Separation of Long DNA Molecules in a Microfabricated Entropic Trap Array

TLDR

A nanofluidic channel device with entropic traps was designed and fabricated to separate long DNA molecules. The device uses narrow constrictions and wider regions to trap DNA size‑dependently at constriction onsets, generating electrophoretic mobility differences that separate DNA without gels or pulsed fields. Long DNA fragments (5 kb–160 kb) were efficiently separated into distinct bands in 15‑mm channels, and parallel multi‑channel devices were demonstrated, indicating that the compact, easily fabricated system could enable practical integrated DNA analysis.

Abstract

A nanofluidic channel device, consisting of many entropic traps, was designed and fabricated for the separation of long DNA molecules. The channel comprises narrow constrictions and wider regions that cause size-dependent trapping of DNA at the onset of a constriction. This process creates electrophoretic mobility differences, thus enabling efficient separation without the use of a gel matrix or pulsed electric fields. Samples of long DNA molecules (5000 to ∼160,000 base pairs) were efficiently separated into bands in 15-millimeter-long channels. Multiple-channel devices operating in parallel were demonstrated. The efficiency, compactness, and ease of fabrication of the device suggest the possibility of more practical integrated DNA analysis systems.