On May 6, the VCC DNA Analysis, Flow Cytometry, and Microarray Facilities hosted a full-day open house to provide researchers with the opportunity to familiarize themselves with the facilities’ equipment, capabilities, and staff. One of the primary purposes of the event was to introduce two recently acquired instruments: the Transgenomic Wave, which offers denaturing high performance liquid chromatography (DHPLC) and the ABI 6100 Nucleic Acid Prep Station, a semi-automated nucleic acid extraction system.
VCC technician Romaica Omaruddin gave a presentation about the DHPLC technology, which capitalizes on differences in DNA thermodynamic properties between perfectly matched base pairs (a homoduplex) and mismatched base pairs (a heteroduplex). This allows for the separation of the two duplexes, providing a means to identify genetic variations. Omaruddin said the technology is very sensitive and far more efficient for detecting gene mutations, polymorphisms, and other genetic changes than older technologies.
"The instrument has two 96-well plates, so a researcher can run many samples at the same time," said Omaruddin. "It takes about eight minutes to run each sample. That's much faster than with other available methods. If a researcher planned to run all those samples using DNA sequencing or even microarray technology, it would take much longer. With this technology, the wild type will have a particular pattern and the mutant will have a different pattern that can be observed very easily, so a researcher can choose to sequence only those few mutant samples that have been identified as having genetic variation. This removes the need to sequence the rest of the samples."
Omaruddin also discussed an example of two novel mutations in the APC (i.e., adenomatous polyposis coli) gene that were detected with DHPLC technology, but missed with single-strand conformational polymorphism and DNA sequencing technologies (G. Wu, et. al., Genetic Testing, 2001), providing evidence of the increased sensitivity of the new technology. Thanks to this discovery, people who are now found to have these mutations and are thus at increased risk for colon cancer can be carefully monitored.
A discussion of the ABI 6100 Nucleic Acid Prep Station, which became available to research clients in July, was led by VCC staff member Meghan Brown. This technology features a 96-well platform that processes samples to provide high yield, high purity gDNA and total RNA in just three hours. The high yield and purity of these products makes this technology valuable to researchers who will be using these products in downstream applications.
Brown said that with the new ABI instrument, gDNA or RNA isolations can be obtained from animal tissue, plant tissue, fresh and frozen whole blood or plasma, tissue culture cells, and buccal swabs. The DNA procured with this technology is delivered free from contaminating proteins such as heme and other cellular macromolecules. The ABI RNA protocol was developed in response to the demand for high quality, high throughput RNA purification for downstream applications such as real-time PCR, microarray analysis, pathogenic material identification, and cell population number analysis.