Color-Coded Quantum Dots For Fast DNA Testing

The technique works like a bar code with each color and intensity combination corresponding to an individual gene. The researchers predict that up to 40,000 genes or proteins could be studied in as little as 10 minutes.

Competing technologies include the lab-on-a-chip, or biochip, in which miniature DNA-decoding troughs are etched onto flat surfaces. These devices can take as long as 24 hours to identify a group of genes.

Researchers have tried for years to use tiny crystals, called quantum dots, as glowing labels for genes, proteins, and other biological molecules. Quantum dots promise faster, more flexible, less costly tests for on-the-spot biological analysis or patient diagnosis. But they have been difficult to collect and manipulate with enough precision to be useful.

"We solved all of the technical problems," said biomedical engineer Shuming Nie, Ph.D., of Indiana University, who led the research published in the July issue of the journal Nature Biotechnology. "The idea is very simple and straightforward, but I think we're the first ones to make it work."

Quantum dots display a rainbow of colors. Each dot is made from semiconductor crystals of cadmium selenide encased in a zinc sulfide shell as small as 1 nanometer in diameter (one-millionth of a millimeter). In ultraviolet light, each dot radiates a brilliant color.

Nie's group found a way to capture the quantum dots in specific quantities and in a wide range of colors and various intensities. Using six colors, each with 10 intensity levels, it would be possible to code for 1 million genes. But the group said that for accurate detection without any spectral overlap, a reasonable range would be 10,000 to 40,000 different codes.

To capture the quantum dots, they made porous microbeads of polystryene (which is used to make Styrofoam brand plastic foam) and seeded these with the zinc sulfide-capped cadmium selenide nanocrystals. They made both the beads and the quantum dots water repellent. This encouraged the quantum dots to move into the pores.

"If they are both water repellent, they will like each other," Nie said. "Just like water and oil don't mix: water likes water and oil likes oil." Once the quantum dots infiltrated the pores, the researchers sealed the pores.

To demonstrate the use of these quantum dots in DNA analysis, the researchers prepared microbeads of three colors, or spectral wavelengths, and attached them to strips of genetic material. Each color corresponded with a specific DNA sequence. These were used as probes to seek out complementary pieces of genetic material in a DNA mixture.

Among the advantages of the quantum dot system is its flexibility. If you want to add a new gene code to the test, you mix a new batch of beads. This takes about half an hour. Adding a new gene to a DNA chip means going back to the manufacturing plant to design and fabricate a new chip.

"We put the biology and engineering together to make this work," Nie said. He plans to test the system on as many as 1,000 genes at a time. But to scale it up to tens of thousands of genes or proteins will be the task of an industrial company.

Nie said the technology has not been licensed, but several companies are engaged in similar research, including Quantum Dot Corporation, which is developing a number of biological uses for quantum dots.

The current work was supported in part by the National Institutes of Health and the Department of Energy. Nie's earlier research in this area was supported by a Biomedical Engineering Research Grant from The Whitaker Foundation and a grant from the Beckman Foundation.