High throughput system for preparing samples for genomic and epigenetic assays

Abstract

Genomic and epigenomic therapies hold great promise for “fixing” faulty genes. In genomics, DNA is sequenced to determine the order of the nucleotides, while in epigenetics, immunoprecipitation of chromatin is used to locate specific proteins of interest. The first step for these therapies is to identify the specific sequence or gene responsible for the disease. To prepare samples for these assays, DNA or chromatin is sheared into fragments, most often using cavitation. However, standard tools such as ultrasonic horns can be highly inconsistent, leading to poor assays. In order to overcome the problems of inconsistent fragmentation, we designed and built a transducer array (free field pressures P + = 30 MPa, P- = 12 MPa) capable of processing samples directly in 96-well microplates. An array of transducers is mounted below a microplate, coupled to a lens array that focuses acoustic energy into each well of a microplate. Intense cavitation is generated in each well. After treatment, gel electrophoresis shows that DNA and chromatin are fragmented to a range of sizes extending as low as 100 base pairs (34 nm). Importantly, this process results in consistent fragmentation that leads to consistent repeatable assays. [Funded by NIH R33CA191135, R21GM111439, R01DK103849 and Life Sciences Discovery Fund #12330479.]