Protocol for effective surface passivation for single-molecule studies of chromatin and topoisomerase II

For single-molecule studies requiring surface anchoring of biomolecules, poorly passivated surfaces can result in alterations of biomolecule structure and function that lead to artifacts. Here, we present a surface passivation assay for single-molecule studies of chromatin and topoisomerase II. We detail steps for preparing a nucleosome array and hydrophobic nitrocellulose-coated flow cell. We then describe procedures for chromatin stretching with an angular optical trap (AOT) and performing a chromatin-topoisomerase experiment. This method is cost effective and potentially applicable to other biomolecules. For complete details on the use and execution of this protocol, please refer to Le et al. ¹.