| We designed, fabricated and tested a nanofluidic channel with submicron constrictions, to separate double-stranded DNA molecules according to their size. This channel consisted of alternating shallow and deep regions, which were fabricated by silicon based lithography and etching techniques. DNA molecules were driven through the channel by electrophoresis, and their motion was observed by fluorescence microscopy.; Because the radius of gyration of DNA used was much larger than the shallow region gap, DNA molecules were trapped when they moved from a deep to a shallow region. This entropic trapping determined the mobility of DNA in the system. The electrophoretic mobility of long DNA molecules in this channel was measured as a function of the electric field applied.; Counterintuitively, longer DNA molecules were found to escape entropic traps faster than shorter ones. DNA molecules overcome the entropic barrier by stretching their monomers into the constriction, and the activation energy barrier for DNA escape is independent of the chain length. However, a larger DNA molecule has a better chance of escaping entropic traps because of the larger contact area with the shallow region gap.; This size-dependent trapping process creates electrophoretic mobility differences between long and short DNA molecules, thus enabling efficient separation without using gel or pulsed electric fields. Samples of long DNA molecules (5 to 166 kilobase pairs) were efficiently separated into bands in 15-millimeter-long channels, typically within 30 minutes. Multiple channel devices operating in parallel were also demonstrated. The efficiency, compactness, and ease of fabrication of the device suggest the possibility of more practical integrated DNA analysis systems.; For the better performance and optimization of the entropic trap array device, effects on separation resolution due to the changes in several structural parameters were studied experimentally. A simple model for the mobility of DNA in the device was constructed and compared with experimental data. It was found that decreasing the both thickness of shallow and deep regions is desirable to get a better separation resolution. Several design standards were suggested for further improvement of the device. |
