Development of a platform for single cell genomics using convex lens-induced confinement

Area of Science:

• Biotechnology
• Microfluidics
• Genomics

Background:

• Single-cell analysis is crucial for understanding cellular heterogeneity.
• Existing methods often face challenges in efficiency and throughput.
• Microfluidic devices offer potential for integrated cellular analysis.

Purpose of the Study:

• To develop an integrated lab-on-a-chip device for comprehensive in situ single-cell analysis.
• To utilize Convex Lens-Induced Confinement (CLIC) for dynamic control of microfluidic dimensions.
• To enable efficient extraction and optical interrogation of genomic DNA from single cells.

Main Methods:

• Integration of micro/nano-fabricated features with a CLIC device.
• Development of a flow-control mechanism for precise buffer exchange and molecule loading.
• Finite element simulation to optimize fluid flow and overcome hydraulic resistance.
• On-chip protocols for cell trapping, lysis, protein digestion, DNA extraction, and linearization.

Main Results:

• Demonstrated a complete cycle of single-cell analysis on-chip.
• Achieved efficient trapping, isolation, and lysis of single cells.
• Successfully extracted and linearized Mbp-long genomic DNA from a single human cell.
• Stretched extracted DNA molecules in nanochannels for optical interrogation.

Conclusions:

• The developed lab-on-a-chip, utilizing CLIC, provides an efficient platform for in situ single-cell genomic analysis.
• Optimized fluid dynamics and confinement are key to overcoming micro/nano-confinement challenges.
• This technology enables the interrogation of large DNA molecules from individual cells, advancing genomic studies.