Gel-on-a-chip: continuous, velocity-dependent DNA separation using nanoscale lateral displacement

Area of Science:

• Polymer physics
• Nanofluidics
• Biomolecular engineering

Background:

• Deterministic lateral displacement (DLD) arrays are micro/nanoscale devices used for particle and cell separation.
• Polymers exhibit complex dynamics in fluid flow, influenced by their size, shape, and flow conditions.
• Efficient separation and fractionation of polymers, such as DNA, are crucial for molecular biology and nanotechnology.

Purpose of the Study:

• To investigate polymer trajectory dynamics in a nanoscale deterministic lateral displacement (nanoDLD) array.
• To demonstrate the potential of nanoDLD devices as a continuous polymer fractionation tool.
• To establish optimal conditions for size-selective separation of double-stranded DNA (dsDNA) fragments.

Main Methods:

• Simulating and analyzing the trajectories of polymers advected and diffusing in a pressure-driven flow through a nanoDLD array.
• Utilizing double-stranded DNA (dsDNA) of varying lengths (100-10,000 base pairs) as a model system.
• Developing a phenomenological model to describe polymer trajectory dependence on gap size and flow velocity.

Main Results:

• Polymers follow size- and velocity-dependent trajectories in nanoDLD arrays.
• dsDNA fragments in the 100-10,000 bp range were separated with a resolution of 200 bp.
• Polymer elongation in shear flow leads to decreased trajectory angles with increasing flow velocity.
• Optimal separation conditions were identified, achieving over 75% recovery and 3-fold concentration of dsDNA fragments.
• Flow velocity was shown to be a key parameter for fine-tuning separation efficiency and resolution.

Conclusions:

• nanoDLD devices offer a continuous, size-selective fractionation method for polymers.
• The velocity-dependent behavior of polymer trajectories provides independent control over separation parameters.
• This technique enables precise separation and concentration of DNA fragments, with potential applications in molecular diagnostics and synthetic biology.