Applying correlative single-molecule fluorescence and force microscopy to study protein-DNA interactions
DNA is both a fundamental building block of life and a versatile natural polymer. A myriad of DNA-binding proteins carry out their biological function by recognizing specific shapes and structures of DNA, or by actively altering the DNA configuration through force generation. Single-molecule techniques are ideally suited for studying these interactions thanks to their ability to follow dynamic processes in real time, while precisely exerting and measuring force on the system of interest. Extensively trained in this field, I have developed a research program that utilizes single-molecule fluorescence visualization and force manipulation to dissect the molecular mechanism of DNA-processing enzymes and DNA-templated machines. In particular, by combining single-molecule fluorescence and force microscopy, we were able to directly correlate the mechanical state of the DNA to the behavior of the protein-DNA complex. This unique approach allowed us to discover that the eukaryotic replicative helicase CMG employs a flexible gate to transition between an unwinding mode on ssDNA and a diffusion mode on dsDNA (Cell 2019), that the SMC complex Smc5/6 stably binds to ssDNA-dsDNA junctions and protects them from collapsing (Nat Commun 2022a), and that the linker histone H1 preferentially coalesces with ssDNA over dsDNA and forms co-condensates exhibiting distinct material properties (NSMB2022). These studies underscore the physical characteristics of DNA as an integral dimension of biological regulation and open a new avenue for interrogating genome transactions.
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Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria.