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  1. Raw Data for "Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway"

    Bonilla, Steve
    [ca. 2015] - 2017

    Matlab files containing single-molecule FRET traces and HMM fits. Please see README.txt for instructions on how to extract data from .proc files.

  2. Dissecting the energy, conformational, and evolutionary landscapes of a ubiquitous RNA tertiary structural motif through single-molecule and high-throughput studies

    Bonilla, Steve
    [Stanford, California] : [Stanford University], 2019.

    RNA's ability to fold into intricate tertiary structures and undergo precise conformational changes is essential for complex biological processes such as translation and pre-mRNA splicing. Although decades of research have revealed important characteristics of the RNA folding process, such as multiple folding pathways and misfolded states, a predictive and quantitative model of RNA folding is lacking. Previous work has revealed modularity of RNA structural motifs, and recent developments have provided evidence for a generalizable model of RNA folding based on reconstitution of the energetic and conformational properties of individual RNA motifs. In this thesis I discuss experimental and conceptual progress towards developing a predictive understanding of the energetic and conformational properties of a ubiquitous class of RNA tertiary contact motifs, the tetraloop/tetraloop-receptor (TL/TLR). First, I discuss the use of single-molecule FRET to dissect the multistep folding pathway of a subclass of TL/TLRs and identify folding steps that are common and distinct between TL/TLR sequence variants. Second, I discuss the use of a novel high-throughput platform to dissect the stability and conformational properties of hundreds of TL/TLR variants and identify types of TL/TLR thermodynamic and conformational behavior. Overall, the work presented in this thesis provides additional support for a reconstitution model in which RNA folding is quantitatively described from the properties of secondary and tertiary structural motifs and provides quantitative datasets that can be used to engineer RNAs with specified stabilities and defined conformational dynamics.

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