Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips
Javier Aguirre Rivera, Guanzhong Mao, Anton Sabantsev, Mikhail Panfilov, Qiqi Hou, Michael K. Lindell, Christelle Chanez, Félix Ritort, Martin Jínek, Sebastian Deindl
Abstract
Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes.