UPPSALA, Sweden—Most current DNA-based technologies are intrinsically high-throughput but there is often a bottleneck in preparing oligonucleotides (oligos) for downstream analysis as technologies like HPLC and gel electrophoresis are traditionally low-throughput. To address this issue, researchers at Uppsala University, Quiatech AB, and at Academia Sinica in Taipei, Taiwan developed a cartridge-based high-throughput oligo purification system, describing the method in Analytical Biochemistry.
Using reverse-phase cartridges in a 96-well format, the scientists loaded oligos generated on a 1536-channel DNA synthesizer, washing the cartridges thoroughly before hitting the resin-bound oligos with 100 percent acetonitrile to trigger precipitation. The scientists then removed the trityl groups with TCA and rapidly eluted the cleaved oligos with a short flush of acetonitrile, thus avoiding large volumes of dilute material.
Using capillary electrophoresis and HPLC, the scientists tested the yields and quality of their method against commercial cartridges and found that the new method compared very favorably, with little sample loss and higher purity. They also tested their oligos in microarray experiments against purchased oligos and found the signal intensities of cartridge-purified oligos were about 9-fold higher.