Electrophoretic and nanopore methods for biomolecule analysis

Nucleic acids are growing in importance as diagnostic molecules for a variety of disease states and responses to treatment, both as indicators of genetic predisposition, and as biomarkers of disease. In many cases, nucleic acid biomarker diagnostic techniques have fallen short of their revolutionary potential, in part due to the difficulty associated with extraction of rare nucleic acids from contaminated samples, and due to the cost and complexity of extraction and analysis techniques. I will present two technologies we have developed to help address these issues. The first, SCODA, is a non-linear electrophoresis technology that uses a form of second-harmonic generation in DNA electrophoresis to generate unique velocity fields in a gel. These allow highly selective extraction of nucleic acids from samples, including sequence-specific extraction. The second is an implementation of force spectroscopy using nanometer scale pores. This technique allows us to detect DNA sequence with single nucleotide resolution, without labeling of the target molecule, and in some cases can be used to uncover heterogeneity of molecule populations by extracting information on individual molecules one at a time. A variety of applications will be presented, ranging from metagenomics of Alberta tar sands, to prion protein stability analysis using nanopore force spectroscopy.