Exploring a new dimension: Single-molecule interaction studies in sequence space

Abstract

Interactions are essential to life. At the cellular level, the most fundamental processes rely on interactions between DNA, RNA, and proteins. Given that the structure and function of these molecules are determined by their sequence, it is ultimately the sequence that dictates the strength and specificity of these interactions. Thus, to improve our understanding of biological processes, and even predict or manipulate them, it is imperative to obtain a comprehensive and quantitative overview of the relationship between sequence and interactions. One valuable method for studying these interactions in detail is single-molecule fluorescence microscopy. However, this technique is expensive and labor-intensive, making it impractical for large sequence libraries. In this thesis, we introduce a novel approach called SPARXS: Single-molecule Parallel Analysis for Rapid eXploration of Sequence space. By integrating single-molecule fluorescence microscopy with next-generation sequencing, this platform enables the simultaneous profiling of interactions with thousands of different DNA or RNA sequences at the single-molecule level.