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Dryad

Deep sequencing datasets from: RNA-catalyzed evolution of catalytic RNA

Data files

Feb 26, 2024 version files 7.24 GB

Abstract

This dataset includes raw and processed sequencing data from evolving RNA populations described in Nikos Papastavrou, David P Horning, Gerald F Joyce. "RNA-Catalyzed Evolution of Catalytic RNA" (submitted). Briefly, directed evolution of a hammerhead ribozyme sequence was carried out over eight rounds of three steps each: 1) templated synthesis of the reverse-complement hammerhead RNA by a polymerase ribozyme; 2) templated synthesis of a new copy of the hammerhead RNA from the reverse-complement by a polymerase ribozyme; 3) selective recovery of hammerhead RNA that cleaved an attached RNA substrate. Cleaved RNA was reverse transcribed, PCR amplified, and archived for sequencing, while a portion was in vitro transcribed with T7 RNA polymerase to initiate the next round of evolution. Two distinct branches of evolution were carried out for 8 rounds, using the '52-2' or '71-89' polymerase ribozymes to replicate RNA, respectively. Sequenced RNA populations were analyzed to determine polymerase ribozyme fidelity and study the evolution of hammerhead sequences replicated by polymerases with low or high RNA copying fidelities. The dataset includes raw sequence files, processed tables of mutations by position along the sequence for each polymerase, processed tables of the sequence frequency distribution from each round in the evolving populations, and spreadsheets containing final processed data used directly in manuscript figures and tables.