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DNA Detection Breakthrough Could Lead To Improved Tuberculosis Treatments

July 29, 2013
Image Caption: This conceptual image shows probe and target complexes at different stages of the reaction that checks for mutations. The red dots represent mutations in a target base pair, while sequences with illuminated green lights indicate that no mutation was found in the reaction. Credit: Yan Liang, L2XY2.com

Brett Smith for redOrbit.com – Your Universe Online

Minor mutations in DNA code can make for major malfunctions, and a breakthrough technique has allowed scientists to spot genetic changes with greater precision than ever.

According to a new report in the journal Nature Chemistry, the new method can look at a specific DNA sequence and pull out a single mutation.

“We’ve really improved on previous approaches because our solution doesn’t require any complicated reactions or added enzymes, it just uses DNA,” said lead author Georg Seelig, a computer scientist at the University of Washington. “This means that the method is robust to changes in temperature and other environmental variables, making it well-suited for diagnostic applications in low-resource settings.”

Along with his UW colleague Sherry Chen and David Zhang, a bioengineer from Rice University, Seelig created DNA probes that can pick out a single mutation for a target stretch of DNA. The team’s probes expand current capabilities tenfold — scanning up to 200 base pairs instead of 20 as provided by current methods.

“In terms of specificity, our research suggests that we can do quadratically better, meaning that whatever the best level of specificity, our best will be that number squared,” Zhang said.

The probes are made to bind with an exact sequence of double-helix DNA via a complimentary DNA sequence. Unlike previous methods, the probe is designed to check both strands of the double helix instead of just one, which translates to increased specificity.

When both the target sequence of DNA and the probe are mixed in a test tube with saltwater, the probe is designed to emit a fluorescent glow if it perfectly aligns with its target. If the scientists don’t see any illumination, it means there is a mutation in the target DNA strand.

The research team performed their study on bacteria because a single nucleotide can confer antibiotic resistance, a major problem for combating diseases like tuberculosis.

“In these tests, our read length was 198 base pairs because that was the length of the region we needed to scan for (single mutations) related to rifampicin resistance,” Seelig told AZONano.com. “We could have designed a longer probe if we’d needed one. There is no inherent limitation to the length of the probe we can make.”

In detecting antibiotic resistant bacteria, selectivity of a DNA probe is a major issue. For example, a person may be infected with one strain of drug-resistant TB and two strains of non-resistant bacteria.

“Maybe only 1 percent of the TB in the patient is resistant to rifampicin,” Zhang said. “If you treat that person with rifampicin, the result is that you will kill the 99 percent and give the drug-resistant variety a chance to become well-established.”

A genetic test would need a selectivity of 100-to-1 to diagnose the patient in Zhang’s example. While some current methods do have that level of selectivity, their procedure requires precise attention to temperature, pH and other conditions.

“Our selectivity was about 12,000-to-1 in this study, and we don’t require any special conditions,” Zhang said.

The researchers said they are currently moving forward in using their newly developed technique to advance diagnostic practices.


Source: Brett Smith for redOrbit.com - Your Universe Online



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