Diagnostic method based on nanoscience could rival PCR

Since the advent of the polymerase chain reaction (PCR) nearly 20 years ago, scientists have been trying to overturn this method for analyzing DNA with something better. The “holy grail” in this quest is a simple method that could be used for point-of-care medical diagnostics, such as in the doctor’s office or on the battlefield.

Now chemists at Northwestern University have set a DNA detection sensitivity record for a diagnostic method that is not based on PCR — giving PCR a legitimate rival for the first time. Their results were published online today (April 27) by the Journal of the American Chemical Society (JACS).

“We are the first to demonstrate technology that can compete with — and beat — PCR in many of the relevant categories,” said Chad A. Mirkin, director of Northwestern’s Institute for Nanotechnology, who led the research team. “Nanoscience has made this possible. Our alternative method promises to bring diagnostics to places PCR is unlikely to go — the battlefield, the post office, a Third World village, the hospital and, perhaps ultimately, the home.”

The new selective and ultra-sensitive technology, which is based on gold nanoparticles and DNA, is easier to use, considerably faster, more accurate and less expensive than PCR, making it a leading candidate for use in point-of-care diagnostics. The method, called bio-bar-code amplification (BCA), can test a small sample and quickly deliver an accurate result. BCA also can scan a sample for many different disease targets simultaneously.

The Northwestern team has demonstrated that the BCA method can detect as few as 10 DNA molecules in an entire sample in a matter of minutes, making it as sensitive as PCR. The technology is highly selective, capable of differentiating single-base mismatches and thereby reducing false positives.

In their experiments, the scientists used the anthrax lethal factor, which is important for bioterrorism and has been well studied in the literature, as their target DNA.

The BCA approach builds on earlier work reported last September in the journal Science where Mirkin and colleagues used BCA to detect proteins, specifically prostate specific antigen, at low levels.

For the DNA detection, the team used commercially available materials to outfit a magnetic microparticle and a gold nanoparticle each with a different oligonucleotide, a single strand of DNA that is complementary to the target DNA. When in solution, the oligonucleotides “recognize” and bind to the DNA, sandwiching the DNA between the two particles.

Attached to each tiny gold nanoparticle (just 30 nanometers in diameter) are hundreds to thousands of identical strands of DNA. Mirkin calls this “bar-code DNA” because they have designed it as a unique label specific to the DNA target. After the “particle-DNA-particle” sandwich is removed magnetically from solution, the bar-code DNA is removed from the sandwich and read using standard DNA detection methodologies.

“For each molecule of captured target DNA, thousands of bar-code DNA strands are released, which is a powerful way of amplifying the signal for a DNA target of interest, such as anthrax,” said Mirkin, also George B. Rathmann Professor of Chemistry. “There is power in its simplicity.”

The technology could be commercially available for certain diseases in one year, Mirkin said.

In addition to Mirkin, other authors on the JACS paper are Jwa-Min Nam and Savka I. Stoeva, from Northwestern University. The research was supported by the Air Force Office of Scientific Research, the Defense Advanced Research Projects Agency, the National Science Foundation and the National Institutes of Health.