{"id":76811,"date":"2025-11-27T11:00:00","date_gmt":"2025-11-27T10:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=76811"},"modified":"2026-04-15T14:00:55","modified_gmt":"2026-04-15T12:00:55","slug":"rna-in-action-filming-a-ribozymes-self-assembly","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science-technology\/rna-in-action-filming-a-ribozymes-self-assembly\/","title":{"rendered":"RNA in action: filming a ribozyme\u2019s self-assembly"},"content":{"rendered":"\n

RNA is a central biological molecule, now widely harnessed in medicine and nanotechnology. Like proteins, RNA often gets its function from its three-dimensional structure. A recent study in Nature Communications<\/a><\/em> has captured, for the first time, a ribozyme in motion \u2014 almost frame by frame. The researchers recorded how this tiny RNA machine folds, flexes, and assembles itself, revealing its intricate choreography in unprecedented detail.<\/p>\n\n\n\n

Using state-of-the-art techniques \u2014 cryo-electron microscopy<\/a> (cryo-EM), small-angle X-ray scattering (SAXS), RNA biochemistry and enzymology, image processing, and molecular simulations \u2014 the scientists observed the assembly of a self-splicing ribozyme \u2013 an RNA molecule that can \u2018cut and paste\u2019 its own sequence, essentially editing itself to become operational. They captured the dynamic \u2018behind-the-scenes\u2019 process by which the self-splicing ribozyme folds into its functional structure. The research was led by the team of Marco Marcia<\/a>, former EMBL Group Leader and currently Associate Professor and SciLifeLab<\/a> Group leader at Uppsala University<\/a>, Sweden.<\/p>\n\n\n\n

This breakthrough was made possible thanks to the cutting-edge facilities and expert services<\/a> at EMBL Grenoble, which enabled the integration of advanced structural biology methods with RNA biochemistry and enzymology. The Marcia group also benefited from close collaboration with the Centre for Structural Systems Biology<\/a> (CSSB) Hamburg, where innovative cryo-EM image processing approaches tailored for this specific project were developed, and the Istituto Italiano di Tecnologia<\/a> (IIT), which provided high-level molecular simulation expertise.<\/p>\n\n\n\n

\u201cDetermining RNA structures is a challenging task \u2013 the inherent flexibility and negative charge make RNA a notoriously difficult target for structural studies,\u201d said Shekhar Jadhav, former Predoctoral Fellow at EMBL Grenoble, now a postdoc at Uppsala University, Sweden. \u201cPersistent efforts and extensive screening on electron microscopes ultimately led us to visualise elusive RNA dynamics.\u201d<\/p>\n\n\n\n

How one domain orchestrates the RNA storyline<\/h2>\n\n\n\n

At the heart of this production is Domain 1 (D1), the ribozyme\u2019s central scaffold and, as it turns out, its director. This domain acts as a molecular gate, cueing the other domains (D2, D3, D4) to enter at precisely the right moment during the folding process.<\/p>\n\n\n\n

Subtle movements in key parts of the D1 molecule prompt one of its sections to open up and make way for the next. Each domain joins the scene only when the previous one is correctly in place, creating a seamless sequence of molecular choreography that prevents structural errors and ensures a flawless finale: the formation of a structure that can catalyse a chemical reaction, essential to the ribozyme’s function.<\/p>\n\n\n\n

Capturing the hidden takes<\/h2>\n\n\n\n

By analysing hundreds of thousands of single RNA particles, the team reconstructed intermediate \u2018takes\u2019 that were invisible in static crystal structures. These fleeting frames show how the RNA explores alternative poses before settling into its final conformation. <\/p>\n\n\n\n

\"\"\/
Dynamic representation of density maps for the two extreme conformational states that the group II intron acquires during folding, through a continuous dynamic movement of its structured helical motifs. Shekhar Jadhav\/EMBL<\/figcaption><\/figure>\n\n\n\n

\u201cTo capture these fleeting frames, we had to develop novel cryo-EM image-processing strategies,\u201d said Maya Topf<\/a>, Group Leader at CSSB<\/a>, Professor at the University Medical Centre Hamburg-Eppendorf, and a collaborator on the study. \u201cThis is a great example of how computational innovation and high-quality cryoEM data can reveal the hidden conformations of molecular machines.\u201d <\/p>\n\n\n\n

SAXS data and molecular dynamics simulations helped the scientists refine each frame and assemble the storyline.<\/p>\n\n\n\n

\u201cOne major strength of this work is the synergy between these cutting-edge new structural data on RNA and our advanced molecular simulations of this challenging system,\u201d said Marco De Vivo<\/a>, Head of Molecular Modeling and Drug Discovery Lab and Associate Director for Computation of Institu Italiano di Technologia<\/a> in Genoa, and one of the collaborators on this study. \u201cThis combined approach has clarified, at an unprecedented atomistic level of detail, the dynamic that drives the entire assembly of this RNA molecule, which now opens new avenues for drug discovery efforts targeting RNA.\u201d <\/p>\n\n\n\n

From ancient scripts to modern spin-offs<\/h2>\n\n\n\n

Group II introns, the ribozymes featured in this molecular film, are thought to be the ancestors of the spliceosome, the complex machinery that edits RNA in human cells. By revealing how these molecules fold efficiently and avoid kinetic traps, the study provides new insight into how early RNA-based life may have evolved its editing tools. Beyond evolutionary lore, this work also sets the stage for RNA design and engineering \u2013 guiding how future biotechnologies might script RNA molecules to fold correctly for use in therapeutics or nanobiotechnology.<\/p>\n\n\n\n

Opening the door to RNA AI<\/h2>\n\n\n\n

The detailed datasets and molecular mechanisms uncovered in this study offer a valuable benchmark for training and testing AI models. Some of the RNA structures resolved here have already been used in international CASP competitions<\/a> \u2014 the same predictive challenge that gave rise to AlphaFold \u2014 as recently described in the journal Proteins<\/a>.<\/p>\n\n\n\n

\u201cThis work is expected to play a key role in shaping artificial intelligence approaches to RNA structure prediction, paving the way towards a new \u2018AlphaFold for RNA\u2019.\u201d said Marcia.<\/p>\n\n\n\n

This convergence of experimental precision and machine learning marks a new phase for RNA structural biology, where AI and cryo-EM can learn from each other to predict, visualise, and understand the dynamics of life\u2019s most versatile molecule.<\/p>\n\n\n\n

\n\n\n\n

ARN en action : mieux comprendre l\u2019auto-assemblage du ribozyme<\/strong><\/h1>\n\n\n\n

Des chercheurs ont visualis\u00e9, avec un niveau de d\u00e9tail sans pr\u00e9c\u00e9dent, la fa\u00e7on dont une grande mol\u00e9cule d\u2019ARN, le ribozyme, s’assemble pour former une machine fonctionnelle.<\/strong><\/h3>\n\n\n\n

L\u2019ARN est une mol\u00e9cule biologique essentielle, aujourd\u2019hui largement exploit\u00e9e en m\u00e9decine et en nanotechnologie. \u00c0 l\u2019instar des prot\u00e9ines, l\u2019ARN tire souvent sa fonction de sa structure tridimensionnelle. Une \u00e9tude r\u00e9cente, publi\u00e9e dans Nature Communications<\/em><\/a>, a pour la premi\u00e8re fois captur\u00e9 un ribozyme en mouvement \u2014 presque image par image. Les chercheurs ont enregistr\u00e9 la fa\u00e7on dont cette minuscule machine d\u2019ARN se plie, se d\u00e9plie et s\u2019assemble, r\u00e9v\u00e9lant une chor\u00e9graphie d\u2019une complexit\u00e9 in\u00e9dite et d\u2019un niveau de d\u00e9tail sans pr\u00e9c\u00e9dent.<\/p>\n\n\n\n

En utilisant des techniques de pointe \u2014 cryo-microscopie \u00e9lectronique (cryo-EM), diffusion des rayons X aux petits angles (SAXS), biochimie et enzymologie de l\u2019ARN, traitement d\u2019images et simulations mol\u00e9culaires \u2014 les scientifiques ont observ\u00e9 l\u2019assemblage d\u2019un ribozyme auto-\u00e9pisseur, une mol\u00e9cule d\u2019ARN capable de \u00ab couper et coller \u00bb sa propre s\u00e9quence, pour s\u2019\u00e9diter en quelque sorte pour devenir op\u00e9rationnelle. Ils ont captur\u00e9 le processus dynamique et \u00ab en coulisses \u00bb par lequel le ribozyme auto-\u00e9pisseur se replie pour adopter sa structure fonctionnelle. La recherche a \u00e9t\u00e9 men\u00e9e par l\u2019\u00e9quipe de Marco Marcia<\/a>, ancien chef d\u2019\u00e9quipe \u00e0 l\u2019EMBL et actuellement professeur associ\u00e9 et chef de groupe SciLifeLab <\/a>\u00e0 l\u2019Universit\u00e9 d\u2019Uppsala<\/a>, en Su\u00e8de.<\/p>\n\n\n\n

Cette avanc\u00e9e a \u00e9t\u00e9 rendue possible gr\u00e2ce aux infrastructures de pointe et \u00e0 l\u2019expertise des services de l\u2019EMBL Grenoble<\/a>, qui ont permis d\u2019int\u00e9grer des approches avanc\u00e9es de biologie structurale \u00e0 la biochimie et \u00e0 l\u2019enzymologie de l\u2019ARN. L\u2019\u00e9quipe Marcia a \u00e9galement b\u00e9n\u00e9fici\u00e9 d\u2019une collaboration \u00e9troite avec le Center for Structural Systems Biology<\/a> (CSSB) \u00e0 Hambourg, o\u00f9 des m\u00e9thodes innovantes de traitement d\u2019images en cryo-EM ont \u00e9t\u00e9 d\u00e9velopp\u00e9es sp\u00e9cifiquement pour ce projet, ainsi qu\u2019avec l\u2019Istituto Italiano di Tecnologia <\/a>(IIT), qui a apport\u00e9 son expertise en simulations mol\u00e9culaires.<\/p>\n\n\n\n

\u00ab D\u00e9terminer la structure de l\u2019ARN est une t\u00e2che ardue : sa flexibilit\u00e9 intrins\u00e8que et sa charge n\u00e9gative en font une cible difficile pour les \u00e9tudes structurales \u00bb, explique Shekhar Jadhav, ancien doctorant \u00e0 l\u2019EMBL Grenoble et aujourd\u2019hui postdoctorant \u00e0 l\u2019Universit\u00e9 d\u2019Uppsala, en Su\u00e8de. \u00ab Des efforts soutenus et un criblage approfondi au microscope \u00e9lectronique nous ont finalement permis de visualiser des dynamiques de l\u2019ARN jusque-l\u00e0 insaisissables. \u00bb<\/p>\n\n\n\n

De cela en r\u00e9sulte le \u201cfilm mol\u00e9culaire\u201d le plus complet \u00e0 ce jour montrant une mol\u00e9cule d\u2019ARN en train de se construire elle-m\u00eame, r\u00e9v\u00e9lant comment elle \u00e9vite l\u2019\u00e9quivalent biologique des prises rat\u00e9es : des \u00e9tats mal repli\u00e9s et non fonctionnels, connus sous le nom de pi\u00e8ges cin\u00e9tiques.<\/p>\n\n\n\n

Le sc\u00e9nario de l’ARN orchestr\u00e9 par le Domaine D1<\/h2>\n\n\n\n

Au c\u0153ur de cette chor\u00e9graphie se trouve le Domaine 1 (D1), le support central du ribozyme et, en quelque sorte, son metteur en sc\u00e8ne. Ce domaine agit comme une entr\u00e9e de sc\u00e8ne mol\u00e9culaire, donnant le signal aux autres domaines (D2, D3, D4) d\u2019entrer \u00e0 un moment exact lors du repliement.<\/p>\n\n\n\n

De subtils mouvements au sein de r\u00e9gions cl\u00e9s de la mol\u00e9cule D1 incitent l\u2019une de ses sections \u00e0 s\u2019ouvrir pour laisser passer la suivante. Chaque domaine n\u2019entre en sc\u00e8ne que lorsque le pr\u00e9c\u00e9dent est correctement positionn\u00e9, cr\u00e9ant une s\u00e9quence fluide de chor\u00e9graphie mol\u00e9culaire qui pr\u00e9vient les erreurs structurelles et garantit un final sans faute : la formation d\u2019une structure capable de catalyser une r\u00e9action chimique, indispensable \u00e0 la fonction du ribozyme.<\/p>\n\n\n\n

Retrouver les prises perdues<\/h2>\n\n\n\n

En combinant plusieurs m\u00e9thodes d\u2019analyse sur des centaines de milliers de particules individuelles, l\u2019\u00e9quipe a pu reconstruire des \u00ab prises \u00bb interm\u00e9diaires invisibles dans les structures cristallines, statiques usuellement observ\u00e9es par cristallographie \u00e0 rayon X. Ces images fugaces montrent comment l\u2019ARN explore des positions alternatives avant de se stabiliser dans sa conformation finale.<\/p>\n\n\n\n

\"\"
R\u00e9solution dynamique des deux \u00e9tats conformationnels extr\u00eames que l’intron du groupe II acquiert lors du repliement, gr\u00e2ce \u00e0 un mouvement dynamique continu de ses motifs h\u00e9lico\u00efdaux structur\u00e9s. Shekhar Jadhav\/EMBL<\/figcaption><\/figure>\n\n\n\n

\u00ab Pour capturer ces mouvements fugaces, nous avons d\u00fb d\u00e9velopper de nouvelles strat\u00e9gies de traitement d\u2019images en cryo-EM \u00bb, explique Maya Topf<\/a>, cheffe d\u2019\u00e9quipe au CSSB<\/a>, professeure au Centre m\u00e9dical universitaire de Hambourg-Eppendorf et collaboratrice de l\u2019\u00e9tude. \u00ab C\u2019est un excellent exemple de la mani\u00e8re dont l\u2019innovation computationnelle et des donn\u00e9es cryo-EM de haute qualit\u00e9 peuvent r\u00e9v\u00e9ler les conformations cach\u00e9es des machines mol\u00e9culaires. \u00bb<\/p>\n\n\n\n

Les donn\u00e9es de SAXS et les simulations de dynamique mol\u00e9culaire ont aid\u00e9 les scientifiques \u00e0 affiner chaque \u00ab image \u00bb et \u00e0 assembler le fil narratif. <\/p>\n\n\n\n

\u00ab L\u2019un des grands atouts de ce travail r\u00e9side dans la synergie entre ces nouvelles donn\u00e9es structurales de pointe sur l\u2019ARN et nos simulations mol\u00e9culaires avanc\u00e9es de ce syst\u00e8me complexe \u00bb, souligne Marco De Vivo<\/a>, responsable du laboratoire de mod\u00e9lisation mol\u00e9culaire et d\u00e9couverte de m\u00e9dicaments, et directeur associ\u00e9 pour le calcul \u00e0 l\u2019Institut Italien de Technologie<\/a> de G\u00eanes, ainsi que l\u2019un des collaborateurs de l\u2019\u00e9tude. \u00ab Cette approche combin\u00e9e a permis de clarifier, avec un niveau de d\u00e9tail atomistique jamais atteint, la dynamique qui gouverne l\u2019assemblage complet de cette mol\u00e9cule d\u2019ARN \u2014 ouvrant ainsi de nouvelles perspectives pour la d\u00e9couverte de m\u00e9dicaments ciblant l\u2019ARN. \u00bb<\/p>\n\n\n\n

De l\u2019ancien manuscrit \u00e0 la spin-off moderne <\/h2>\n\n\n\n

Les introns de groupe II, les ribozymes mis en sc\u00e8ne dans ce film mol\u00e9culaire, sont consid\u00e9r\u00e9s comme les anc\u00eatres du spliceosome, la machinerie complexe qui \u00e9dite l\u2019ARN dans les cellules humaines. En montrant comment ces mol\u00e9cules se replient efficacement et \u00e9vitent les pi\u00e8ges cin\u00e9tiques, l\u2019\u00e9tude offre un nouvel \u00e9clairage sur la mani\u00e8re dont les premi\u00e8res formes de vie fond\u00e9es sur l\u2019ARN ont pu d\u00e9velopper leurs outils d\u2019\u00e9dition.<\/p>\n\n\n\n

Au-del\u00e0 de l\u2019aspect \u00e9volutif, ces travaux pr\u00e9parent \u00e9galement le terrain pour la conception et l\u2019ing\u00e9nierie de l\u2019ARN : ils orientent la mani\u00e8re dont les biotechnologies de demain pourront programmer des mol\u00e9cules d\u2019ARN capables de se replier correctement pour des usages th\u00e9rapeutiques ou en nanobiotechnologie.<\/p>\n\n\n\n

Ouvrir la voie \u00e0 l\u2019IA pour l\u2019ARN<\/h2>\n\n\n\n

Les jeux de donn\u00e9es d\u00e9taill\u00e9s et les m\u00e9canismes mol\u00e9culaires mis au jour dans cette \u00e9tude constituent une r\u00e9f\u00e9rence pr\u00e9cieuse pour l\u2019entra\u00eenement et l\u2019\u00e9valuation des mod\u00e8les d\u2019IA. Certaines des structures d\u2019ARN r\u00e9solues ici ont d\u00e9j\u00e0 \u00e9t\u00e9 utilis\u00e9es dans les comp\u00e9titions internationales CASP<\/a> \u2014 le m\u00eame d\u00e9fi pr\u00e9dictif qui a donn\u00e9 naissance \u00e0 AlphaFold \u2014 comme r\u00e9cemment d\u00e9crit dans la revue Proteins<\/em><\/a>.<\/p>\n\n\n\n

\u00ab Ces travaux devraient jouer un r\u00f4le cl\u00e9 dans l\u2019\u00e9laboration d\u2019approches d\u2019intelligence artificielle d\u00e9di\u00e9es \u00e0 la pr\u00e9diction de la structure de l\u2019ARN, ouvrant la voie vers un nouvel \u201cAlphaFold de l\u2019ARN\u201d \u00bb, d\u00e9clare Marcia.<\/p>\n\n\n\n

Cette convergence entre pr\u00e9cision exp\u00e9rimentale et apprentissage automatique marque une nouvelle \u00e9tape pour la biologie structurale de l\u2019ARN, o\u00f9 l\u2019IA et la cryo-EM peuvent s\u2019enrichir mutuellement pour pr\u00e9dire, visualiser et comprendre la dynamique de la mol\u00e9cule la plus polyvalente du vivant.<\/p>\n","protected":false},"excerpt":{"rendered":"

Researchers have visualised, in unprecedented detail, how a large RNA molecule assembles itself into a functional machine.<\/p>\n","protected":false},"author":179,"featured_media":77361,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[17591],"tags":[4718,17279,3718,37,1748,70,76,251,35],"embl_taxonomy":[9792,19331,19017],"class_list":["post-76811","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science-technology","tag-artificial-intelligence","tag-cryo-electron-microscopy","tag-engineering","tag-grenoble","tag-press-release","tag-rna","tag-service","tag-small-angle-x-ray-scattering-saxs","tag-structural-biology","embl_taxonomy-embl-grenoble","embl_taxonomy-marcia-group-visiting","embl_taxonomy-marco-marcia"],"acf":{"vfwp-news_embl_taxonomy":[19331,19017,9792],"featured":true,"show_featured_image":false,"field_target_display":"embl","field_article_language":{"value":"english","label":"English"},"article_intro":"

Researchers have visualised, in unprecedented detail, how a large RNA molecule assembles itself into a functional machine<\/p>\n","related_links":[{"link_description":"Marcia Group","link_url":"https:\/\/www.embl.org\/groups\/marcia\/"},{"link_description":"Electron Microscope Facility","link_url":"https:\/\/www.embl.org\/services-facilities\/grenoble\/cryoem\/"}],"source_article":[{"publication_title":"Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy","publication_link":{"title":"","url":"https:\/\/www.nature.com\/articles\/s41467-025-65502-8","target":""},"publication_authors":"Jadhav S., et al. ","publication_source":"Nature Communications","publication_date":"11November 2025","publication_doi":"https:\/\/doi.org\/10.1038\/s41467-025-65502-8"}],"in_this_article":[{"heading_description":"","anchor":""}],"press_contact":"EMBL Generic","article_translations":[{"translation_language":"Fran\u00e7ais","translation_anchor":"#FR"}],"languages":"","vf_locked":false},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"b14d3f13-5670-44fb-8970-e54dfd9c921a\";i:1;s:36:\"89e00fee-87f4-482e-a801-4c3548bb6a58\";i:2;s:36:\"8f81131e-d37c-470c-848f-618fce652295\";}","parents":[],"name":["EMBL Grenoble"],"slug":"embl-grenoble","description":"Where > All EMBL sites > EMBL Grenoble"},{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"fc528877-4017-438f-85b4-de2b54c443f1\";i:2;s:36:\"da5e1956-e83f-40da-af52-60b91bd63b67\";}","parents":[],"name":["Marcia Group (Visiting)"],"slug":"marcia-group-visiting","description":"What > Structural Biology (EMBL Grenoble) > Marcia Group (Visiting)"},{"uuid":"a:2:{i:0;s:36:\"4428d1fd-441a-4d6d-a1c5-5dcf5665f213\";i:1;s:36:\"d7b7dd88-87fb-478e-9a19-11be34646f75\";}","parents":[],"name":["Marco Marcia"],"slug":"marco-marcia","description":"Who > Marco Marcia"}],"yoast_head":"\nRNA in action: filming a ribozyme\u2019s self-assembly | EMBL<\/title>\n<meta name=\"description\" content=\"Researchers have captured, in unprecedented detail, how a large RNA molecule assembles itself into a functional machine\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science-technology\/rna-in-action-filming-a-ribozymes-self-assembly\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"RNA in action: filming a ribozyme\u2019s self-assembly | EMBL\" \/>\n<meta property=\"og:description\" content=\"Researchers 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