Exploring the space of self-reproducing ribozymes using generative models

Camille N. Lambert, Vaitea Opuu, Francesco Calvanese, Polina Pavlinova, Francesco Zamponi, Eric J. Hayden, Martin Weigt, Matteo Smerlak and Philippe Nghe ()
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Camille N. Lambert: Université PSL
Vaitea Opuu: Université PSL
Francesco Calvanese: Université PSL
Polina Pavlinova: Université PSL
Francesco Zamponi: Sapienza Università di Roma
Eric J. Hayden: Boise State University
Martin Weigt: UMR 7238
Matteo Smerlak: Université PSL
Philippe Nghe: Université PSL

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Estimating the plausibility of RNA self-reproduction is central to origin-of-life scenarios. However, this property has been shown in only a handful of catalytic RNAs. Here, we compare models for their generative power in diversifying a reference ribozyme, based on statistical covariation and secondary structure prediction, and experimentally test model predictions using high-throughput sequencing. Leveraging statistical physics methods, we compute the number of ribozymes capable of autocatalytic self-reproduction from oligonucleotide fragments to be over 1039, with sequences found up to 65 mutations from the original sequence and 99 mutations away from each other, far beyond the 10 mutations achieved by deep mutational scanning. The findings demonstrate an efficient method for exploring RNA sequence space, and provide quantitative data on self-reproducing RNA that further illuminates the potential pathways to abiogenesis.

Date: 2025
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DOI: 10.1038/s41467-025-63151-5

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