Faster DNA Testing

tkjtkj writes "Physorg.com is reporting that a Rochester,NY, company, 'Thermal Gradients, Inc' has produced a new method of DNA analysis that can reduce the required time from hours to minutes that the usual 'Polymerase Chain Reacion' (PCR) takes to produce the large quantity of sample DNA needed to identify the donor. This could,conceivably, make "Instant DNA Identification" a reality! Will air travel now require one to arrive at the airport 5 minutes earlier than usual, to provide a skin-swab sample before boarding the plane?"

Comments

Whoa giddy.

[LiquidCoooled]

They have a tiny oven which can:
While other miniature PCR devices exist, they are limited in the rate at which they can change temperature, Grover said. "Our first prototype has demonstrated that we can expose the sample to the required temperatures at unprecedented rates," he said.

Now, lets look at just whats needed to do the PCR reaction (just one of the variations taken from here:

If you are using DNA Thermal Cycler (TCI, the DNA Thermal Cycler Model 4800 or any thermal cycler requiring light mineral oil overlay.

        * Place the tubes in the thermal cycler and begin thermal cycling as follows:
        * For the first cylce only, ramp to 96 C for 1-5 minutes to completely denature DNA template then proceed with sequencing PCR steps.
        * Rapid thermal ramp to 96C
        * 96C for 30 seconds
        * Rapid thermal ramp to 50C
        * 50C for 15 seconds
        * Rapid thermal ramp to 60C
        * 60C for 4 minutes
        * Repeat Step 2 for 25 cycles
        * Rapid thermal ramp to 4C and hold. Samples can be started in the evening and purified the next day if necessary
        * Proceed with Purifying Extension Products.

They might be able to change temperature quicker, but they haven't invented a new way to perform the reaction.

minor upgrade, no digg.

Re:Whoa giddy.

[Reblet]

minor upgrade, no digg.

Exactly. Having actually performed DNA analysis in the lab, I can tell you that while very rapid temperature changes are benificial, you still need to take some time to let the new DNA strands form. In addition, there's more steps involved in actual DNA analysis (isolating the DNA, running it through a poly-acrylamide gel to get the familiar stipe patterns, etc), some of which can take far longer than the actual replication of the DNA itself. I doubt we'll be seeing machines that can perform DNA-analysis in mere minutes anytime soon. Reblet

Re:Whoa giddy.

[Noehre]

The problem is that this press release is incredibly short on details. They appear to be making the claim that they have a product that will replace conventional PCR equipment when, in fact, this is not the case.

Microfluidic heating methods only significantly increase PCR rates in cases in which the amplicon length is less than 1,000bp. In fact, the average amplicon length in a recent review of microfluidic PCR devices (Analytical Chemistry, 77(12):3887-93) is only 330bp. Dependending on what polymerase is used, a 330bp piece of DNA can be replicated in 10-20 seconds. This, obviously, is a completely different situation from one in which a researcher is amplifying a 7kb vector in which elongation is the rate-limiting step. I'm sure that microfluidic devices could be adapted to work with amplicon lengths >1kb, but at that point the reaction rate improvements become negligible. Microfluidic PCR lends itself primarily to SNP genotyping, not general research.

Furthermore, the difficulty inherent in working with nanoliter volumes of reagents makes these microfluidic PCR devices somewhat less useful for general lab use. Naturally, they mesh well when coupled with lab-on-chip applications, but again that is currently a niche use.

Traditional thermocyclers aren't going anywhere any time soon. They're cheap, they're functional, and they're flexible.

This doesn't seem so great...

[sowalsky]

Many companies have produced faster thermocyclers. And indeed, the rate of heat cycling is a major factor in the time needed for a 30- or 35-cycle PCR. However, what this article omits are necessary wait periods to permit the annealing, elongation, and melting stages in typical PCR. Unless they have also re-engineered a DNA polymerase and can sufficiently prove that denaturation and annealing stages can be completed much faster, we're talking about maybe a 30 to 45 minute decrease in PCR. That's it. I've never seen anything less than 30-30-30 before, even in the smallest of genotyping markers.

Re:The next stage of biometrics?

[n0dalus]

Normal hairs you shed off don't contain a usable DNA tag; contrary to what most believe.
Not always (unless a root is intact), but Mitochondrial DNA can still usually be found. mDNA, while more expensive to test and not as conclusive, is still useful and I think it's been used in some high profile murder cases.

Re:Only 5 minutes??

[AndersOSU]

Ignoring the fact that this is all impossible becasue DNA analysis consists of more than PCR and that PCR is never going to take 5 minutes - its just the kinetics of the reaction.

The only real way to get rapid DNA testing is a test that forgoes the amplification step and can identify single strands of DNA. Of course you then have the what if they get someone elses DNA because I just kissed my mom^H^H^H girlfriend goodby.

If all of those were accomplished I see no problem implementing such a solution, because as we all know airports are the hallmarks of efficiency.

Re:Accuracy

[inputsprocket]

I didn't read anything in the article which says it can amplify DNA like a traditional PCR in minutes. Of course it can only be as fast as the speed of the reaction - 15-30" to efficiently denature a 3kb strand, the speed of the enzyme (~60nt/sec) and of course the primer annealing step - one of the nice things about current PCR (walled tubes) is that the temperature drops to the annealing temperature gradually. If the temperature drop was instantaneous, then you risk mal-annealed primers. At any rate, if you say 30" to allow annealing, and 1 minute for the enzyme to amplify ~3.5kb DNA, then you still have to wait 1 hour for a 30-cycle reaction.

And of course, there are the thermodynamic encumbrances imposed by walled PCR tubes - unless the machine was disposable, I wouldn't like to eliminate the security of x-contamination of using disposable tubes.