Nanofluidic technologies for DNA replication analysis by optical mapping

DNA replication is essential to maintain genome integrity, and its anomalous progression is hallmark of tumorigenesis. Here we report on two complementary techniques to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. We apply them to detect deregulations of the replication program induced by an antitumor drug [1].

Nanofluidics is exploited to force the longitudinal spreading of DNA molecules through entropic constraints induced by the walls of the nanochannel ([2], left panel of the Figure). DNA molecules are then observed by fluorescence microscopy, and we detect replication patterns associated to the doubling of fluorescence intensity in replicated regions, which contain twice more DNA than unreplicated regions (right panel of the Figure).

REFERENCES:

1. “Analysis of DNA replication by optical mapping in nanochannels” J. Lacroix, S. Pélofy, C. Blatché, M.-J. Pillaire, S. Huet, C. Chapuis, J.-S. Hoffmann, A. Bancaud Small (2016) DOI: 10.1002/smll.201503795.
2. “Conformational manipulation of DNA in nanochannels using hydrodynamics” Q. He, H. Ranchon, P. Carrivain, Y. Viero, J. Lacroix, C. Blatché, E. Daran, J. M. Victor, A. Bancaud Macromolecules (2013) 46: 6195–6202.

Figure legend: The upper left series of images correspond to the setting up of the nanofluidic technology for DNA manipulation. The system consists of arrays of nanochannels of ~200 nm in cross-section, as shown by the Scanning electron micrographs. They are placed on an inverted microscope, and DNA transport is forced with hydrodynamic actuation. The time series at the lower left corresponds to the transport of one single chromosome fragment in the nanochannel. The time series at the right represents to a patterned molecule with replication tracks along its contour.