Professor Lewis Rothberg of the University of Rochester Chemistry Department received a NYSTAR grant in August 2006 to continue working on a recent discovery by Huixiang Li, a research associate in his group: how to rapidly test DNA to improve our health and make sure we're drinking clean water and eating uncontaminated food. In fact, his new method can be used to help forensics labs identify criminals, test ponds and pools before children swim in them, and identify harmful genetic sequences in medical research, to name only a few applications. Rothberg's innovative procedure quickly and inexpensively identifies genetic sequences in any sample of DNA.
The technology is a novel fluorescent DNA screening assay, which rapidly determines whether specific DNA target sequences are present in an analyte. In simple terms, the analyte contains the DNA target sequences as well as other DNA sequences, and the assay filters out only the targets. Professor Rothberg's assay is based on the electrostatic properties of DNA.
The principle underlying the method is that single-stranded DNA and double-stranded DNA have significantly different affinities for attaching to ionically charged gold nanoparticles. Because ions have electric charges, having gained or lost electrons, they attract their opposites. An anion with a negative electric charge will attract positive charges, a cation with a positive charge will attract negative charges. Single-stranded DNA adsorbs on negatively charged citrate ions on the gold nanoparticles while double-stranded DNA does not. Given that both single-stranded and double-stranded DNA are (nominally) negatively charged, this proven phenomenon intrigues the research group.
The new assay determines whether a fluorescently-tagged short probe sequence of single-stranded DNA matches a sequence in the target analyte. When it does not, the fluorescently tagged probe adsorbs on a gold nanoparticle and its fluorescence is quenched. If the probe sequence is able to hybridize to the target, it will not adsorb on the gold and its fluorescence persists.
The new method is simple and effective. It costs very little, and it's very quick.
The most widespread and common method of screening DNA is called gel electrophoresis. Each test takes 1 hour and can cost as much as $1.00. Setting up a lab for gel electrophoresis requires a capital expenditure of $5,000. By contrast, Professor Rothberg's technique only requires 5 minutes, and it costs approximately $0.05 (literally five cents) per test. The capital expenditure to set up a lab with the new technique is only $600.
It's as simple as that, yet nobody's ever done it before. The method is so new that the University of Rochester filed patents for it in 2004 and 2006. In May 2005, Professor Rothberg created a company called Diffinity Genomics, Inc. with two partners to further study and commercialize his technique.
Professor Rothberg's method is part of a much larger process that analyzes DNA. First, a technician extracts the DNA from the blood, tissue, or food. This typically take up to an hour. Second, there is generally not enough DNA to analyze, so it must be chemically amplified. This also takes apprximately one hour. The new process comes after these two steps, saving a final hour of work for the technician, who ordinarily would be doing gel electrophoresis.
Perhaps more important than the savings in time and money, the new method works to determine single-base mutations in DNA, whereas gels cannot do this without even further processing. Professor Rothbergs concludes, "This could be very important for applications in personalized medicine where a particular DNA sequence will be linked to a prescribed therapy. In fact, we see this happening already."
For further details, see:
Li, H., Rothberg, L.J., "Label-free colorimetric detection of specific sequences in genomic DNA amplified by polymerase chain reaction," J. Am. Chem. Soc. 2004, 126, 10958-10961.
Li, H., Rothberg, L.J., "Rapid DNA sequence detection using selective fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles," Anal. Chem. 2004, 76, 5414-5417.
Dr. Lewis Rothberg | EurekAlert!
A Map of the Cell’s Power Station
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau
On the way to developing a new active ingredient against chronic infections
21.08.2017 | Deutsches Zentrum für Infektionsforschung
Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.
As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...
Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.
Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...
For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.
While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...
An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.
The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...
A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.
Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...
16.08.2017 | Event News
04.08.2017 | Event News
26.07.2017 | Event News
22.08.2017 | Power and Electrical Engineering
22.08.2017 | Medical Engineering
22.08.2017 | Awards Funding