Single-Molecule Visualization of BLM-DNA2-Mediated DNA End Resection Using DNA Curtains

Abstract

Homologous recombination (HR) is the principal pathway undertaken by a cell for the error-free repair of DNA double-strand breaks that are frequently encountered by the cell. HR can be initiated at the sites of DNA double-strand breaks by generating long stretches of single-stranded 3' DNA overhang through a process called DNA end resection. In one DNA end resection pathway, this is achieved via the concerted effort of specialized machinery involving the RecQ family helicase BLM, the helicase/endonuclease DNA2, and a single-strand DNA binding protein complex RPA. BLM unwinds the DNA at the sites of DNA damage. The DNA unwound by BLM is cleaved in a 5' to 3' direction by DNA2 leaving behind a long single-stranded 3' DNA tail which is rapidly coated with RPA. This long single-stranded DNA provides the loading platform for recombinase proteins to form nucleoprotein filaments which initiate the homology search to undergo HR-based repair. Most of the insights into these processes have been gained using ensemble biochemical methods. However, these approaches have proven to be challenging for dissecting complex molecular mechanisms, especially because of the dynamic nature of these processes. Experiments involving single-molecule techniques have enabled us to counter these issues by allowing us to gather information on intermediates that are heterogeneous and transient in nature. We have developed a single-molecule technique called DNA curtains where we can study hundreds of protein-nucleic acid interaction events in real time. Here, we describe a method to prepare a single-tethered double-stranded DNA curtain to visualize, in combination with total internal reflection microscopy (TIRFM), the BLM- and DNA2-mediated DNA end resection in real time.

Keywords: BLM; DNA curtains; DNA end resection; DNA2; Homologous recombination; RPA; Single-molecule.