Label-Free, Sequence-Specific, Inexpensive Fluorescent DNA Sensors

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By Karen McNulty Walsh | April 28, 2014

Newswise Using principles of energy transfer more commonly applied to designing solar cells, scientists at the U.S. Department of Energys Brookhaven National Laboratory have developed a new highly sensitive way to detect specific sequences of DNA, the genetic material unique to every living thing. As described in a paper published in the journal Chemistry of Materials, the method is considerably less costly than other DNA assays and has widespread potential for applications in forensics, medical diagnostics, and the detection of bioterror agents.

The sensors weve developed use a light-absorbing polymer to amplify the fluorescent signal of a dye that emits light only when it binds between two matched pieces of DNA, said Mircea Cotlet, a physical chemist at Brookhavens Center for Functional Nanomaterials, who led the research and who is also an adjunct professor at Stony Brook University. The system is sensitive enough to detect individual mismatches between the bases that make up the rungs of the twisted-ladder DNA double helix molecule, making it highly specific with no false positives, Cotlet said.

Plus, the method is rapid and requires no expensive equipment, just a conventional laboratory fluorimeter. It has high potential to be made field deployable for rapid analysis of crime-scene evidence and to mount a more knowledgeable, speedy response to bioterror threats.

DNA, show thyself!

The idea of using glowing dyes to sniff out DNA sequences is not entirely new. But finding an inexpensive fluorescent dye that inserts itself between every complementary base pair of a DNA moleculeand using a light absorbing/emitting polymer to amplify the fluorescent signal without the need for additional chemical taggingmakes the Brookhaven approach a big advance.

The dye we use is hundreds of times cheaper than popular commercial intercalating dyes, said Zhongwei Liu, a graduate student from Stony Brook University working with Cotlet and first author of the paper. Unbound, the green colored molecule absorbs red light but does not emit light. But when it inserts itself in the grooves of the DNA, the dye becomes fluorescent. And so far it is the only dye that can intercalate so densely with DNAmeaning exactly one dye molecule binds between each complementary base pair of the DNA double helixthe T-A and G-C matches that make up the genetic code.

That means the strength of the fluorescent signal is directly related to how many dye molecules are boundand how closely an unknown DNA sample matches a probe strand used for testing. As soon as theres a mismatch, even at just one rung on the DNA ladder, a dye molecule wont bind and the signal will weaken. Two mismatches results in a proportional drop in signal strength, and so on. That gives us a large range for the detection of sequence mismatch, Cotlet said.

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Label-Free, Sequence-Specific, Inexpensive Fluorescent DNA Sensors