Contact :
Ron Brown
504 388-3867
e-mail: [email protected]
Steven Soper
LSU Chemistry Department
504 388-1527
BATON ROUGE -- Using $1.5 million in grants from the National Institutes of Health, LSU chemist Steven Soper is on the verge of saving researchers millions of dollars and years of work.
Soper and his colleagues, Robert Hammer in the chemistry department and Richard Bruch in the zoology and physiology department, have devised a method of decoding genes that is 10 times faster and 50 times cheaper than current methods. Their work, which is part of the Human Genome Project, has implications for medicine, forensics, pharmacology and business.
The Human Genome Project, an international effort begun in October of 1990, is dedicated to discovering all of the 60,000 to 80,000 human genes (the human genome) and determining the complete sequence and function of each set of genes in the 3-billion base set of human chromosomes.
A number of important strides have already been made, said Soper, with the identification of the BRCA 2 and 3 genes that predispose women to breast cancer, and the discovery of the genes that cause cystic fibrosis.
But with roughly 1.29 percent of the human genome sequenced, at the current rate of sequencing it will take more than 200 years to complete the project. Worse than that, because of the high cost of the consumables needed in the process, the cost to sequence the genome will exceed $1 billion.
"We have three goals in this project," Soper said. "Increase the speed, increase the accuracy and lower the cost."
All these goals could be met by the end of next summer, he said.
What Soper and his colleagues have done is decrease the size of the device that sequences DNA from a box the size of a one-drawer filing cabinet to a piece of Plexiglas one inch square. Using the facilities at LSU's Center for Advanced Microstructures and Devices, they created a tiny, undulating tube in a piece of Plexiglas that can be filled with a porous gel. When an electric field is applied, pieces of DNA will flow through the gel at different rates, depending on their size. This reduces the amount of time it takes for the DNA to move through the gel from 120 minutes with current equipment to between 10 and 20 minutes, Soper said.
It also reduces the quantity of chemicals that have to be used by 1,000 percent. "It costs between 25 and 50 cents to identify one pair of bases," he said. "But with this system it should cost significantly less."
A base is one of four nucleic acids, identified as A, T, C and G, that pair up to make the rungs of the ladder that link one strand of spiral DNA to the other. A and T will pair only with each other, as will G and C. Discovering the order which the bases follow on the strands is done by a complex process called the Sanger method. One of the difficulties in determining this order is that strands of DNA, which have millions of bases, must be cut up into pieces with no more than 1,000 bases each. Knowing how to reassemble the strands as they were before they were cut is essential to mapping the genome properly.
Ordinarily this is done by adding a fluorescent dye to each half of the cut so that when the sensor detects two greens, for example, the researcher knows these two ends fit together. But Soper and his team have improved on that.
Rather than using dyes that fluoresce in certain colors, they use dyes that fluoresce for a certain length of time. Soper said this new method improves the accuracy of identifying cuts to 99 percent.
"By far the most important contribution we've made is that we're doing microbiology on a nanoliter scale. If we do a million bases a day on the nano scale it will cost us $25 in reagents rather than the $25,000 a day it costs researchers currently," Soper said.
The completion of the project will also put LSU at the forefront of genetic research. One of the possibilities Soper mentioned was the development of food products with specific taste and nutritional qualities. There are also veterinary, forensic, diagnostic and pharmaceutical applications for the work.
"We have three of the five subsystems (necessary for the entire instrument) functional," Soper said. "Even if this works at half the projected efficiency, it will still have some unique capabilities."
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