Grant: Engage Grants Program

Separation of DNA strands by size and subsequent isolation of specific fragment size ranges (size selection) isa requisite step for genomic analysis techniques and biotechnology applications that involve DNA. Gelelectrophoresis (GE) is the most common technique for size selection. In GE, the solution containing DNAstrands of different lengths is flowed through a gel via an external electric field. Due to the porosity of the gel,short strands move faster through the gel than long strands. Thus, after some time, strands of different lengthswill be at different locations in the gel. The section containing the desired strands can then be cut out of the geland purified for further analysis. While this approach is inexpensive and reliable, it does suffer somedrawbacks: it is time and labour intensive, prone to variability, and requires a large experimental setup that isindependent of the setup required for the actual genetic analysis. Coastal Genomics develops and sellsautomated solutions for separation by size via gel electrophoresis. This automation addresses the issue of beinglabour intensive and prone to variability, but the other drawbacks remain. Dr. de Haan has developed a novelnanopore design in which there is a large cavity between narrow entrance and exit pores. Simulations of thisgeometry for a generic polymer model demonstrate that this device is able to sort polymers by size - and it canin fact be tuned to have chains of an intermediate length pass through the device quickest with both shorter andlonger strands lagging behind. As opposed to GE, this technology is intrinsically automated, shows potential tobe time efficient and effective for a wide range of DNA sizes, and could be directly integrated into a largernano/micro-fluidic device in which the device is an in-line precursor to further downstreamanalysis/modification. This technology thus shows potential as a disruptive development for DNA sorting forgenomic and biotechnology applications and thus is of great interest for Coastal Genomics. The goal of thisgrant is to perform detailed simulations that reflect applications of interest to Coastal Genomics as a practicaltest of the technology to inform decisions for further development.