DNA molecules deviate from shortest trajectory when driven through hydrogel

Area of Science:

• Biophysics
• Polymer Science
• Nanotechnology

Background:

• Understanding DNA behavior in complex media is crucial for gene delivery and DNA sequencing.
• Agarose hydrogels present a challenging environment due to their mesh-like structure.

Purpose of the Study:

• To investigate the motion of DNA molecules in agarose hydrogels under DC electric fields.
• To quantify the off-axis diffusion and trajectory deviations of DNA driven through hydrogels.

Main Methods:

• Dynamic fluorescence-based single-molecule imaging.
• Applying DC electric fields (2-16 V/cm) to drive lambda-DNA (λ-DNA) through agarose hydrogels.
• Analyzing off-axis displacement distributions and trajectory paths.

Main Results:

• DNA molecules exhibit significant mobility orthogonal to the applied electric field.
• Off-axis dispersion increases with higher electric field strength.
• Time-normalized off-axis displacement follows a master curve, with time dependence varying with field strength (t^0.25 to t^0.6).
• Deviations from the shortest path increase as electric field strength decreases.

Conclusions:

• Hydrogel entanglement significantly influences DNA trajectory, leading to orthogonal diffusion.
• Electric field strength modulates DNA path tortuosity and off-axis dispersion.
• These findings have implications for manipulating and separating large DNA molecules in microfluidic devices.