A new DNA biosensor that simulates the biochemical pathways of the nucleus

Since their development in the 1990s, DNA microarrays have become a fundamental tool in laboratories around the world. DNA biosensors, an evolution of the DNA microarray technology, have exhibited extremely rapid growth in the past ten years. They couple a biological component to a detector component allowing scientists to obtain DNA sequence specific information quickly and simply.

DNA biosensors typically contain nucleic acid arrays consisting of specific sequences immobilized upon a transducing element that can measure optical or electrochemical changes. This nucleic acid array can be used to probe a solution containing molecules of interest, whether that be a new drug, proteins or enzymes, or other nucleic acids, and the response measured. For example, labeled DNA in a solution will hybridize, or bind, only to nucleic acid probes with the complimentary DNA sequence. When the DNA in solution hybridizes to the nucleic acid probe, a signal is generated, which will be detected and measured via the transducing element. In this case the DNA biosensor could be used to measure the relative concentrations of DNA between solutions. Probes are generally designed so that their sequence matches that of genes of interest. Target DNA binding to the probes must have originated from the gene that the probe is designed for, allowing analysis of gene expression levels between samples.

Recent work by researchers at the University of Texas, Dallas, has led to the development of a novel biosensor technology based on DNA biosensors. The researchers started by allowing double-stranded DNA to self-assemble onto gold electrode pads. The DNA complexed pads can then be connected to electrochemical testing equipment to form a DNA biosensor. Building upon this, the researchers, led by associate professor of physics Dr. Jason Slinker, added various proteins and enzymes to simulate particular cell activities. They then added membranes to the assembly in order to mimic the nuclear and cytoplasmic organization found in cells. The result was the generation of a simulated nucleus, complete with nuclear membrane and cytoplasm, allowing the study of complex biochemical reactions within a simulated cell environment.

According to the researchers their approach allowed them to control which factors could be included in their simulated cell. This is an important consideration given that many diseased cells exhibit very different biochemistries compared to their healthy counterparts. For example, the expression of many genes can vary significantly between cancerous cells and normal cells. These differences can dramatically affect the efficiency of a particular drug. This new technology would allow researchers to test new anticancer drugs to ensure that they are toxic to cancer cells, while remaining benign in healthy cells.
In order to test the functionality of their device the researchers examined the repair of DNA damage generated by a chemical compound known as beta-lapachone (β-lap). β-lap is a naphthoquinone compound with two active oxygen groups fused to a central aromatic ring. The compound is bioactived by the enzyme NQO1, which generates highly reactive oxygen species (ROS). The generation of these reactive molecules results in oxidative DNA damage, which in turn activates DNA repair processes that can ultimately lead to the cell’s death. NQO1 is often overexpressed in cancer cells, making β-lap a potential anticancer drug. Using their system, the researchers were successfully able to track the effects of β-lap mediated DNA damage and repair in simulated healthy and cancerous cells – reactions that could normally only be observed in cellular environments.

Whilst still in early development, this technology could have profound implications in public health, particularly in the rapidly growing arena of personalized medicine. In the near future this type of device could be used by oncologists to determine the best drug cocktail, or treatment regime, to treat cancers on a patient by patient basis.

About the author: Stephen Moore is a fourth year PhD candidate at Northeastern University in Boston. His research is focused on the role of base excision repair, a DNA damage repair pathway, during early embryogenesis, and how DNA damage may influence gene expression.


Source: Dimithree Kahanda, Gaurab Chakrabarti, Marc A. Mcwilliams, David A. Boothman, Jason D. Slinker. Using DNA devices to track anticancer drug activity. Biosensors and Bioelectronics, 2016; 80: 647 DOI: 10.1016/j.bios.2016.02.026

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