Optical Mapping of Stretched DNA

For optical mapping, the DNA in 4 mm wide agarose fractions was stained with YOYO-1 (Invitrogen) and partially denaturated to produce the DR maps (Supplementary Information). Basic design and working principle of the device used in the experiment is described elsewhere^{11 (link),28 (link)}. Compared to the previous device design^{11 (link),28 (link)}, the present device has been modified so that the slit length is shorter (200 µm) and the cross-shaped slit is narrower at its centre (see Supplementary Fig. S1). Thus shorter molecules (>200 µm) can be stretched and imaged. Stretched DNA molecules were imaged with an Olympus IX81-ZDC2 microscope equipped with 100x/1.40 oil UPlanSApo objective. Images were recorded with an Andor’s iXon3 897 camera using 50-ms exposure and maximum electron multiplying (EM) gain. Molecule images presented in this paper were prepared with ImageJ^{58 (link)} and stitched with the ImageJ plugin Stitching^{59 (link)}. DR maps were aligned with the theoretical prediction for the melting profile of the hg19 human reference genome as previously described in^{11 (link),27 (link),28 (link)}.