ArticleNucleic acids research2021
Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids.Journal of molecular evolution · 2025Article
- CHiTA: A scarless high-throughput pipeline for characterization of ribozymes.Methods (San Diego, Calif.) · 2025Article
- Protocells by spontaneous reaction of cysteine with short-chain thioesters.Nature chemistry · 2025Article
- Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.Nucleic acids research · 2024Article
- Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme.Nucleic acids research · 2024Article
- Prebiotic chiral transfer from self-aminoacylating ribozymes may favor either handedness.Nature communications · 2024Article
- Protocell Effects on RNA Folding, Function, and Evolution.Accounts of chemical research · 2024Article
- Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis.RNA (New York, N.Y.) · 2023Article
- Article
- Sequence dependent UV damage of complete pools of oligonucleotides.Scientific reports · 2023Article
- Article
- Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes.Nature communications · 2022Article
- RNA-Cleaving Deoxyribozymes Differentiate Methylated Cytidine Isomers in RNA.Angewandte Chemie (International ed. in English) · 2021Article
- Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
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4 authors.
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Abstract
Characterizing genotype-phenotype relationships of biomolecules (e.g. ribozymes) requires accurate ways to measure activity for a large set of molecules. Kinetic measurement using high-throughput sequencing (e.g. k-Seq) is an emerging assay applicable in various domains that potentially scales up measurement throughput to over 106 unique nucleic acid sequences. However, maximizing the return of such assays requires understanding the technical challenges introduced by sequence heterogeneity and DNA sequencing. We characterized the k-Seq method in terms of model identifiability, effects of sequencing error, accuracy and precision using simulated datasets and experimental data from a variant pool constructed from previously identified ribozymes. Relative abundance, kinetic coefficients, and measurement noise were found to affect the measurement of each sequence. We introduced bootstrapping to robustly quantify the uncertainty in estimating model parameters and proposed interpretable metrics to quantify model identifiability. These efforts enabled the rigorous reporting of data quality for individual sequences in k-Seq experiments. Here we present detailed protocols, define critical experimental factors, and identify general guidelines to maximize the number of sequences and their measurement accuracy from k-Seq data. Analogous practices could be applied to improve the rigor of other sequencing-based assays.
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