New sensor would simplify diagnostics
Aim is to create tool for hospital, field use
Research on a new sensing device that can simultaneously identify more than 3,000 biological materials shows great promise, says Ravi Saraf of Virginia Tech’s chemical engineering department. Saraf and his supporters at the Optical Science and Engineering Research Center (OSER) and Carilion Biomedical Institute (CBI) expect the device will have medical, military and industrial applications.
A key advantage of the sensor is its ability to detect a specific biological agent in concentrations lower than one part per billion (femoto-molar levels) in water and blood. Saraf's chip for untagged biomolecule sequencing (CUBS) is new generation microarray technology that can detect target DNA, RNA, or proteins. As a potentially portable unit, it will allow sophisticated diagnosis in the field. Knowing quickly which chemical(s) a soldier has been exposed to or what pathogens are present in body fluids, in advance of clinical symptoms, facilitates immediate treatment. The new detection device will also be able to monitor soil, water, and air to identify the presence of such pathogens as viruses, bacteria, and protozoa.
And CUBS can be used for genetic profiling, which will enhance personalized medicine, says Sam English, manager of research projects at CBI. For example, a person can be tested to see if the breast cancer susceptibility gene is present in her DNA. If detected, a physician could then customize preventative care.
Saraf's prototype and the biochip under development in collaboration with researchers in Virginia Tech's College of Veterinary Medicine and Battelle's Northwest Division is based on several modern technologies. The rapidly growing knowledge of the human genome and the functions of proteins, as well as the genetic profiles of many pathogens, is combined with thin-film technology that allows layers of different materials only a few molecules thick to be built up on a chip with different capabilities in each layer. The veterinary researchers will provide sample material with pathogenic markers from in-vitro and in-vivo experiments. Battelle is providing an existing device to separate and purify nucleic acid and proteins from the fluid. Saraf provides CUBS and a detection device to read the chip. Add a laptop computer, and the entire operation can fit on the top of a desk.
So
far, the researchers can achieve detection sensitivity 10 times better than
the best of today's technology available in scientific laboratories. "The level
of sensitivity means we can determine how long an invading organism has been
present based on the number of genes switched on in the pathogen and the maturity
of the immune response. Thus, we know when the infection occurred. We can also
determine the species of the source based on the genetic profile of the infecting
organism.
"My goal is to bring this technology to hospitals and pathology labs, which is the reason OSER has supported this work and CBI has licensed it," says Saraf, who has 27 U.S. patents, including several developed at IBM before he joined the Virginia Tech faculty.
The problem Saraf's technology will solve is the intermediate necessity of processing a sample to copy the DNA so there is enough to analyze, which is done using a process called PCR (polymerase chain reaction). PCR is also used to tag specific sequences in a portion of a gene with florescent dye or radioactive molecules so the sequence will become visible if it encounters its complementary pair or sequence in a probe. "PCR was an amazing, revolutionary invention and a great tool -- but it requires a high level of skill. And the necessity of copying the DNA and then analyzing the copies creates complications for the diagnostic environment," says Saraf.
CUBS does not require that a sample be tagged. It places many single strands of DNA in an environment where a target sequence of nucleic acids can react to a nearby probe -- the complementary sequence to a portion of the DNA. The probe and target portion may be only 20 to 100 units long. In the case of proteins, the probe and target molecules may be antibody-antigen pairs. CUBS' simplicity will allow it to be integrated with complex microfluidic units for separating the markers (DNA, RNA, and proteins) in order to develop so called "lab on a chip" technology.
"We are working with other groups to develop such a fully integrated technology, which essentially requires miniaturization of existing unit operations involving fluids," says Saraf. "There is already technology to make miniaturized pumps and fluid channels at 100 micron scales. The challenge is to develop efficient mixers and separation processes that will allow for complex processing of biofluids. Then the realization of a commercial application will, of course, depend upon manufacturability and cost, which is a complex interplay of process materials and required operations."
Saraf says he would like to see the entire operation, from the as received fluid to the complete molecular analysis, on a monolithic substrate. "This, I think, will ultimately be the best performance requiring the least amount of material. It would be the most cost effective and cheapest to manufacture.
"As an engineer, my goal is a product that is simple to fabricate using established manufacturing tools. The novelty is the design of the device. Our hope is to advance our security and health care."
- Karen Gilbert, College of Engineering
For details, visit www.che.vt.edu/Saraf/index.htm or call 540-231-6774.
Content of this column may be reused so long as credit is given to Virginia Tech and the researchers.