The researchers also will investigate whether certain compaction and expansion states might be indicative of cancer or other diseases.
"Our current study describes the platform technology necessary to try to understand larger questions," Dr. Garner said. "The next step will involve using the technique to look at different types of cancer cells to see whether this type of assay could be a diagnostic tool."
Other techniques have be used to examine the compactness of DNA, but only a small piece of DNA at a time, said Ryan Weil, a UT Southwestern biophysics graduate student and the study's lead author. "One of the advantages of our array is that it sorts through lots of pieces of DNA and gives us information about each segment all at once."
Currently, scientists determine which genes are turned on, or expressed, in a cell by extracting RNA and measuring how much of it is being produced for each gene. An RNA microarray, or "gene chip," is the standard equipment used to measure RNA expression levels.
"Only a small fraction of genes are making sufficient RNA to be detected with RNA microarrays," said Dr. Garner. "Many of the genes that make very small quantities of RNA are nonetheless very important, but they fall below the threshold of detection for current techniques."
The UT Southwestern technique allows researchers to study genes that previously weren't accessible because there was not enough RNA to make a measurement of their activity.
"We can get information on a much larger number of genes, and whether or not they are in a state in which they can make RNA, using this technique than by using traditional RNA microarrays," Dr. Garner said. "This technology can tell us not only whether the DNA for a given gene is present or not, but also whether it
Contact: Amanda Siegfried
UT Southwestern Medical Center