially enantioenriched, however, stalling of chain growth may occur, whimsically termed in the case of nucleic acids as “the problem of original syn”. 2 In studying a novel prebiotically plausible route to proteinogenic peptides reported by Powner, 3-5 we discovered that the reaction favors heterochiral ligation, i.e., the ligation of l monomers with d monomers. While this finding appears problematic for the prebiotic emergence of homochiral l-peptides, we demonstrate, paradoxically, that this heterochiral preference provides a mechanism for enantioenrichment in homochiral chains. Symmetry breaking, chiral amplification, and chirality transfer processes occur for all reactants and products in multicomponent competitive reactions even when only one of the molecules in the complex mixture exhibits an imbalance in enantiomer concentrations (non-racemic). Solubility considerations lead to chemical purification and enhanced chiral amplification. Experimental data and kinetic modeling support this prebiotically plausible mechanism for the emergence of homochiral biological polymers. Organic Chemistry prebiotic chemistry homochirality peptide ligation catalysis Figures Figure 1 Figure 2 Figure 3 Full Text Additional Declarations The authors declare no competing interests. Supplementary Files SupportingInformation11102023.pdf 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-3694563","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":256586204,"identity":"66ca52f9-f7b1-48e0-a1bb-a66f2ca2538c","order_by":0,"name":"Min Deng","email":"","orcid":"","institution":"Scripps Research","correspondingAuthor":false,"prefix":"","firstName":"Min","middleName":"","lastName":"Deng","suffix":""},{"id":256586205,"identity":"1532bd03-1a4e-49e2-a60f-36c35620c390","order_by":1,"name":"Jinhan Yu","email":"","orcid":"","institution":"Scripps Research","correspondingAuthor":false,"prefix":"","firstName":"Jinhan","middleName":"","lastName":"Yu","suffix":""},{"id":256586206,"identity":"87912fa6-c6b4-4f70-b4cd-096649bb2846","order_by":2,"name":"Donna G. Blackmond","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA4ElEQVRIiWNgGAWjYBACA3YGBsYGIIMfxEuACuLXwgzVItlAshaDA0iCeLWYMzM//DgzxybP+PzhZx8e7rhjz8DevE0CnxbLZjZjyY3b0orNbqQZz0g88yyxgedYGV4tBocZzBgfbjucuO0GDzNDYtvhBAaJHDMCWti/gbVs7j8D1mLPIP+GkBYeM8aNQC0bGHLAWhgbJHjwa7Fs5imWnLktLXEG0C8MIL+08aQVW+DTYs7evvFj7zabxP7+w48ZfwJDjJ/98MYb+LSgAsaGAwxsxCuHaRkFo2AUjIJRgA4A70lMdfc/4oMAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0001-9829-8375","institution":"Scripps Research","correspondingAuthor":true,"prefix":"","firstName":"Donna","middleName":"G.","lastName":"Blackmond","suffix":""}],"badges":[],"createdAt":"2023-12-01 22:03:28","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-3694563/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-3694563/v2","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":49148184,"identity":"3572f07a-5792-4c97-962c-7d3b9c28cdec","added_by":"auto","created_at":"2024-01-03 21:35:58","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":203464,"visible":true,"origin":"","legend":"\u003cp\u003eCatalytic peptide ligation and chiral amplification under prebiotically relevant\u003c/p\u003e\n\u003cp\u003econditions. Panel a, Reaction between amidonitriles 1 and amino acids, amino amides, or peptides\u003c/p\u003e\n\u003cp\u003e2 catalyzed by thiols 4 or 5. Stereogenic center denoted as *. Panel b, Table, left: selected results\u003c/p\u003e\n\u003cp\u003efor different substrates and catalysts. Diastereomeric ratio (dr) = heterochiral:homochiral 3; Bar\u003c/p\u003e\n\u003cp\u003egraph, right: dr for different amino acid, amino amide, and dipeptide substrates 2 reacting with rac-\u003c/p\u003e\n\u003cp\u003eLeu-CN 1 using catalyst 5. Panel c, Left: enantiomeric excess of homochiral dipeptide product 3,\u003c/p\u003e\n\u003cp\u003eee3,homo, written in terms of the initial ee values of substrates 1 and 2 (eq. (a)) or homochiral product\u003c/p\u003e\n\u003cp\u003econcentrations 3LL and 3DD (eq. (b)); see Supporting Information for derivation of eq (a); Middle:\u003c/p\u003e\n\u003cp\u003e3D simulations of homochiral product 3 ee for reaction of equimolar 1 and 2 for a range of\u003c/p\u003e\n\u003cp\u003ekhetero:khomo values and initial ee values of 1 and 2 from 0 ≤ ee ≤ 1; Right: selected 2D slices from the\u003c/p\u003e\n\u003cp\u003e3D plot. Panel d, Experimental data and model simulations for the reaction of Panel a employing\u003c/p\u003e\n\u003cp\u003eLeu-CN 1 and Val 2 at different ee values. Symbols: experimental data; solid lines: model\u003c/p\u003e\n\u003cp\u003esimulations. Left: homochiral product 3 ee as a function of initial ee values of 1 and 2. Right:\u003c/p\u003e\n\u003cp\u003etemporal ee values for 1 and 2 and homochiral 3 as a function of conversion in the case shown in\u003c/p\u003e\n\u003cp\u003ethe upper plot with eei,1 = eei,2 = 0.5.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-3694563/v2/53af374804e91b341c8dffce.png"},{"id":49148340,"identity":"373fe0ae-11e0-42ed-ae7e-e8e5f42cf6e7","added_by":"auto","created_at":"2024-01-03 21:43:58","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":122339,"visible":true,"origin":"","legend":"\u003cp\u003eLigation reactions in complex mixtures. Panel a, Rate equations and simulation results\u003c/p\u003e\n\u003cp\u003efor competitive reactions of substrate 1 with either substrate 2 or 2’ for different cases of khetero:khomo\u003c/p\u003e\n\u003cp\u003ewith eei,1 = 0; eei,2 = 0 and eei,2’ = 0.5 (50%). Panel b, Experimental data and model prediction for\u003c/p\u003e\n\u003cp\u003ethe reaction of Leu-CN 1 (200 mM) with Leu 2 (50 mM) and Val 2’ (150 mM); eei,1 = 0 (squares)\u003c/p\u003e\n\u003cp\u003eor 3% ee (circles), eei,2 = 0; eei,2’ = 50%; catalyst 5 (400 mM), pD = 9.5, 5 oC, D2O.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-3694563/v2/b5ecd7e9240521afcdf15e1f.png"},{"id":49148186,"identity":"d3a6b9ba-43e3-4ebd-ba11-5dda1994ab76","added_by":"auto","created_at":"2024-01-03 21:35:58","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":255759,"visible":true,"origin":"","legend":"\u003cp\u003ePhysical processes leading to chemical purification and chiral amplification of\u003c/p\u003e\n\u003cp\u003edipeptide product 3. Panel a, Reaction of Leu-CN 1 (400 mM) and Val 2 (100 mM) with achiral\u003c/p\u003e\n\u003cp\u003ecatalyst 5 (400 mM) in D2O at pD = 9.5. Solution phase concentration equals % yield. Left: rac-\u003c/p\u003e\n\u003cp\u003eLeu-CN 1 and enantiopure L-Val 2. Right: rac-Leu-CN 1 and rac-Val 2. Panel b, Crystal structures\u003c/p\u003e\n\u003cp\u003eof sequential cosolvate products 3 from the ligation reaction between rac-Leu-CN 1 and rac-Val 2.\u003c/p\u003e\n\u003cp\u003e(heterochiral 3LD+3DL and homochiral 3LL+3DD). Experimental results and workflow shown for\u003c/p\u003e\n\u003cp\u003esolution phase ee3,homo and product 3 dr after reaction and after each precipitation event starting\u003c/p\u003e\n\u003cp\u003efrom 20% ee L-Leu-CN 1 and 20% ee L-Val 2.\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-3694563/v2/874cc634b7d5a7ff80c67c81.png"},{"id":49148531,"identity":"b55b2956-e19d-4f30-ba39-4db625deaadd","added_by":"auto","created_at":"2024-01-03 22:00:04","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":506991,"visible":true,"origin":"","legend":"","description":"","filename":"Nature20230814722BDec22.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3694563/v2_covered_8c3c9824-1bd0-4614-9543-256d6135712c.pdf"},{"id":49148187,"identity":"29b6eb5e-647c-48f6-bd4a-4671a3c36116","added_by":"auto","created_at":"2024-01-03 21:35:59","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":23719276,"visible":true,"origin":"","legend":"","description":"","filename":"SupportingInformation11102023.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3694563/v2/25f89426b8b361a7197e1968.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eSymmetry Breaking and Chiral Amplification in Prebiotic Ligation Reactions\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[{"identity":"9c092973-6b9e-4dda-aec0-a65fe1cf1fa5","identifier":"10.13039/100000893","name":"Simons Foundation","awardNumber":"SCOL 287625","order_by":0}],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"Scripps Research Institute","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":"prebiotic chemistry, homochirality, peptide ligation, catalysis","lastPublishedDoi":"10.21203/rs.3.rs-3694563/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3694563/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eA general rationalization of the single chirality of biological molecules, a signature of life, remains a challenging goal.\u003csup\u003e 1\u003c/sup\u003e Research has commonly focused on initial symmetry breaking and subsequent enantioenrichment of monomeric building blocks – sugars and amino acids – that comprise the genetic polymers RNA, DNA, and peptides. If these building blocks are only partially enantioenriched, however, stalling of chain growth may occur, whimsically termed in the case of nucleic acids as “the problem of original syn”.\u003csup\u003e2\u003c/sup\u003e In studying a novel prebiotically plausible route to proteinogenic peptides reported by Powner,\u003csup\u003e3-5\u003c/sup\u003e we discovered that the reaction favors heterochiral ligation, i.e., the ligation of l monomers with d monomers. While this finding appears problematic for the prebiotic emergence of homochiral l-peptides, we demonstrate, paradoxically, that this heterochiral preference provides a mechanism for enantioenrichment in homochiral chains. Symmetry breaking, chiral amplification, and chirality transfer processes occur for all reactants and products in multicomponent competitive reactions even when only one of the molecules in the complex mixture exhibits an imbalance in enantiomer concentrations (non-racemic). Solubility considerations lead to chemical purification and enhanced chiral amplification. Experimental data and kinetic modeling support this prebiotically plausible mechanism for the emergence of homochiral biological polymers.\u003c/p\u003e","manuscriptTitle":"Symmetry Breaking and Chiral Amplification in Prebiotic Ligation Reactions","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2024-01-03 21:35:53","doi":"10.21203/rs.3.rs-3694563/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":"2023-12-06 03:52:17","doi":"10.21203/rs.3.rs-3694563/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":"9a346e88-b133-4936-8cc4-b42e54a51114","owner":[],"postedDate":"January 3rd, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":27103029,"name":"Organic Chemistry"}],"tags":[],"updatedAt":"2023-12-06T03:52:17+00:00","versionOfRecord":[],"versionCreatedAt":"2024-01-03 21:35:53","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-3694563","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3694563","identity":"rs-3694563","version":["v2"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}