Microfluidics platform simplifies preparation of long DNA strands for optical mapping

When drawn taut in a line, larger DNA fragments allow researchers to use genomic optical mapping techniques to determine structural features of single cell samples, such as tumor subpopulations and embryos, across broad swaths of the human genome. Designing methods for handling long strands of single-cell DNA, however, often requires extensive planning to take everything from fluid actuation to reagent cross-reactions into account. A team of researchers has announced in Biomicrofluidics a new technique that leverages hydrogel encapsulation for handling these long fragments of DNA more easily.

The team demonstrated a water-in-oil droplet microfluidics technique to prepare alginate microparticles (AMP) to encapsulate, handle and then lyse (dissolve) cells using traditional benchtop protocols. The platform allows simplified manipulation and lysis of cells within the easily made AMP, followed by their release on-demand by dissolving the AMP.

Long DNA molecules trapped in AMP can be prepared for various types of optical mapping experiments. The team demonstrated the technique’s ability to house purified lymphoblast DNA fragments larger than 11 millimeters long, diffuse reagents within the AMP to selectively bind the DNA for visualization, and then transfer them to a microfluidic device for further processing.

Up to a chromosome in length, the strands have radii of gyration larger than AMP’s pore size, allowing for effective molecular isolation. Fragments are protected from shear forces during pipetting and can be introduced onto a microfluidic device largely intact.

Next the team will incorporate this platform for multiplex uses, especially in assays geared toward understanding epigenetic gene control, the silencing or enhancing of gene function over large areas of DNA through the use of various methods such as histone proteins.

Source: “Hydrogel droplet single-cell processing: DNA purification, handling, release, and on-chip linearization,” by Philip Zimny, David Juncker, and Walter Reisner, Biomicrofluidics (2018). The article can be accessed at https://doi.org/10.1063/1.5020571 .