Shape-Shifting DNA

Posted on Tuesday, December 3rd, 2019

A variety of cereal grains
Ochratoxin A can contaminate foods such as grains if they are stored in warm, humid conditions that promote mold growth.

U of G researchers develop new way to detect food contaminants that is simpler and cheaper.

Food contaminants such as Ochratoxin A (OTA) must be highly regulated to keep consumers safe. OTA is produced by mold that forms when foods are stored in warm, humid conditions. It may contaminate foods such as grains, nuts, coffee beans, and grapes. OTA is a possible human carcinogen that is especially damaging to the kidneys, resulting in kidney disease or even failure. Due to potential health risks, it is important to measure levels of OTA in our food supply and ensure that safety regulations are met.  Current detection methods require expensive, specialized lab equipment. This problem particularly affects developing countries that lack access to such specialized equipment, so they cannot confirm whether their food products are safe and cannot sell their foods to countries with strict safety regulations.  More recent strategies for OTA detection include biosensor-based platforms that seek to eliminate the need for complex instrumentation to deliver rapid, on-site detection.  In this regard, short strands of DNA called ‘aptamers’ can be used as cost-affordable biosensors to detect substances like OTA. Aptamers are chains consisting of four repeated molecules (DNA bases) in a specific order that bind targets, such as OTA, with high affinity and specificity.  

A research team led by University of Guelph chemistry professor Richard Manderville developed a new aptasensor that provides a simpler, cheaper way to detect food contaminants.  DNA with lots of G bases can form a structure called a G-quadruplex (GQ), where four guanines come together. The team took advantage of the inherent ability of GQ structures to form two different shapes, called parallel and anti-parallel. Instead of detecting changes between single- or double-stranded DNA and GQ structures, which requires expensive, specialized equipment, the team found that they could create an aptamer that binds OTA and has a different GQ shape depending on whether OTA is bound or not. This finding is a key step towards a more inexpensive method to detect OTA during food safety testing. The aptamer begins in an anti-parallel shape. A fluorescent dye is added, which binds the aptamer, causing the GQ shape to change to parallel. Then, if OTA is present, it ‘kicks out’ the fluorescent dye and binds to the aptamer, resulting in change back to anti-parallel and producing fluorescence that can be detected.

 “This new detection method could eventually be implemented as a handheld device that provides rapid and cheap on-site detection of any substance that can bind GQ,” says Manderville. “Aptamers could be designed for a variety of small molecules and proteins that contaminate our food. A device like this could be especially beneficial for developing countries that need inexpensive ways to test the safety of their food products.” 

This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC).

Deore PS, Gray MD, Chung AJ, Manderville RA. 2019. Ligand-induced G-quadruplex polymorphism: a DNA nanodevice for label-free aptasensor platforms. J. Am. Chem. Soc. doi: 10.1021/jacs.9b06533

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