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A digitally magnified image shows DNA density by varying brightness. There are anywhere from 200 to 300 silica microspheres in each dot.  (Source: Lawrence Berkeley National Laboratory)
Detecting specific genes and pathogens in DNA and RNA is typically quite expensive and time consuming. But that's about to change.

Analyzing DNA and RNA -- examining it for things like certain genes, mutations and pathogens -- has become somewhat more commonplace in the past few years. One problem is that it requires equipment and expertise that few of even the best medical centers posses. A group at the Department of Energy's Lawrence Berkeley Laboratory may change that with their new DNA microarray analysis technique.

One area of great interest to medical researchers is personalized medicine. Each person's body reacts differently to diseases, infections, and viruses and the same can be said for medicines and other treatments. But knowing a person’s genetic makeup by analyzing their DNA can give treatment specialists insight on what drug or treatment may work best for a certain individual.

Unfortunately, though the technology exists and works, as mentioned previously, it presently lies in the hands of a few advanced institutions worldwide. Fluorescence detection is the most utilized method of DNA analytics, but it takes specialized equipment and high power devices to implement. Not to mention time for an analysis to take place.

The Berkeley team's method uses none of these things, instead relying on a relatively simple approach based on electrostatics. It requires no chemicals markers, no high energy excitation, and best of all, no microscopes. They boast that the imaging can be done with nothing more complex than a cell phone camera if necessary.

They start off with a standard hybridized DNA microarray, set on a positively charged base. DNA hybridization is a fairly standard technique in which complementary single strands of DNA combine to form a double-stranded hybrid. Some DNA will not find complementary strands and will remain single. Then, after the array is placed in a well chamber, a solution of negatively-charged silica microspheres is disbursed over the surface of the microarray using gravitational sedimentation. As the base is positively charged and the microspheres are negatively charged, the silica spheres will adhere to it in most places.

The trick is that DNA, hybridized or not, is also negatively charged, with hybridized segments more so than single strands. This negative charge causes the silica beads to be repelled and hover above the spots that contain the DNA. The beads hover at a state of equilibrium based on the repulsion of the negatively charged DNA samples and the force of gravity. This causes a slightly frosted look in areas where samples are present, with hybridized samples standing out more due to the distance of the beads from the surface. Images of the areas can be analyzed for known genes, mutations or pathogens based on their charge-density and Brownian motion.

While the technique is much less expensive and complex than fluorescence detection, the group says they still have room for improvement and intend to move in that direction. They will be further testing their method on higher density arrays and experimenting with the absolute limit of resolution available to the method. Ultimately, it could be used to examine millions of strands of DNA simultaneously.

This kind of technology could serve to put genetic profiling for medical purposes like personalized medicine into the hands of doctors in hospitals worldwide. Rather than relying on a standard treatment, ushering in an era of personalized medicine may save hundreds of thousands of lives, or more, world-wide where these blanket treatments are sometimes ineffective. This type of analytics is looking very promising for the future of medicine, and groups like Berkeley's are making it more and more possible every day.

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Interesting, but....
By Rugar on 7/1/2008 8:46:13 AM , Rating: 2
I'm not sure how revolutionary this really is. Fluorescence techniques like RiboGreen are well developed and widely available. I perhaps don't have enough vision, but this just looks like another methodology to accomplish the same end. I don't see it as making the instrumentation any cheaper (at least not for quite a while) either since most of the expense is in the development of the assay and the licensing of the various components.

/me shrugs.

RE: Interesting, but....
By tmouse on 7/1/2008 9:22:12 AM , Rating: 2
In fairness this is for high throughput analysis. Ribogreen is not used in microarrays; it is simply a nonspecific nucleic acid binding agent. Arrays generally use fluro-conjugated nucleic acids in either single or dual channel modes. This is a single channel mode assay as are many others commercial systems like Affymetrix and Illumina.

RE: Interesting, but....
By Rugar on 7/1/2008 10:49:09 AM , Rating: 2
Well, my ignorance of microarrays shows through. I'm more of a qPCR kind of guy myself and haven't done any microarrays. With that said, I still don't see the "value" in this alternate methodology. But again, I'm probably not seeing some larger picture.

RE: Interesting, but....
By DNAgent on 7/1/2008 10:32:46 PM , Rating: 2
One of the most amazing things about our electrostatic detection method is that it requires nothing more than the naked eye to read out results that currently require chemical labeling and confocal laser scanners

You'll notice that the image of their microarray with dots of varying intensity is just that--an image, taken by some sort of digital camera. The attractiveness of this method lies in its simplicity and low cost. Current technologies developed by Illumina, Agilent, and Affymetrix require 3+ days of sample processing before the chips are ready for scanning, even streamlined for the production environment at our company. Removing the need for dye labeling could potentially shorten this time significantly.

The cost barrier to accessing a technology like this right now is very high--laser scanning machines like those required for Illumina cost upwards of $50,000.00, putting them out of reach for many smaller research groups. Not that the proprietary reagents accompanying many of these assays are going to get any cheaper, but this is certainly a promising new direction.

RE: Interesting, but....
By tmouse on 7/2/2008 8:23:24 AM , Rating: 2
This work will most certainly NOT significantly decrease the time, since the majority of the time is involved with the hybridization NOT the labeling which usually takes only a few hours. As I noted in one of my posts the Illumina system costs around 400-500k depending on bells and whistles. 50k is not that much for a major piece of equipment and these types of systems are never for individual groups they are for facilities, as will be the system being developed by this group. I do not know why you think this will be faster, for example while the Illumina protocol takes 3 days the bulk of the first day is for the invitro transcription reaction which is as much for amplification as labeling this will not change (aprox 4-14 hours). The second day is almost exclusively hybridization; this too will not change (aprox 17-24 hours). The third day is washing and scanning which is around 3 hours. Even if you save on the wash you lose on the additional hybridization they require. It MAY be a little cheaper but as I said after the original outlay (which is steep) the cost per array is usually around $200 I do not see that getting much cheaper. The fluorescent labeling adds maybe $20 to the costs of a array experiment.

RE: Interesting, but....
By geddarkstorm on 7/2/2008 1:12:40 PM , Rating: 2
There's a major flaw with this system though--sensitivity. Since hybridized or not, the DNA/RNA will repel the silicon beads, you end up having to subjectively score whether an intensity means you had hybridization or not, or more DNA/RNA bound to the chip there, or the beads didn't distribute right there, or what not. Man, the error rate on this will be huge if they don't think of something. There's already enough subjective trouble with fluorescent detection in microarrays as it is.

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