Correlative imaging by fluorescence and atomic force microscopy provides a versatile tool to extract orthogonal information on structurally heterogeneous biomolecular assemblies. In this chapter, we describe an integrated setup for correlative fluorescence and force microscopy. We present factors influencing data quality, as well as step-by-step protocols for sample preparation, data acquisition, and data processing that yield nanoscale topographic resolution, high image registration accuracy, and single-fluorophore sensitivity. We demonstrate the capabilities of the approach through simultaneous characterization of mesoscale geometry and composition in a multipart nucleoprotein complex.
Keywords: Atomic force microscopy (AFM); Correlative imaging; Protein-DNA interactions; Single-molecule localization microscopy (SMLM); Stepwise photobleaching.