Together with the new probe design, they have also developed a new algorithm, tailored to the new probe pattern, that uses the information obtained from the probes to reconstruct the original sequence.
Preparata and Upfal want to test chemical compounds called universal bases for use as the gaps in DNA probes. A perfect universal base would attach itself to all four bases in DNA.
If the universal bases behave closely to ideal, this is by far a superior method, Preparata said. It would be a fundamental change in the way of doing sequencing.
For this work, he and a group of colleagues have received a National Science Foundation grant of $850,000 over two years. During the research, the computer scientists are designing and analyzing algorithms, and Brown biochemists are using probes that consists of mixtures of DNA bases and universal bases to test how well the mathematical models work.
The potential power of our findings may change the way medical diagnosis is practiced, said chemistry professor Kathlyn Parker, who is leading the chemistry part of the research. The research will also help scientists learn about fundamental interactions of DNA, which will have many applications.
The research project is unusual because it integrates biochemistry and computer science, two disciplines that dont easily mix. They are two really different languages, said Upfal.