Towards Single-Molecule Genomics: Muti-Color Localization in a Single Frame

The genome is composed of the genetic DNA code and a rich repertoire of epigenetic chemical DNA modifications, the epigenome, that form distinct signatures in health and disease. Unmasking the interplay between different genomic features is critical for understanding the operating system of life and is the key for effective personalized medicine. Nevertheless, there is no method today that can integrate multiple genomic observables, on the same genome and at the same time. To address this problem we propose a novel single-molecule fluorescence imaging setup for simultaneous acquisition of high-content genomic information from long DNA molecules stretched in nanochannel arrays. With the proposed optical concept which codes spectral information into spatial information in the image plane, we are able to acquire a spectral image that reports both on fluorescent markers locations as well as on their color with a single camera’s frame. In this talk, I will present preliminary results, showing the system’s ability to perform simultaneous multi-color, single-molecule imaging with continuously variable spectral resolution, thus enabling to map simultaneously up to 5 distinct genetic and epigenetic markers on the same large DNA molecule. This optical concept enables to co-localize multi-color markers in dynamic environments with unprecedent accuracy. The new approach will provide for the first time a holistic, high-content view of large genomic regions, elucidating the genetic and epigenetic variation between individual chromosomes. Moreover, this concept opens up new exciting applications such as imaging protein-protein and protein-DNA interactions, and probing protein dynamics by multi-color single-molecule FRET.