Extending chromosomal DNA in microstructures using electroosmotic flow

TLDR

Extending chromosomal DNA is essential for high‑resolution gene mapping, such as extended‑fibre FISH. The study introduces a micro‑device that integrates cell positioning, DNA extension, and fiber anchoring on a chip. The device employs a flow chamber with multi‑phase electrodes to generate controllable electroosmotic flow, micro‑pockets to position cells, and chemically modified pillars to anchor the hydrodynamically extended DNA. Controllable EOF reduces DNA breakage, producing fibers suspended a few microns above the surface that remain accessible to probes.

Abstract

The extension of chromosomal DNA is a key technique in high-resolution gene location such as extended fibre fluorescent in situ hybridization. In this paper, we propose a new micro-device designed for on-chip integration of three functions, (1) positioning of cells, (2) extending chromosomal DNA from the cells, and (3) anchoring the extended DNA fibres. The device has a flow chamber equipped with (a) multi-phase electrodes to create electroosmotic flow (EOF) of variable direction, (b) a set of micro-fabricated pocket-like structures for cell positioning, and (c) a micro-pillar array whose surface is chemically modified to anchor DNA fibres. First, unidirectional EOF is induced, by which cells are carried into the micro-pockets and positioned, one cell at each pocket. After rupturing the cells, chromosomal DNA from each cell is hydrodynamically extended by EOF. When the EOF direction is rotated through 90°, the fibres are made to contact with the pillars to be anchored. Because the velocity of the EOF is controllable, the breakage of DNA during the process can be minimized. Thus immobilized DNA fibres are suspended a few microns above the surface, allowing free access of probe molecules.