Nanotech News

November 7, 2005

DNA Sensing with a Single Quantum Dot

Using standard quantum dots attached to DNA probes, researchers at Johns Hopkins University have developed a rapid and highly sensitive method for detecting small amounts of specific DNA sequences. The researchers, who published their work in the journal Nature Materials, have already used their method to detect a mutation associated with some types of ovarian cancer.

Tza-Huei Wang, Ph.D., and his coworkers developed the fluorescent quantum dot DNA sensor to accomplish three tasks: to capture specific DNA targets, concentrate them, and provide a strong fluorescent signal without the need to use PCR technology or perform cumbersome purification steps. The researchers make use of a physical phenomenon called FRET, short for fluorescence resonance energy transfer, to achieve these goals.

FRET occurs when two fluorescent molecules come close enough in space to one another so that they can transfer energy from one of the molecules to the other. This energy exchange produces an extraordinarily bright fluorescent signal. Dr. Wang and his colleagues use the quantum dot as one of the two FRET probes and a fluorescent dye known as Cy5 attached to a short stretch of DNA as the other central component.

To conduct the assay, the researchers mix two different DNA probes and a quantum dot with a clinical DNA sample. Both pieces of DNA are designed to bind to a specific DNA sequence of interest – a cancer-related gene, for example. A Cy5 molecule is attached on the end of one of the two DNA probes, and a molecule called biotin is attached to the end of the other DNA probe. The quantum dot is coated with a third molecule, called streptavidin that binds tightly to biotin. If the target DNA is present in a sample, the two probes wrap themselves around that piece of DNA and then stick to the nanosized quantum dot, which brings the Cy5 molecule close enough to the quantum dot to produce a FRET response. Since each quantum dot can bind dozens of probe DNAs to their target, the resulting FRET signal is quite bright. In the absence of the target DNA, there is virtually no fluorescent signal from just the DNA probes and the quantum dot.

As a proof of principle, the researchers used their system to screen clinical samples from patients with ovarian tumors. Using DNA probes designed to recognize a mutation associated with one form of ovarian cancer, the researchers were able to identify those patients who had that gene mutation without the need to separate the DNA from the clinical sample prior to running the assay.

This work is detailed in a paper titled, “Single-quantum-dot based DNA nanosensor.” This paper was published online in advance of print publication. An abstract is available through the journal’s website.
View abstract.