Electrodes And Nanoprobes Signal New DNA Detection Method

Northwestern scientists used a synthetic sequence of DNA that models the anthrax lethal factor to test a technology that could displace polymerase chain reaction (PCR) and conventional fluorescence probes in clinical diagnostics and make point-of-care DNA testing possible in the doctor’s office and on the battlefield. A simple electrical signal indicates that target DNA has been detected, and hundreds of pathogenic agents could be monitored simultaneously.

Results will be published in the Feb. 22 issue of the journal Science. Notably, the new DNA detection method eliminates the expensive and currently necessary step of heating the gene chip and also improves upon optical detection methods reported previously by Northwestern in Science.

Once optimized, the technology could be used to quickly and easily detect biological weapons such as anthrax and smallpox as well as a wide range of genetic and pathogenic diseases, from genetic markers for cancer and neurodegenerative diseases to HIV and other sexually transmitted diseases. Results could be available in a matter of minutes instead of days.

The technology, which has not been fully optimized yet, is 10 times more sensitive and 100,000 times more selective than conventional methods. It can pinpoint single-base mismatches that are missed by conventional fluorescence technology. This opens up opportunities in the rapidly growing area of single-nucleotide polymorphism (SNP) detection.

"Because this system is based on conventional microelectrodes, tests could be produced for a fraction of what conventional technologies cost," said Mirkin, also George B. Rathmann Professor of Chemistry, "and take a fraction of the time to process and interpret results."

Currently, companies in the business of gene chip technology use PCR coupled with fluorescence to do DNA testing. The gene chips are read using a confocal microscope, a complex instrument costing more than $60,000. The whole process requires a long series of complicated steps.

Northwestern’s electrical DNA detection method could eliminate the expense of PCR and fluorescence and allow testing for thousands of different biological targets on one chip.

Using this method, various DNA tests can be placed on a glass slide, each test made up of single strands of synthesized DNA, or oligonucleotides, with a sequence designed to bind with its complementary target DNA. These "capture" oligonucleotides are placed in between a pair of electrodes, one test for each pair. The slide then is placed in solution containing the target. Perfect and partial matches alike bind to the oligonucleotides on the slide’s surface. The gold nanoparticle probes, each covered with 200 oligonucleotide strands, latch on to these pairings.

The probes are then amplified using modified photographic developing solution. Each gold nanoparticle becomes covered with silver and grows in size, closing the gap between the electrodes and carrying a current. The crucial next step is to eliminate the perfect match from a close match.

Temperature, or a thermal stringency wash, is the conventional tool for differentiating between the perfect and close match. With the new method, this complicated step is eliminated. Instead, a change in the concentration of a salt solution can be used to break apart any mismatches. Only the perfect matches remain, allowing the silver-coated gold nanoprobes to carry a measurable electrical signal across the gap between electrodes.

The researchers made the important observation that these nanoparticle probes are very sensitive to changes in salt concentration, allowing them to replace the conventional thermal stringency wash with a "salt stringency wash."

To illustrate the superiority of their method, the researchers took on the challenge of what is called the "G:T wobble," a single-base mismatch of DNA that is difficult for conventional methods to distinguish from the perfect match of the target DNA. Such difficulty in discrimination can lead to false positives.

The Northwestern method was able to distinguish between the match of two perfectly complementary DNA strands and the near-perfect match where just one base pair was wrong. The conventional fluorescence method would be unable to effectively distinguish the two.

In addition to clinical diagnostics, other applications of the electrical DNA detection method include SNP analysis, the fabrication of high-density electrical gene chips, and portable field sensors for the defense of biological warfare and terrorism. The technology has been licensed to Nanosphere of Northbrook, Ill., for commercialization.

Other authors on the paper are So-Jung Park (lead author), of Northwestern, and T. Andrew Taton, formerly of Northwestern and now of the University of Minnesota. The research was supported by the Air Force Office of Scientific Research, the Army Research Office and the Defense Advanced Research Projects Agency (DARPA).