Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO®-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent “barcode” corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells.

We describe high-resolution lithography based on transfer of a pattern from an elastomeric "stamp" to a solid substrate by conformal contact: a nanoscale interaction between substrate and stamp on macroscopic scales that allows transport of material from stamp to substrate. The stamp is first formed by curing poly(dimethy1 siloxane) (PDMS) on a master with the negative of the desired surface, resulting in an elastomeric solid with a pattern of reliefs, typically a few microns deep, on its surface. The stamp provides an "ink" that forms a self-assembled monolayer (SAM) on a solid surface by a covalent, chemical reaction. Because SAMs act as highly localized and efficient barriers to some wet etches, microcontact printing forms part of a convenient lithographic system not subject to diffraction or depth of focus limitations while still providing simultaneous transfer of patterned features. Our study helps to define the strengths and limitations of microcontact printing with SAMs, a process that is