Detecting Single Molecule Deoxyribonucleic Acid in a Cell Using a Three-Dimensionally Integrated Nanopore

Area of Science:

• Nanotechnology
• Genomics
• Biophysics

Background:

• Genetic variation analysis is crucial for personalized medicine.
• Current methods often require complex amplification steps.
• Single-molecule detection offers a more direct approach.

Purpose of the Study:

• To develop an amplification-free method for in situ single-molecule DNA detection within cells.
• To demonstrate a novel 3D-integrated nanopore device for ionic current measurements.
• To explore the potential for on-chip sequencing and multi-omics analysis at the single-cell level.

Main Methods:

• Fabrication of a 3D-integrated nanopore device using SiO2 and SiNx membranes on a Si wafer.
• Application of a high electrostatic field for single-cell lysis and multinanopore focusing.
• Detection of intracellular molecules via ionic current measurements as they pass through the nanopore sensing zone.

Main Results:

• Successful demonstration of single-cell lysis using a focused electrostatic field.
• Observation of unique telegraphic current signatures corresponding to DNA molecule folding within the nanopore.
• Establishment of a direct, amplification-free method for analyzing single DNA molecules in situ.

Conclusions:

• The 3D-integrated nanopore device enables direct, amplification-free detection of single DNA molecules in cells.
• The observed current signatures provide insights into polynucleotide folding dynamics.
• This technology holds promise for advancing on-chip single-molecule sequencing and single-cell multi-omics.