Imagine a handheld device that could identify a person infected with HIV in seconds with a drop of their blood. As great as this would be, it is just the tip of the iceberg of options made possible by new technology pioneered at UCSB.
A research group headed by UCSB professors Kevin Plaxco and Alan Heeger with visiting postdoc Chunhai Fan has recently taken the first steps toward developing an extremely versatile DNA sensor. The sensor could be used to detect diseases, warn of biochemical attacks or test meat for contamination, as well as perform a huge variety of other biological identification tasks.
The technology used to make such a sensor work has been already been built and tested in Plaxco’s lab. The remaining work needed to transform the new technique into real devices lies in improving the sensitivity of the system.
A new type of DNA sensor
Plaxco, Heeger and Fan have developed a way to sense specific, short segments of DNA. This simple ability gives rise to very powerful and beneficial devices.
“Biochemistry is really the study of how evolution solves various engineering, chemical and physical challenges; we are trying to exploit some of the tricks biology learns to our ends,” Plaxco said.
The DNA sensor project is a bit of a change for pure scientists who are not used to working towards developing a product.
“I’ve got to admit, I am starting to enjoy the engineering aspects of it. It’s nice having a very specific goal in mind that’s more concrete than just esoterically revealing science,” Plaxco said.
“It was a good example of interdisciplinary collaboration work, where everybody brings something and what comes out is bigger than the sum of the parts,” Heeger said.
Plaxco brought his expertise in chemistry, Heeger shared his knowledge of physics and chemistry, and Fan offered his help with biochemistry.
The DNA sensor reveals the presence of small amounts of a specific segment of DNA by changing an electrical signal. Each sensor must be custom-made for the detection of a segment of DNA. For example, a sensor may be manufactured to sense HIV DNA, while another may sense a biochemical attack.
“The Dept. of Homeland Security, like most of us, would like a device that could sit in subway stations and sniff the air looking for pathogens,” Plaxco said.
Building blocks of DNA
A DNA molecule consists of two long chains of amino acids that twist around each other in a structure called a double helix. There are four types of acids, which form complementary pairs: Adenine pairs with guanine; thymine pairs with cytosine. One chain of the double helix is the complement of the other chain, so the information in a DNA molecule is stored twice. This allows copies to be made from one side of the helix.
Scientists often describe a short length of DNA by just listing abbreviations for its amino acids – AATCGTGCTA, for example. A single letter, which actually represents an amino acid and its complement, is called a base pair. An entire DNA molecule for a human consists of about 3 billion base pairs. That would make almost 200,000 newsprint pages filled with only AGTCGTCG…
DNA in an organism
Every known living thing uses DNA to store its genetic code. It is this code that determines everything about the organism. The code is like a cookbook that contains instructions on how to construct a biological entity.
Identical copies of the DNA are stored in most cells of the organism (unique cells for reproduction, namely sperm and eggs, are an exception). When a cell divides in normal growth, it makes a copy of the DNA it contains and places a copy into each new cell.
The DNA molecule can be divided into sections called genes that determine how to genetically build something. For example, a subset of DNA that is 100,000 base pairs long could describe how to make lactase, an enzyme that digests milk in the small intestine. People who are lactose intolerant are not producing the enzyme because their bodies are not reading that piece of DNA correctly.
A cancer is a growth of cells whose DNA has become corrupted. Cancers can be very devastating because their corrupted DNA causes the cell to reproduce far more quickly than normal. This leads to malignant tumors that can impede the function of a body’s organs.
Bent out of shape
“I think [Fan] was the first one to see the whole thing clearly – to say ‘we can do that,’ ” Heeger said. “We all agreed it was a great idea.”
Fan said the sensor consists of a gold electrode that is coated with special loop-shaped DNA molecules. Each molecule has two shapes it can assume. In the looped shape, the tail of the molecule is held close to the gold surface. In the stretched shape, the tail is held further away from the gold. The molecule changes shape when it finds and bonds with its complement segment.
The segment can be picked out of a large mess of other things like blood and can be identified even when it is part of a larger DNA molecule. This is similar to the way in which a specific key matches with and turns a lock. Hundreds of wrong keys can be tried, but none will turn the lock.
The tail of the molecule contains an electrochemical agent that allows an electric current to flow when it is close to the gold electrode, but restricts the current when pulled away from the gold. The tail moves a small amount in such a situation.
“It can be a few nanometers,” said Fan.
The electric current stops flowing when the molecule changes shape. It is then amplified and displayed by an electric circuit.
There are similar DNA sensors being designed at other universities; however, the UCSB sensor has the distinct advantage of not needing any separate chemicals, called reagents, to do the test.
“Ours has an advantage over those other electronic techniques in that it is reagent-less. All of the components required to do the assay are tied to the surface,” Plaxco said. “Because of that, our sensor is reusable.”
How do the DNA sensor molecules return to their looped state? Easy: Just pour hot water on them. Fan said that the DNA molecules are joined with hydrogen bonds, which are sensitive to heat. Just washing the gold electrode with hot water will wash away the bonded molecules and ready the sensor for another test.
There’s always a catch
“One of the issues, still, is sensitivity,” Plaxco said. “There’s material there, but not enough to make the sensor go off.”
This means that the sensor isn’t quite ready to detect HIV in normal blood samples yet.
“Sensitivity is about 10 picomolar,” Plaxco said. “That’s about 150 milligrams of DNA in an Olympic swimming pool.”
A picomolar is a unit that defines how concentrated a mixture is.
“From the biologist’s perspective, that’s very poor, because that still corresponds to 6 billion molecules per milliliter,” Plaxco said. “So if you’re looking for the HIV genome, that’s 6 billion virons [complete viruses] in a milliliter. Long before you have 6 billion HIV virons in a milliliter, you’ll be dead.”
In other words, a person infected with HIV typically has far fewer viruses in his or blood than can be detected with the current sensor.
“In principle the sensitivity here can be enormous. We are nowhere near the limits that we are currently sensing,” Heeger said.
Some of the issues that affect sensitivity may be dirt, which covers the sensor and clogs it, and other chemicals that partially damage the sensor. Changing the sensor so its form is less susceptible to dirt and more inert may solve the problems.
The project was a good example of collaboration among experts of different fields.
“It was great fun, because it crosses so many boundaries: electrochemistry, … biology. And it has great applications,” Heeger said.
Improving sensitivity will be the next goal for scientists and engineers working to get this technology into commercial products. Once the sensors are able to detect pathogens in normal blood samples, a medical revolution will be underway to build sensors that can detect any choice of diseases. It is entirely possible to build a sensor that could detect a dozen diseases at one time. Placing an assortment of sensor molecules on the same electrode could do this. Such a system would be useful for rapidly screening patients against diseases.
“Scenarios that we envision are things like a device that your doctor carries in his pocket, that is a quick assay for some pathogen – HIV is an obvious case,” Plaxco said.
And a small device that could do that would be a giant step forward in medicine – and not just one step, but the first of many to follow in quick succession.