Trapping and separating objects in free solution by exploiting conformation-dependent electrophoretic mobility

Rensselaer Polytechnic Institute, Troy NY

Investigators

Abstract

The molecular structure of DNA gives rise to its twisting, ladder-like, double helix structure. Charged chemical groups link along the length of the ladder, forming the backbone for the sequence of base pairs that encodes genetic material. The double helix is folded and looped to fit within a cell, and the folded shape is dependent upon the sequencing of base pairs. Both the charging and shape of DNA provide a means to isolate and identify DNA. The response of DNA to an electric field (electrophoresis) has enabled laboratory isolation, sequencing, and unlocked the genetic code. To enable more rapid diagnostics, isolation can be accelerated by using the response of DNA to flow through microchannels, which is highly sensitive to shape, and thus sequencing. This project will develop and validate the theory necessary to simultaneously use charge and flow to isolate biomarkers, such as specific DNA sequences and viruses. Charged objects have an electrophoretic mobility that depends on their conformation. Conformation of folded molecules, in turn, is influenced by flow. This project will use computational methods to explore the fundamentals for isolation of deformable charged molecules in flow fields. Straight channels will be used to study cases in which separation occurs by different residence time through the device. Cross-slot channels will be used to study cases in which some molecules are trapped at the center of the device. Experiments with double-stranded DNA will be performed with the best device designs as validation of the mechanism for deformable polymers. Rigid orientable rods can resist compressional forces from the flow and electric field, which leads to an additional mechanism for trapping and separation. Simulations of rods with different flexibilities (from very rigid to very flexible) will determine how stiff the rods must be for this other mechanism to be present. The project will train two graduate students and two undergraduates, and incorporate the research into courses and online interactive tools that highlight application of mathematical modeling to biological separations. The project is the first step in developing next generation diagnostics for rapid identification of biological markers in a portable, small, and rapid device. This project is co-funded by the Molecular Separations program in the Division of Chemical, Bioengineering, Environmental and Transport Systems, and the Chemical Measurement and Imaging program in the Division of Chemistry. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.