Restriction mapping in nanofluidic devices

Time-resolved restriction mapping of λ-DNA in nanochannels. (a) Restriction of three λ-DNA (48.5 kbp) molecules by using SmaI in channels of ≈120 nm × 120 nm cross-section. The DNA is stretched to ≈40% of its contour length. (Left) Individual 10-ms frames. (Right) Time traces, in which each line corresponds to intensity along the nanochannel in a single frame. From the known DNA sequence, we expect fragments of 19.4, 12.2, 8.3, and 8.6 kbp, in that order. (b) Restriction of three λ-DNA molecules by using SacI in channels of 140 nm × 180 nm cross-section. (Left) Individual 10-ms frames. (Right) Time traces. The DNA is expected to stretch to ≈25-30% of its contour length in channels of these dimensions. We expect fragments of 22.6, 0.9, and 24.8 kbp. The smallest 0.9-kbp segment is in general not visible. (c) Cutting 61-kbp DNA with PacI. The top panels are time traces of cutting in roughly 120 nm wide nano-channels, where we expect a stretch of 40%. (Right) Pulsed-field gel electrophoresis separation of the digestion product of an unpurified 61-kbp DNA and cloning vector. Lane 1,λ-DNA ladder; lane 2, long-range PFGE ladder; lanes 3 and 4, digestion product after Pacl.