Optical Tweezers Controlled Nanopore Detection of Nucleosomes along a DNA

Abstract

Nucleosomes, the fundamental packaging unit of DNA inside eukaryotic cells, have both structural as well as functional roles in gene regulation. Genome-wide maps of nucleosome positions have significantly contributed towards our general understanding of regulation at transcription start sites, promoter regions and promoter boundary demarcations, but very little is known about the nucleosome positioning at local, single gene level. This calls for sensitive single-molecule tools to probe nucleosome positioning along a chromatin fiber. Nanopores have been used as a structural biosensor for DNA, DNA-bound proteins and very recently for nucleosomes [1]. Translocation of a biomolecule through the nanopore results in characteristic changes in the nanopore current which provides a direct readout of the molecular volume of the translocating complex. Resolving specifically positioned nucleosomes on DNA is however challenging due to lack of control on the speed of translocation. Here we use an optical tweezers assay to control the translocation of nucleosome arrays through a nanopore. An array of nucleosomes along a single DNA molecule is tethered to an optically trapped bead and the molecule is inserted into a nanopore at a controlled speed. Simultaneous measurements of force and nanopore current signals provide data on the position of nucleosomes on DNA. These experiments extend the reach of the nanopore platform into the study of chromatin biology.[1] Soni and Dekker, Nano Lett. (2012).