Fig. 1.

Experimental setup and chip design. (A) Schematic of how the chip, fluidic chuck, and heater are assembled and integrated in an experiment. A retaining ring held the chip clamped against a fluidic chuck via eight o-ring seals. The chuck was designed so that pneumatic pressure could be applied to bring fresh DNA into the nanoslit from the loading channels. In addition, the chuck was designed with a built-in “hot plate” so that the chip could be heated during experiments. A cartridge heater (Omega) was inserted into a cylindrical aluminum insert that was then gently pressed against the chip’s back surface. In order to monitor the temperature in situ, a thermocouple was threaded through the insert and placed in a hole drilled halfway through the silica sample. (This hole was located 2 mm away from the nanogroove region.) The hot-plate surface was painted with thermally conductive grease (Omegatherm) to enhance heat transfer. Thermocouple measurements of the chip surface temperature show that the measured thermal difference across the chip is comparable to the expected absolute accuracy of our thermocouple readings (∼1–2 °C). The fluctuations in thermocouple readings are ∼0.1 °C. (B) Three-dimensional diagram of the nanogroove and nanochannel arrays interfaced to microscale loading channels (1 μm deep, 50 μm wide). The nanochannels are etched first (120 nm), followed by the nanoslit (30 nm), to create nanogrooves within the open nanoslit region. Cartoon DNA molecules are shown in red. (C) Photograph of the chuck-chip-heater assembly on the microscope stage with external tubing for applying pressure. (D) Photograph of a chip clamped to the chuck via the aluminum retaining ring. (E) Low-magnification SEM micrograph of the nanochannels. (F) High-magnification SEM micrograph of a nanochannel (150 nm wide, 120 nm deep). (G) Raw image of λ-DNA molecules in nanochannels at 28 °C in 50% formamide (with background removed). (H) Example of single λ-DNA molecule from G with accompanying “time trace” of intensity integrated transverse to nanochannel axis plotted for all frames. (I Bottom) Time trace for molecule shown in H with thermal fluctuations “smoothed out” via rescaling procedure. (I Top) Intensity profile obtained by averaging over rescaled frames. The barcode shown below the plot is graphed data displayed as a grayscale plot. The scale bars are equal to 2 μm.