Pushing Limits of DNA Sequencing: DNA Capture and Sequencing Using Nanopore-Coupled Zero-Mode Waveguides

We are developing a new platform for high-throughput single molecule, real-time (SMRT) sequencing of DNA and RNA molecules. The system integrates the familiar zero-mode waveguides (ZMWs), optical wells in which single-dye fluorescence signals are acquired during DNA replication, with pore-containing membranes, which allow electrophoretic molecular focusing of charged analytes into the ZMWs for subsequent interrogation. We observe in interesting packaging process of DNA into the waveguides, length dependence, and anomalously long residence times, which we attribute to entanglement of the DNA inside the ZMWs.

Dr. Meni Wanunu is an Assistant Professor of Physics and Chemistry at Northeastern University. His research involves studying biosystems at the nanoscale (macromolecular and sub-molecular levels). Subtle changes in the chemical structure of biomolecules can enormously impact their function: In the morning sickness drug thalidomide, the enantiomeric form (mirror image of the same exact molecule) causes severe birth defects; a single base substitution in a gene, aka a mutation, is sufficient to cause disease by producing a malfunctioning protein; subtle changes in molecular structure to DNA, such as the addition of a methyl group, are now known to regulate gene expression. Many of the mechanisms by which miniscule chemical changes affect biomolecular function are unknown to date.