Color-Coded DNA

Color-Coded DNA Image Credit: National Human Genome Research Institute

Many people now get their DNA tested for hereditary diseases, including Huntington’s Disease and some cancers. But soon, DNA may also be used to diagnose infectious diseases, from salmonella to HIV. In this Science Update, you’ll hear about a developing technology that could make this possible.


Seeking out DNA. I'm Bob Hirshon and this is Science Update.

Most people associate DNA analysis with paternity tests and criminal investigations. But it can also be important for diagnosing illness.

Bruce Armitage is a chemist at the Center for Light Microscope Imaging and Biotechnology. He’s working on basic technology that could become a quick and easy way to screen for bacterial and viral DNA in the blood.

He says it’s based on a molecule called PNA and a group of special dyes. PNA is a lab-created version of DNA. It can be made so that it will seek out and connect to a specific DNA sequence.


By designing our PNA to have the right shape we can distinguish a viral DNA or a bacterial DNA from a human DNA.

Armitage and his colleagues found that they can see if the PNA has found its target by adding special dyes to the mix.


What we’ve found is that certain types of cyanine dyes will stick to a ladder where one of the strands is DNA, and one of the strands is PNA. And when they stick, they change color from blue to purple.

Armitage says right now the test is only used in the research lab, but it could be improved for wider applications. For the American Association for the Advancement of Science, I'm Bob Hirshon.

Making Sense of the Research

Bacterial and viral infections can be hard to spot. Often, a diagnosis is made based on symptoms. In the case of viral infections, even a firm diagnosis is done indirectly, by looking for antibodies that the body makes to fight the virus.

This technique may make it possible to diagnose infections more quickly, efficiently, and confidently. The key player in the technology is PNA, an artificial version of DNA, the molecule that contains a living thing’s genetic code. (PNA can also mimic RNA, a DNA-like molecule that viruses use instead.)

PNA can be made to look like any specific strand of DNA or RNA. If it comes near a strand that matches, the PNA will stick to it. Since the genetic code of each organism is unique, it’s possible to manufacture PNA strands that will stick to bacterial or viral DNA, but not to human DNA.

Armitage says it’s easier to do this with PNA than with actual DNA for two reasons: First, because you can synthesize as much PNA as you want, and make it exactly how you want it. Second, because PNA is more stable than DNA, it binds more firmly to its target and doesn’t tend to come apart.

Once the PNA binds to its target, the question is, how do you see it? That’s where the dye, called cyanine, comes in. Cyanine dyes are the same light-absorbing dyes that are used in color photography. When PNA binds to DNA, the attached dye molecules end up stacking tightly on top of each other, and the apparent color changes from blue to purple. You can see this happen with the naked eye; all you need to do is put a couple of drops of cyanine dye in a small well where a DNA sample – from the blood, for example – is mixed with PNA. If it changes color, the bacteria or virus is present; if not, it isn’t.

Armitage says it isn’t easy to make just the right strand of PNA. That’s because the strands of DNA and RNA don’t lie flat in living tissue: they’re all tangled up like spaghetti. Sometimes a strand of PNA can’t bind to its target, because the section of DNA it matches up with isn’t exposed. So the researchers have to keep trying until they find a strand of PNA that works.

Although the idea here is to diagnose infectious diseases, this isn’t the only potential use for this technology. It could also be used to diagnose genetic diseases more easily. If scientists could manufacture a strand of PNA that matched up to a genetic sequence that causes a disease, they could turn it loose on a blood sample to see if the defective gene is there – even if the patient doesn’t have any symptoms yet.

Now try and answer these questions:

  1. What is PNA? How is it different from DNA or RNA?
  2. How can it be used to spot bacterial or viral DNA?
  3. Why are the cyanine dyes essential to this technique?
  4. What are the advantages of this technique, compared with looking for the antibodies to a virus? Compared with diagnosing an illness based on the symptoms?
  5. Some kinds of genetic testing – for example, for incurable diseases – have provoked controversy. Why do you think that is? Can you think of possible arguments for and against this kind of testing?

For Educators

For general information on DNA for grades 4 and up, see DNA: The Instruction Manual for All Life on The Tech Museum of Innovation website.

Learn about The Human Genome Project, an international effort to understand the complete human genetic code, on The National Human Genome Research Institute (NHGRI) website.

If you want to look at DNA, try Finding DNA, an activity which uses cow thymus (sweetbreads), available at a butcher shop.

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